Quantifying E. coli Proteome and Transcriptome with Single-molecule Sensitivity in Single Cells

Devil in the Detail Genetically identical cells in the same environment can show variation in gene expression that may cause phenotypic variation at the single-cell level. But how noisy are most genes? Taniguchi et al. (p. 533; see the Perspective by Tyagi) now report single-cell global profiling of both messenger RNA (mRNA) and proteins in Escherichia coli using a yellow fluorescent protein fusion library. As well as a common extrinsic noise in high-abundance proteins, large fluctuations were observed in low-abundance proteins. Remarkably, in single-cell experiments, mRNA and protein levels for the same gene were uncorrelated. Measurement of protein and messenger RNA copy numbers in single Escherichia coli cells gives a system-wide view of stochastic gene expression. Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size. At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell’s protein and mRNA copy numbers for any given gene are uncorrelated.