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PNAS Papers on Coronavirus Enzyme, Phylogenetic Tree Modeling, Sponge Symbiont Microbes

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

Loyola University Chicago researchers characterize interactions involving an EndoU endoribonuclease enzyme that coronaviruses in general use to dodge host immune sensors. Using cell line experiments, RNA sequencing, gene editing, and other approaches, the team assessed activity by beta-CoV mouse hepatitis virus and alpha-CoV porcine epidemic diarrhea virus strains with wild type or altered versions of the EndoU enzyme. The results suggest that coronavirus EndoU enzymes can chop up specific viral sequences that would normally trigger host immune sensors, the author report, prompting them to suggest that "EndoU may be one of several immune antagonists targeted for generating an attenuated and recombination-resistant [coronavirus] vaccine."

A University of Illinois at Urbana-Champaign team takes a genomics-informed, statistical modeling look at phylogenetic tree topology. In an effort to understand consistent topology and diversification burst features in phylogenetic trees, the researchers put together a model that encompasses everything from speciation and niche inheritance to niche construction. Among other things, their analyses suggest that "phylogenetic tree topology is scale-invariant due to a singularity arising from large niche fluctuations that follow extinction events," the authors note, while underscoring the "bursty" nature of diversification patterns over time. "These results show, in principle, how dynamical scaling laws of phylogenetic trees on long timescales may emerge from generic aspects of the interplay between ecological and evolutionary processes," they conclude.

Finally, in a paper set to appear in PNAS this week, investigators in Switzerland, the US, Germany, and New Zealand describe the complex and chemically diverse microbiome associated with a marine sponge called Mycale hentscheli and its symbiotic partners. Using metagenomic sequencing, expression profiling, mass spec-based proteomic profiling, and other approaches, the team assessed M. hentscheli samples collected at marine sites off of New Zealand's South Island, demonstrating that the sponge and its symbionts  "jointly generate chemical diversity" stemming from the microbiome, together producing a proposed microtubule inhibitor and anti-cancer compound called peloruside and other chemicals of interest. "[W]e identified extensive biosynthetic potential distributed among a broad phylogenetic range of bacteria," the authors report.