Understanding RNA Organization in Living Bacteria

Revealing how individual mRNAs shape bacterial gene expression

Gene expression is not determined only by which genes are transcribed. After transcription, each mRNA enters a crowded and highly organized cellular environment where it can be translated, stored, or degraded. These competing outcomes shape how bacteria grow, adapt, and survive, yet the principles that determine mRNA fate remain poorly understood.

Much of what we know about bacterial RNA regulation comes from ensemble-average measurements or fixed-cell experiments. While powerful, these approaches often miss the dynamic and heterogeneous behavior of molecules inside living cells. The Ortiz Lab uses quantitative super-resolution microscopy and single-molecule imaging to bridge this gap. Super-resolution microscopy maps nanoscale organization beyond the diffraction limit,While single-molecule imaging follows individual mRNAs over time to reveal how location, interactions, and environment influence fate.

Research Directions

Spatial organization of bacterial gene expression

Bacterial cells are small, crowded, and highly organized. Chromosomes, ribosomes, RNA-processing machinery, biomolecular condensates, and regulatory factors create intracellular environments that influence where mRNAs move and how they function. Our lab investigates how this spatial organization shapes gene expression during growth, stress, and adaptation.

RNA fate and biomolecular condensates

Every mRNA faces multiple possible outcomes. These decisions are shaped by ribosomes, RNA-binding proteins, RNA-processing enzymes, biomolecular condensates, and the physical organization of the cytoplasm. Our previous work showed that bacterial ribonucleoprotein bodies, known as BR bodies, can switch between distinct material states that alter their function and regulate RNA stability. Building from this discovery, we seek to understand how dynamic intracellular compartments influence RNA fate.

Single-molecule views of RNA regulation

Population-level measurements reveal average RNA abundance and stability, but individual mRNAs can follow very different trajectories. By observing single mRNAs in living cells, our lab aims to uncover how molecular motion, transient interactions, and condensate association relate to outcomes such as degradation or storage.

Vision

The Ortiz Lab aims to transform bacterial RNA biology from a field built largely on population averages into one where the life history of individual mRNAs can be observed directly inside living cells.