Correlative imaging of gene expression and metabolic activity by combining single-molecule mRNA FISH and nanometer-scale secondary ion mass spectrometry
- Populations of genetically identical cells that share the same environment can differ markedly in their phenotypes. This phenomenon has been termed phenotypic heterogeneity. While a few molecular mechanisms that lead to heterogeneity in gene expression have been elucidated, it remains unclear how heterogeneity in gene expression is transmitted to heterogeneity in activity; especially in metabolism. Metabolic activity of single bacterial cells can be quantified by labeling the substrate with stable isotopes and by measuring label uptake with nanometer-scale secondary ion mass spectrometry (NanoSIMS). Here we combined NanoSIMS with single-molecule mRNA fluorescence in situ hybridization (smFISH) to link heterogeneity in gene expression and metabolism in nitrogen fixing bacteria. We find that gene expression and metabolic activity are decoupled in single cells. However, heterogeneity in gene expression is correlated with heterogeneity in metabolic activity on the population level. GenePopulations of genetically identical cells that share the same environment can differ markedly in their phenotypes. This phenomenon has been termed phenotypic heterogeneity. While a few molecular mechanisms that lead to heterogeneity in gene expression have been elucidated, it remains unclear how heterogeneity in gene expression is transmitted to heterogeneity in activity; especially in metabolism. Metabolic activity of single bacterial cells can be quantified by labeling the substrate with stable isotopes and by measuring label uptake with nanometer-scale secondary ion mass spectrometry (NanoSIMS). Here we combined NanoSIMS with single-molecule mRNA fluorescence in situ hybridization (smFISH) to link heterogeneity in gene expression and metabolism in nitrogen fixing bacteria. We find that gene expression and metabolic activity are decoupled in single cells. However, heterogeneity in gene expression is correlated with heterogeneity in metabolic activity on the population level. Gene expression kinetics can provide insights into the molecular mechanisms that lead to heterogeneity in metabolism.…