Simultaneous measurements of translation rate and transcriptome in single bacterial cells by scTR-seq uncovers linked regulation within a specialized active cell population.

Cell-to-cell variation within clonal bacterial populations provides bacterial communities important advantages including opportunities for bet-hedging and metabolic division of labor. In recent years the extent of bacterial heterogeneity has been documented both at the transcriptome level and with physiological measurements of cell growth rate and translation rate. However, methods that link physiological parameters to a single cells full transcriptomic state are lacking, making it difficult to identify the regulatory mechanisms that couple physiology and transcriptional output. Here we introduce a method that combines click-chemistry enabled labeling of nascent polypeptides to measure translation rates in single cells alongside microfluidic encapsulation and single cell transcriptomic measurements, providing a tandem measurement of translation rate and transcriptome in thousands of single Bacillus subtilis cells. In a culture experiencing nutrient limitation, we identified a subpopulation of cells with a higher rate of protein translation that uniquely overexpresses genes for several metabolic processes including acetoin production and arginine synthesis. Using a genetic approach informed by the gene expression in this subpopulation, we identified a regulatory mechanism that couples the increase in protein abundance of a transcriptional regulator AlsR with expression of alsR regulated genes in this subpopulation.