Structure and assembly of an augmented Sm-like archaeal protein 14-mer

Mura, Cameron; Phillips, Michael R.; Kozhukhovsky, A.; Eisenberg, David

doi:10.1073/pnas.0538042100

Cited by 51 publications

(50 citation statements)

References 37 publications

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“…At present we do not know which subunits carry such sites. Structural studies on the SmAP3 (archaeal Lsm protein) homoheptamer and the homooctamer formed by yeast Lsm3 in bacteria reveal that the residues in the C-terminal extension could facilitate intersubunit interactions within the Lsm ring and between two Lsm rings (Mura et al 2003b;Naidoo et al 2008). These observations suggest that the CTD of Lsm1 may also make contacts with the Lsm2 through Lsm7 or Pat1 subunits.…”

Section: Discussionmentioning

confidence: 99%

Both Sm-domain and C-terminal extension of Lsm1 are important for the RNA-binding activity of the Lsm1–7–Pat1 complex

Chowdhury¹,

Raju²,

Kalurupalle³

et al. 2012

RNA

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Lsm proteins are a ubiquitous family of proteins characterized by the Sm-domain. They exist as hexa-or heptameric RNAbinding complexes and carry out RNA-related functions. The Sm-domain is thought to be sufficient for the RNA-binding activity of these proteins. The highly conserved eukaryotic Lsm1 through Lsm7 proteins are part of the cytoplasmic Lsm1-7-Pat1 complex, which is an activator of decapping in the conserved 59-39 mRNA decay pathway. This complex also protects mRNA 39-ends from trimming in vivo. Purified Lsm1-7-Pat1 complex is able to bind RNA in vitro and exhibits a unique binding preference for oligoadenylated RNA (over polyadenylated and unadenylated RNA). Lsm1 is a key subunit that determines the RNA-binding properties of this complex. The normal RNA-binding activity of this complex is crucial for mRNA decay and 39-end protection in vivo and requires the intact Sm-domain of Lsm1. Here, we show that though necessary, the Sm-domain of Lsm1 is not sufficient for the normal RNA-binding ability of the Lsm1-7-Pat1 complex. Deletion of the C-terminal domain (CTD) of Lsm1 (while keeping the Sm-domain intact) impairs mRNA decay in vivo and results in Lsm1-7-Pat1 complexes that are severely impaired in RNA binding in vitro. Interestingly, the mRNA decay and 39-end protection defects of such CTD-truncated lsm1 mutants could be suppressed in trans by overexpression of the CTD polypeptide. Thus, unlike most Sm-like proteins, Lsm1 uniquely requires both its Sm-domain and CTD for its normal RNA-binding function.

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Section: Discussionmentioning

confidence: 99%

Both Sm-domain and C-terminal extension of Lsm1 are important for the RNA-binding activity of the Lsm1–7–Pat1 complex

Chowdhury¹,

Raju²,

Kalurupalle³

et al. 2012

RNA

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“…The Lsm1 and Lsm2 proteins have been shown to be associated in vivo (28), so they might also form heteromeric complexes. Crenarchaeota have an additional Lsm protein, Lsm3, which * This work was supported by the Deutsche Forschungsgemeinschaft contains a traditional Sm domain fused to a second domain by a flexible linker (29,30).…”

mentioning

confidence: 99%

“…The Lsm2 protein from Archaeoglobus fulgidus has been reported to form a hexameric (34) or a heptameric (31) complex. The Lsm3 protein has also been shown to form 14-mer complexes (30), a process of which some of the Lsm1 proteins are also capable (35).…”

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confidence: 99%

The Archaeal Lsm Protein Binds to Small RNAs

Fischer

Benz

Späth

et al. 2010

Journal of Biological Chemistry

100

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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...

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“…Members include eukaryotic Lsm (Salgado-Garrido et al, 1999), Sm (Kambach et al, 1999) and SMN/Gemin proteins (Selenko et al, 2001;Ma et al, 2005), archaeal Lsm proteins (Collins et al, 2001), the bacterial protein Hfq (Schumacher et al, 2002) and a recently identified Lsm homolog of cyanophage origin (Das et al, 2009). Eukaryotic genomes can contain up to 16 Lsm and 7 Sm proteins (Albrecht & Lengauer 2004), yet 2-3 Lsm proteins are generally encoded in archaea (Collins et al, 2001;Toro et al, 2002;Mura et al, 2003) and only a single form is evident in bacteria and cyanophage (Schumacher et al, 2002;Das et al, 2009). A characteristic feature of the Lsm proteins is their natural tendency to form ring-shaped quaternary complexes, each of a precise composition related to cellular location and RNA target (Beggs, 2005;Spiller et al, 2007).…”

Section: Phylogeny Of Lsm Protein Sequencesmentioning

confidence: 99%

“…This protein is suggested to be dimeric in solution (Ling et al, 2008). The archaeal protein Pa-Sm3 contains an Lsm-like domain in addition to a C-terminal domain of unknown function adopting an /-fold (Mura et al, 2003).…”

Section: Phylogeny Of Lsm Protein Sequencesmentioning

confidence: 99%