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PNAS Papers on Convergent Pathogen Effectors, Lineage-Related RNA Mutations, Desiccation-Tolerant Grass

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

A team from Belgium, Japan, and Germany describes a mitogen-activated protein kinase (MAPK)-targeting peptide motif that appears to have arisen via convergent evolution in pathogenic bacteria and multiple viral lineages. With kinase immunoprecipitation assays, mass spectrometry, and other experiments, the researchers tracked down a short linear motif present in multiple viruses and in Yersinia bacteria that binds to MAPK p90-ribosomal S6-kinase (RSK) enzymes, prompting their ongoing activation. "Remarkably, while viruses and bacteria evolved an identical mechanism of kinase activation, [the] downstream effect diverged, effectively disarming different arms of the immune system according to their own need," they suggest. "This is a prominent illustration of trans-kingdom convergent evolution across microbial pathogens to usurp key signaling kinases."

Researchers at Xiamen University and other centers in China describe an algorithm for gleaning cell lineage features from mitochondrial RNA mutations in individual cells. The team's "label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis" (LINEAGE) algorithm involves the interpretation of endogenous lineage markers in mitochondrial RNA sequences rather than barcodes that have been exogenously added to the cells. When they used the computational method to assess simulated and real scRNA-seq data from BRAF-mutated melanoma cells, for example, the authors tracked down genes suspected of contributing to BRAF inhibitor resistance. Moreover, they argue that the approach "removes most of the technical hurdles of lineage analysis on scRNA-seq and will dramatically accelerate its application in biological research."

A team led by investigators in Mexico and the US searches for genomic features that distinguish the desiccation-tolerant grass plant Sporobolus stapfianus from a related, desiccation-sensitive species called S. pyramidalis. Using high-quality genome assemblies for the plant species, together with transcript sequence data from hydrated and dehydrated samples, the researchers saw signs that desiccation tolerance in vegetative parts of S. stapfianus plants may stem from relatively recent tweaks to mechanisms that seeds used to survive dry spells. "Our results also show that the desiccation response is largely unique, indicating a recent evolution of this trait within the angiosperms," the authors note, "and that inhibition of senescence during dehydration is likely critical in rendering a plant desiccation tolerant."