Journal Article

CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis

Stallings, Christina L., Zhu, Dennis X., Garner, Ashley L., Galburt, Eric A.

2019

Overview

The ability to regulate gene expression through transcription initiation underlies the adaptability and survival of all bacteria. Recent work has revealed that the transcription machinery in many bacteria diverges from the paradigm that has been established in Escherichia coli. Mycobacterium tuberculosis (Mtb) encodes the RNA polymerase (RNAP)-binding protein CarD, which is absent in E. coli but is required to form stable RNAP-promoter open complexes (RPₒ) and is essential for viability in Mtb. The stabilization of RPₒ by CarD has been proposed to result in activation of gene expression; however, CarD has only been examined on limited promoters that do not represent the typical promoter structure in Mtb. In this study, we investigate the outcome of CarD activity on gene expression from Mtb promoters genome-wide by performing RNA sequencing on a panel of mutants that differentially affect CarD’s ability to stabilize RPₒ. In all CarD mutants, the majority of Mtb protein encoding transcripts were differentially expressed, demonstrating that CarD had a global effect on gene expression. Contrary to the expected role of CarD as a transcriptional activator, mutation of CarD led to both up- and down-regulation of gene expression, suggesting that CarD can also act as a transcriptional repressor. Furthermore, we present evidence that stabilization of RPₒ by CarD could lead to transcriptional repression by inhibiting promoter escape, and the outcome of CarD activity is dependent on the intrinsic kinetic properties of a given promoter region. Collectively, our data support CarD’s genome-wide role of regulating diverse transcription outcomes.

• Publisher: National Academy of Sciences
• Subject: Adaptability / Bacteria / Bacterial Proteins - metabolism / Bacterial Proteins - physiology / Biological Sciences / DNA-directed RNA polymerase / DNA-Directed RNA Polymerases - metabolism / E coli / Gene expression / Gene Expression Regulation, Bacterial - genetics / Gene sequencing / Gene silencing / Genome, Bacterial - genetics / Genomes / Microbiology / Mutation / Mycobacterium tuberculosis / Mycobacterium tuberculosis - genetics / Mycobacterium tuberculosis - metabolism / PNAS Plus / Promoter Regions, Genetic - genetics / Promoters / Proteins / Ribonucleic acid / RNA / RNA polymerase / Stabilization / Transcription initiation / Tuberculosis / Viability