Transcriptomic profiling of the deletion of NUDIX hydrolases in Sulfolobus acidocaldarius
Nudix hydrolases comprise a large and ubiquitous protein superfamily that catalyzes the hydrolysis of a nucleoside diphosphate linked to another moiety X (Nudix). S. acidocaldarius possesses four Nudix domain-containing proteins (SACI_RS00730, SACI_RS02625, SACI_RS00060/Saci_NudT5 and SACI_RS00575). Deletion strains were generated for the four individual Nudix genes as well as for both Nudix genes annotated to encode ADP-ribose pyrophosphatases (SACI_RS00730, SACI_RS00060). RNA-seq was used to establish the transcriptomic profiles of the Nudix deletion strains, revealing a large number of differentially regulated genes, most notably in the ?SACI_RS00730/SACI_RS00060 double knock-out strain and the ?SACI_RS00575 single deletion strain, with each deletion strains presenting a distinct transcriptomic profile. While the deletion strains did not show a distinct phenotype compared to the wild-type strain under standard growth conditions, the Nudix hydrolases indirectly affect transcription as shown by a large number of differently regulated transcriptional regulators in the deletion strains. We observed downregulation of the lysine biosynthesis and the archaellum operons in the stationary phase, as well as upregulation of two genes involved in the de novo NAD+ biosynthesis pathway. Furthermore, the deletion strains exhibited upregulation of two thermosome subunits (a, ß) and the putative ribonuclease toxin VapC together with its antitoxin VapB, which are implicated in the archaeal heat shock response. Our results uncover a defined set of pathways that involve archaeal Nudix protein activities and assist in their functional characterization.