In Science this week, researchers at the University of Arizona report that a lateral transfer of fungal genes underlies the red pea aphid's ability to produce carotenoids. Nancy Moran and Tyler Jarvik found that the aphid genome "encodes multiple enzymes for carotenoid biosynthesis" by performing phylogenetic analyses, they were able to show that red aphids have a 30-kb region encoding a single carotenoid desaturase derived from fungal genes, which green aphids do not have.
A team led by investigators at the Department of Energy's Joint Genome Institute present a draft genome sequence for Xenopus tropicalis — the western clawed frog — in Science this week. The X. tropicalis genome, the team writes, encodes more than 20,000 protein-coding genes, "including orthologs of at least 1,700 human disease genes." The authors conclude that the western clawed frog genome "exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage."
In a perspectives piece, Jeremy Gunawardena of Harvard Medical School writes that "'systems' thinking has always been present in biology, even if its importance has waxed and waned with changes in experimental capabilities." He suggests that mathematical tools become important as the field shifts to understand the collective function of disparate disciplines. "What is different today is that the molecular details are at the bottom of the biological hierarchy," he writes. "Now there is nowhere left to go but up."
Meanwhile, in Science Signaling, investigators in the US and China report that the protein phosphatase 1α isoform interacts with Krüppel-associated box domain-associated protein 1 under basal conditions — in which PP1β only interacts with KAP1 in response to genotoxic stress. Differential abundance of PP1α and PP1β, the authors show, affects the phosphorylation and small ubiquitin-like modifying protein "SUMOylation" in response to DNA double-strand breaks. Using ChIP and re-immunoprecipitation approaches, the team shows that "PP1β-dependent SUMOylation of KAP1 occurred by mechanisms that were dependent and independent of the phosphorylation status of Ser-824."