Small RNAs of the halophilic archaeon <i>Haloferax volcanii</i>

Soppa, Jörg; Straub, Julia; Brenneis, Mariam; Jellen-Ritter, Angelika; Heyer, Ruth; Fischer, Susan M.; Granzow, M; Voss, Bjoern; Hess, Wolfgang R.; Tjaden, Brian; Marchfelder, Anita

doi:10.1042/bst0370133

Cited by 28 publications

(26 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The red/green ratio denotes the average signal strengths of cDNAs generated from RNA co-purified with the FLAG-Lsm protein divided by the average signal strengths of a negative control cDNA generated from RNA purified from cultures only expressing the FLAG peptide. RNAs termed "sRNA" were previously identified as sRNAs in Haloferax (37,38). RNAs termed "H" and "p" had been predicted as sRNAs using bioinformatic approaches.…”

Section: Proteinmentioning

confidence: 99%

“…Interestingly, Methanocaldococcus jannaschii lacks a classical Lsm gene (9,36) Recently, it has been shown that H. volcanii also has an sRNA population potentially involved in gene expression regulation (37,38). To investigate whether the Haloferax Lsm is involved in sRNA regulation and to clarify its biological function, we generated a deletion strain for Lsm and analyzed the in vivo and in vitro function of this protein.…”

mentioning

confidence: 99%

See 1 more Smart Citation

The Archaeal Lsm Protein Binds to Small RNAs

Fischer

Benz

Späth

et al. 2010

Journal of Biological Chemistry

Self Cite

100

View full text Add to dashboard Cite

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...

show abstract

Section: Proteinmentioning

confidence: 99%

mentioning

confidence: 99%

The Archaeal Lsm Protein Binds to Small RNAs

Fischer

Benz

Späth

et al. 2010

Journal of Biological Chemistry

Self Cite

100

View full text Add to dashboard Cite

show abstract

“…They led to the elucidation of sRNAs in all tested archaeal species, i.e., Archaeoglobus fulgidus, 27 Sulfolobus solfataricus, 28 Methanosarcina mazei 29 and H. volcanii. 30,31 In summary, the picture emerged that the presence of sRNAs is widespread in archaea and that the number is comparable to the number of sRNAs in bacteria.…”

Section: Introductionmentioning

confidence: 99%

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

Babski¹,

Tjaden²,

Voss³

et al. 2011

RNA Biology

Self Cite

View full text Add to dashboard Cite

“…Subsequently, RNomics revealed the presence of additional sRNAs in two archaeal organisms: Sulfolobus solfataricus and Archaeoglobus fulgidus [11,12]. Since that time, sRNAs have been identified in several archaeal species [13][14][15][16][17][18][19][20][21]. In addition to the already identified snoRNAs, cis-encoded antisense RNAs and trans-encoded sRNAs were identified (for a review, see [22]).…”

mentioning

confidence: 99%

Regulatory RNAs in Haloferax volcanii

Fischer

Benz

Späth

et al. 2011

Biochemical Society Transactions

Self Cite

View full text Add to dashboard Cite

In organisms of all three domains of life, a plethora of sRNAs (small regulatory RNAs) exists in addition to the well-known RNAs such as rRNAs, tRNAs and mRNAs. Although sRNAs have been well studied in eukaryotes and in bacteria, the sRNA population in archaea has just recently been identified and only in a few archaeal species. In the present paper, we summarize our current knowledge about sRNAs and their function in the halophilic archaeon Haloferax volcanii. Using two different experimental approaches, 111 intergenic and 38 antisense sRNAs were identified, as well as 42 tRFs (tRNA-derived fragments). Observation of differential expression under various conditions suggests that these sRNAs might be active as regulators in gene expression like their bacterial and eukaryotic counterparts. The severe phenotypes observed upon deletion and overexpression of sRNA genes revealed that sRNAs are involved in, and important for, a variety of biological functions in H. volcanii and possibly other archaea. Investigation of the Haloferax Lsm protein suggests that this protein is involved in the archaeal sRNA pathway.

show abstract

Small RNAs of the halophilic archaeon Haloferax volcanii

Cited by 28 publications

References 30 publications

The Archaeal Lsm Protein Binds to Small RNAs

The Archaeal Lsm Protein Binds to Small RNAs

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

Regulatory RNAs in Haloferax volcanii

Contact Info

Product

Resources

About