Dormant bacterial spores encrypt a long-lasting transcriptional program to be executed during revival

Sigal Ben-Yehuda ¹ Bing Zhou ¹ Yifei Xiong ¹ Yuval Nevo ² Tamar Kahan ³ Oren Yakovian ^1,4 Sima Alon ¹ Ilan Rosenshine ¹ Lior Sinai ¹

¹Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, the Hebrew University of Jerusalem, 9112001, Jerusalem, Israel.
²Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
³Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
⁴The Racah Institute of Physics, Faculty of Science,, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel

Cellular dormancy is a strategy shared across the tree of life from bacteria to fungi and plants. It enables species to endure adverse conditions, spread into new niches and reproduce. Bacteria belonging to the Bacillus and Clostridium genera form durable dormant spores, an extreme type of cellular quiescence, that are capable of rapid germination under propitious conditions. Yet, it is elusive how the spore revival transcriptional program is memorized for years. We revealed that in dormant spores, core RNA polymerase (RNAP) resides in a central chromosomal domain, where it remains paused in a standby mode, on a subset of intergenic promoter regions, holding the cue for RNAP positioning. These promoters regulate genes encoding for most essential cellular functions, such as rRNAs and tRNAs. Promptly upon germination, halted RNAP recruits key transcriptional components, including sigma factor, necessary to drive the expression of the adjacent downstream genes, allowing spore awakening. This transcriptional pattern is abrupted in mutants devoid of spore specific DNA-binding proteins that exhibit a disperse pattern of RNAP nucleoid localization, and subsequently disordered firing of gene expression during germination. RNAP resting could provide a mechanism to sustain transcriptional hierarchy in a plethora of organisms displaying a quiescent life form.