Transcriptome Analysis of US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of -acyl-l-homoserine Lactone Accumulation.

In most bacteria, a bifunctional Rsh responsible for (p)ppGpp metabolism is the key player in stringent response. To date, no transcriptome-wide study has been conducted to investigate the Rsh regulon, and the molecular mechanism of how Rsh affects the accumulation of -acyl-l-homoserine lactone (AHL) remains unknown in sphingomonads. In this study, we identified an gene by sequence analysis in US6-1, a member of the sphingomonads. RNA-seq was used to determine transcription profiles of the wild type and the ppGpp-deficient deletion mutant (∆). There were 1540 genes in the Rsh regulon, including those involved in common traits of sphingomonads such as exopolysaccharide biosynthesis. Furthermore, both RNA-seq and quantitative real-time polymerase chain reaction (qRT-PCR) showed essential genes for AHL production ( and ) were positively regulated by Rsh during the exponential growth phase. A degradation experiment indicated the reason for the AHL absence in ∆ was unrelated to the AHL degradation. According to RNA-seq, we proposed σ, DksA, Lon protease and RNA degradation enzymes might be involved in the Rsh-dependent expression of and . Here, we report the first transcriptome-wide analysis of the Rsh regulon in sphingomonads and investigate the potential mechanisms regulating AHL accumulation, which is an important step towards understanding the regulatory system of stringent response in sphingomonads.