Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources

Seth E Lyon; Freya D R Wencker; Chrishan M Fernando; Kimberly A Harris; Ronald R Breaker

doi:10.1093/pnasnexus/pgae075

Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources

PNAS Nexus. 2024 Feb 12;3(2):pgae075. doi: 10.1093/pnasnexus/pgae075. eCollection 2024 Feb.

Authors

Seth E Lyon¹, Freya D R Wencker², Chrishan M Fernando¹, Kimberly A Harris³, Ronald R Breaker^{1

2

3}

Affiliations

¹ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
² Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.
³ Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

Abstract

Ornate, large, extremophilic (OLE) RNAs comprise a class of large noncoding RNAs in bacteria whose members form a membrane-associated ribonucleoprotein (RNP) complex. This complex facilitates cellular adaptation to diverse stresses such as exposure to cold, short-chain alcohols, and elevated Mg²⁺ concentrations. Here, we report additional phenotypes exhibited by Halalkalibacterium halodurans (formerly called Bacillus halodurans) strains lacking functional OLE RNP complexes. Genetic disruption of the complex causes restricted growth compared to wild-type cells when cultured in minimal media (MM) wherein glucose is replaced with alternative carbon/energy sources. Genetic suppressor selections conducted in glutamate MM yielded isolates that carry mutations in or near genes relevant to Mn²⁺ homeostasis (ykoY and mntB), phosphate homeostasis (phoR), and putative multidrug resistance (bmrCD). These functional links between OLE RNA, carbon/energy management, and other fundamental processes including protein secretion are consistent with the hypothesis that the OLE RNP complex is a major contributor to cellular adaptation to unfavorable growth conditions.

Keywords: Mn2+; bTOR; noncoding RNA; protein secretion; ykoY.