Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-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 N-acyl-l-homoserine lactone (AHL) remains unknown in sphingomonads. In this study, we identified an rshUS6⁻1 gene by sequence analysis in Novosphingobium pentaromativorans US6-1, a member of the sphingomonads. RNA-seq was used to determine transcription profiles of the wild type and the ppGpp-deficient rshUS6⁻1 deletion mutant (∆rsh). There were 1540 genes in the RshUS6⁻1 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 (novI and novR) were positively regulated by RshUS6⁻1 during the exponential growth phase. A degradation experiment indicated the reason for the AHL absence in ∆rsh was unrelated to the AHL degradation. According to RNA-seq, we proposed σE, DksA, Lon protease and RNA degradation enzymes might be involved in the RshUS6⁻1-dependent expression of novI and novR. 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.
['Lu|Hang|H|', 'Huang|Yili|Y|']
D015107:4-Butyrolactone D000595:Amino Acid Sequence D020869:Gene Expression Profiling D015964:Gene Expression Regulation, Bacterial D020043:Genes, Essential D011135:Polysaccharides, Bacterial D018085:Regulon D017422:Sequence Analysis, DNA D042301:Sphingomonadaceae D059467:Transcriptome
Novosphingobium pentaromativorans US6-1 Rsh regulon N-acyl-l-homoserine lactone sphingomonads RNA-seq ppGpp