high-throughput genetics
Editor's Pick Research Article | Molecular Biology and PhysiologyGapMind: Automated Annotation of Amino Acid BiosynthesisMany microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool,...
Research Article | Molecular Biology and PhysiologyOxidative Pathways of Deoxyribose and Deoxyribonate CatabolismDeoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified...