A Proterozoic microbial origin of extant cyanide-hydrolyzing enzyme diversity

In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation

A Proterozoic microbial origin of extant cyanide-hydrolyzing enzyme diversity

In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families.

Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted. As a result, several computational methods have been developed for inferring the root of unrooted gene trees. However, the accuracy of such methods has never been systematically evaluated on prokaryotic gene families, where horizontal gene transfer is often one of the dominant evolutionary events driving gene family evolution. In this work, we address this gap by conducting a thorough comparative evaluation of five different rooting methods using large collections of both simulated and empirical prokaryotic gene trees. Our simulation study is based on 6000 true and reconstructed gene trees on 100 species and characterizes the rooting accuracy of the four methods under 36 different evolutionary conditions and 3 levels of gene tree reconstruction error. The empirical study is based on a large, carefully designed data set of 3098 gene trees from 504 bacterial species (406 Alphaproteobacteria and 98 Cyanobacteria) and reveals insights that supplement those gleaned from the simulation study. Overall, this work provides several valuable insights into the accuracy of the considered methods that will help inform the choice of rooting methods to use when studying microbial gene family evolution. Among other findings, this study identifies parsimonious Duplication-Transfer-Loss (DTL) rooting and Minimal Ancestor Deviation (MAD) rooting as two of the most accurate gene tree rooting methods for prokaryotes and specifies the evolutionary conditions under which these methods are most accurate, demonstrates that DTL rooting is highly sensitive to high evolutionary rates and gene tree error, and that rooting methods based on branch-lengths are generally robust to gene tree reconstruction error

Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported

Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.ISSN:2045-882