Simultaneous measurements of translation rate and transcriptome uncovers linked regulation within an active bacterial...

Cell-to-cell variation within clonal bacterial populations provides bacterial communities with 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 cell's 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 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 the expression of alsR-regulated genes in this subpopulation.