UC Berkeley

The survival of bacterial cells requires the coordinated regulation of genes and proteins so that cells can quickly and efficiently respond to opportunities for rapid cell growth and to stresses of different environments. Many of the networks and mechanism for the coordinated regulation of genes and proteins involve the control the production, degradation and translation of messenger RNAs (mRNAs). This dissertation focuses on the relationship between translation and the regulation of mRNA production and degradation that occurs without (direct translational control) and with (indirect translational control) the action of small non-coding RNAs (sRNAs). The results shine a light on the designing process of circuits in bioengineering and the mystery of complicated bacterial stress responses and adaptations.

In the first chapter, we developed a new metric named threshold overlap score (TOS) that measures colocalization between biomolecules. TOS describes whether two or three biomolecules occur in the same place more than chance. Specifically, TOS quantifies the percentage of overlapping signals between two or three channels with respect to the uniformly distributed random signals and rescales this value so that it is easily interpretable. The TOS metric was used in the third chapter to quantify sRNA localization in the nucleoid, which provided novel insight into their role in mRNA transcription, degradation and translation.

In the second chapter, we built an open source tool (ImageJ plugin) with an easy-to-use user interface called EzColocalization. EzColocalization gives biologists without programming experience access to imaging segmentation, data visualization, and colocalization analyses including TOS, other classic colocalization metrics and custom colocalization measurements. A form of EzColocalization was used in the first chapter to demonstrate and valid TOS as useful metric and it was used in the third chapter to measure sRNA colocalization and understand the role in mRNA in mRNA transcription, degradation and translation.

In the third chapter, we studied the subcellular localization of sRNAs to elucidate their roles in mRNA production, degradation and translation. Based on our data, we concluded that sRNAs can but mRNAs cannot enter the densely packed nucleoid. This phenomenon is due to the active translation and larger size of mRNAs. These findings indicate that sRNAs have the potential to regulate nascent mRNAs in the nucleoid prior to the completion of mRNA transcription, which increases their potential impact and efficiency as a regulator.

In the fourth chapter, we constructed mathematical models that capture “real-world” regulation. Unlike the classic central dogma model where mRNA production and degradation and protein production and degradation are all completely independent, the real-world model includes the effects of translation on premature transcription termination and mRNA degradation. The simulations reproduce key experimental observations and show that the coupling of translation to mRNA production and degradation to increase quality control occurs at the cost of efficiency.

Together, the four chapters in this dissertation provide novel insight into the direct and indirect control of mRNA concentrations by sRNA localization and translational feedbacks, and how these sophisticated regulatory processes may benefit bacterial growth and adaptation.