Summary: In this project we seek to investigate how modularity of transcriptional programs generated through expansions of general transcription factors (GTFs) begets the extraordinary success of microbes in adapting to diverse niches. Duplications or even small changes to the regulation or interactions of a GTF dramatically alters the modularity of a transcriptional regulatory network. We have discovered that modular changes in a transcriptional regulatory network may govern the coordinated recruitment of specialized ribosomes to transcripts encoding proteins required for adaptation to a new environment. This interplay of transcription and translation likely occurs through physical interactions of GTFs with specific ribosomal subunits, which recruits the specialized ribosomes to coordinately transcribed genes, including transcripts encoding those subunits. We hypothesize that by preferentially translating the conditionally expressed subunits, the specialized ribosome creates a feed forward loop to drive rapid physiological transitions. If confirmed, this mechanism would explain how archaea and bacteria adapt to unfavorable environments by synthesizing proteins from newly made transcripts that are lower in abundance by orders of magnitude, relative to transcripts of the preceding active growth state. Specifically, we will investigate how mutations in a GTF that changes the modularity of the transcriptional program in Halobacterium salinarum dramatically alters its fitness landscape across environments. We will profile changes in the transcriptome, ribosome footprints, and proteome during environmental adaptation of GTF mutants, and characterize how changes in modularity of transcription proportionally changes ribosome recruitment and translational efficiency of specific pools of transcripts to manifest in phenotype. We will also map environment-specific changes in the composition and physical interactions within and across the transcriptional and the translational apparatus to generate mechanistic hypotheses. We will test the mechanistic hypotheses by engineering the regulation of specialized ribosomal subunits to force phenotypic transitions in the absence of environmental cues.

Tags: Halobacterium, transcription, translation, General Transcription Factors, Riboseq

Relevant Publications: PMID: 32723790, PMID: 22108796

Team Members: Chris, Alan

Model Organism(s): Halobacterium salinarum