Proteins of the Lsm family, including eukaryotic Sm proteins and bacterial Hfq, are key players in RNA metabolism. Little is known about the archaeal homologues of these proteins. Therefore, we characterized the Lsm protein from the haloarchaeon Haloferax volcanii using in vitro and in vivo approaches. H. volcanii encodes a single Lsm protein, which belongs to the Lsm1 subfamily. The lsm gene is co-transcribed and overlaps with the gene for the ribosomal protein L37e. Northern blot analysis shows that the lsm gene is differentially transcribed. The Lsm protein forms homoheptameric complexes and has a copy number of 4000 molecules/cell. In vitro analyses using electrophoretic mobility shift assays and ultrasoft mass spectrometry (laser-induced liquid bead ion desorption) showed a complex formation of the recombinant Lsm protein with oligo(U)-RNA, tRNAs, and an small RNA. Co-immunoprecipitation with a FLAG-tagged Lsm protein produced in vivo confirmed that the protein binds to small RNAs. Furthermore, the co-immunoprecipitation revealed several protein interaction partners, suggesting its involvement in different cellular pathways. The deletion of the lsm gene is viable, resulting in a pleiotropic phenotype, indicating that the haloarchaeal Lsm is involved in many cellular processes, which is in congruence with the number of protein interaction partners.Sm and Sm-like (Lsm) proteins constitute a large family of proteins known to be involved in RNA metabolism. Representatives of this family are found in all three domains: bacteria, archaea, and eukarya. All of them share a common bipartite sequence motif, known as the Sm domain, consisting of two conserved segments separated by a region of variable length and sequence. The bacterial family member is the Hfq protein (1, 2), which has a plethora of functions (3). Hfq is a highly conserved protein encoded within many bacterial genomes (4). Although the protein does not show a high similarity to the Lsm proteins on the primary structure level, it possesses striking similarities in both function and tertiary and quaternary structure to the eukaryotic Lsm proteins (3, 5). Hfq monomers assemble to form highly stable hexamers (6), which bind preferentially to A/U-rich sequences (7, 8) but have a relaxed RNA binding specificity and participate in many stages of RNA metabolism. It was therefore proposed that Hfq is an ancient, less specialized form of the Lsm proteins (9). One of the identified functions of Hfq is its interaction with sRNAs (10). It has been proposed that the protein acts as an RNA chaperone that might simultaneously recognize the sRNA and its target and facilitate its interaction. An Escherichia coli hfq insertion mutant showed pleiotropic phenotypes including decreased growth rates and yields, increased cell sizes, and an increased sensitivity to stress conditions (11-13). These defects are at least in part a reflection of the fact that Hfq is required for the function of several sRNAs including DsrA, RprA, Spot42, OxyS, and RhyB (14 -17).Eukaryotes have t...

To elucidate the role of small noncoding RNAs (sRNAs) in archaea we applied RNomics to identify sRNAs in the halophilic archaeon Haloferax volcanii. Using a size-selected cDNA library, 39 different previously uncharacterized sRNAs were identified ranging in size from 130 to 460 nucleotides. Twenty-one of these sRNAs are located in intergenic regions and 18 in antisense orientation. One of the intergenic sRNAs codes for a peptide. Only a minor fraction of sRNA genes were preceded by promoter elements (15 of 39), indicating that the majority might be generated by processing from larger precursors. Northern blot analyses of the intergenic sRNAs revealed differential expression for several sRNAs. Deletion mutants of two sRNAs were constructed, demonstrating that this approach is suitable to elucidate their biological function. Both mutant strains showed a defined phenotype: sRNA(30) gene deletion mutant was less resistant to higher temperatures and sRNA(63) gene deletion mutant resulted in a severe growth defect at low salt concentrations. Proteome analyses revealed clear differences between wildtype and deletion strains. These results represent the first reported examples of experimentally characterizing the function of sRNAs, excepting snoRNAs, in archaea. Taken together, we showed that haloarchaea encode sRNAs, some of which are differentially expressed and which have the potential to fulfil important biological functions in vivo.

In recent years, sRNAs (small non-coding RNAs) have been found to be abundant in eukaryotes and bacteria and have been recognized as a novel class of gene expression regulators. In contrast, much less is known about sRNAs in archaea, except for snoRNAs (small nucleolar RNAs) that are involved in the modification of bases in stable RNAs. Therefore bioinformatic and experimental RNomics approaches were undertaken to search for the presence of sRNAs in the model archaeon Haloferax volcanii, resulting in more than 150 putative sRNA genes being identified. Northern blot analyses were used to study (differential) expression of sRNA genes. Several chromosomal deletion mutants of sRNA genes were generated and compared with the wild-type. It turned out that two sRNAs are essential for growth at low salt concentrations and high temperatures respectively, and one is involved in the regulation of carbon metabolism. Taken together, it could be shown that sRNAs are as abundant in H. volcanii as they are in well-studied bacterial species and that they fulfil important biological roles under specific conditions.