Abstract
Signaling networks allow adaptation to stressful environments by activating genes that counteract stressors. Small proteins (≤ 50 amino acids long) are a rising class of stress response regulators. Escherichia coli encodes over 150 small proteins, most of which lack phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we identify stress-induced small proteins using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, several of them transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, underscoring their physiological significance in low magnesium stress. Most remarkably, we elucidate an unusual connection via a small membrane protein YoaI, between major signaling networks – PhoR-PhoB and EnvZ-OmpR in E. coli, advancing our understanding of small protein regulators in cellular signaling.
Synopsis
Ribo-RET identifies 17 small proteins induced under low magnesium (Mg2+) stress in E. coli
Many of these proteins are transcriptionally activated by PhoQP signaling system
Half of the stress-induced small proteins localize to the membrane
Deletion or overexpression of specific small proteins affects growth under stress
Small protein YoaI connects PhoR-PhoB and EnvZ-OmpR signaling networks
Competing Interest Statement
The authors declare no competing interests. P.S. a director at an RNA-therapeutics startup.
Footnotes
Changes to title, abstract, consolidation of a few figures, minor changes to the text following the methods and change in citation style.
