Small regulatory RNAs

Small RNAs are known as important players in gene regulation in Bacteria and Eukarya. To date not much is known about small RNAs as regulators of gene expression in Archaea. To elucidate the function of small RNAs in Archaea we used different experimental approaches to identify sRNAs in the halophilic archaeon Haloferax volcanii. As experimental approaches we used "traditional "cloning of cDNAs from size selected RNA fractions and deep sequencing of several RNA populations isolated from cells grown under different conditions. Together, the two experimental approaches identified 111 intergenic sRNAs and 38 antisense sRNAs. To investigate the biological function of the identified sRNAs we generated deletion mutants of the intergenic sRNA genes and overexpressed the genes for the identified antisense sRNA. These strains are currently being investigated.

An important player in the bacterial sRNA pathway is the Hfq protein. Therefore, we investigated the Hfq homolog in Haloferax, the HvoLsm protein in detail using in vitro and in vivo methods. Immuno-precipitation of a tagged HvoLsm protein revealed several protein- and RNA-interaction partners. Furthermore, a deletion of the lsm gene was generated and analysed in detail.

The picture shows the pathways. To date quite a lot is known about the function of bacterial and eukaryotic small RNAs. Most of the bacterial sRNAs act at the 5´ end of a target mRNA and often the Hfq protein is required. Sometimes an RNase is sequestered which degrades the RNA. Eukaryotic miRNAs target often the mRNA 3´ end. The mode of action of archaeal sRNAs is not known yet. They might require the Lsm protein and/or an RNase but nothing is known about that process yet. ATG: start codon on the mRNA, TAA: stop codon on the mRNA, RBS: ribosome binding site.
To date quite a lot is known about the function of bacterial and eukaryotic small RNAs. Most of the bacterial sRNAs act at the 5´ end of a target mRNA and often the Hfq protein is required. Sometimes an RNase is sequestered which degrades the RNA. Eukaryotic miRNAs target often the mRNA 3´ end. The mode of action of archaeal sRNAs is not known yet. They might require the Lsm protein and/or an RNase but nothing is known about that process yet. ATG: start codon on the mRNA, TAA: stop codon on the mRNA, RBS: ribosome binding site.