Detection of differentially expressed growth dependent noncoding RNAs in Sulfolobus solfataricus

Noncoding RNA mediated gene regulation exists in all the three kingdoms of life including prokaryotes, eukaryotes and archaea. In prokaryotes, the ncRNAs typically bind to the 5’ end of the messenger RNAs to facilitate its activation or repression. The repression of gene expression in eukaryotes by ncRNAs is regulated by its binding to the 3’-untranslated region. A significant amount of information is available on the ncRNA mediated gene regulation in eukaryotes and prokaryotes. However, the data on ncRNA interference mechanisms in archaea are largely based on bioinformatics predictions. More than 300 noncoding RNAs have been bioinformatically predicted to exist in the hyperthemophilic archeon Sulfolobus solfataricus. The main objective of this study was to ascertain the growth dependent differential expression of certain ncRNAs in S. solfataricus. The northern blot analysis confirms that certain ncRNAs are differentially expressed at particular phases of growth while others are constitutively expressed in all phases of growth. One of the three ncRNAs, RNA 22 was expressed constitutively whereas the other two ncRNAs, RNA 43 and RNA 115 was expressed at specific points of growth. In addition, we also attempt to predict the putative mRNAs that are targeted by specific ncRNAs. In conclusion, our study states that in term with the constitutive expression of ncRNAs 22, the predicted targets include a drug resistance transporter and transposase protein which should be down regulated during the normal growth of Sulfolobus. The second candidate, ncRNA 43 was specifically expressed at the late log phase with putative targets that includes critical metabolic proteins. The third RNA analyzed was ncRNA 115. The expression of ncRNA 115 was at the mid-log phase with the predicted target being the Translation recovery factor (TRF). These predictions with functional classifications of the mRNAs relevant in specific growth points out that ncRNAs plays significant role in gene regulation in S. solfataricus.