Oligomerization behavior of the archaeal Sm2‐type protein from Archaeoglobus fulgidus

Abstract

As part of a functional analysis of archaeal Sm-related proteins, we have studied the oligomerization behavior of the Sm-2 type protein from the euryarchaeon Archaeoglobus fulgidus using gel filtration chromatography and noncovalent mass spectrometry. Our experiments show that the oligomeric state of the protein depends on the pH and presence of RNA. The protein forms a hexamer at acidic pH in the absence of RNA. The addition of RNA (oligo U 10 ) induces the formation of a heptamer over the whole pH range studied. The stability of both the hexamer and the RNA-bound heptamer increases at lower pH.Keywords: archaea; Sm-like protein; Sm fold; RNA binding; heptamer; hexamer; noncovalent mass spectrometry The Sm protein family is characterized by a conserved bipartite sequence motif of ;70 amino acids, which is called the Sm domain. The domain contains two conserved sequence segments, known as the Sm1 and Sm2 motifs, separated by a loop region which differs in length and sequence among the family (Séraphin 1995; SalgadoGarrido et al. 1999). b-Strands 1, 2, and 3 constitute the first motif, and b-strands 4 and 5 constitute the second motif of the Sm domain. The overall architecture of the Sm monomer, a barrel-type OB-fold structure, is completed by the N-terminal a-helix (Fig. 1). In eukaryotes, seven distinct Sm or Sm-like (Lsm) proteins, together with various RNAs that contain the short, single-stranded, uridine-rich Sm site, form the core domain of the small nuclear ribonucleoprotein particles (snRNPs), which are essential for several RNA-processing events such as (Mattaj et al. 1993;Hermann et al. 1995;Will and Lührmann 2001), and telomerase activity (Seto et al. 1999). Sm-related proteins have also been identified in archaea and eubacteria through database searches (Salgado-Garrido et al. 1999;Møller et al. 2002). The in vivo function of the archaeal Sm proteins is widely unknown; however, experimental results from our laboratory suggest their potential involvement in transfer RNA (tRNA) maturation (Törö et al. 2001). Archaeal Sm proteins share the common Sm fold, bind to U-rich RNA sequences, and form ringshaped homo-hexameric or -heptameric complexes. The assembly of the protein complexes is primarily maintained through interactions between the b4 and b5 strands of adjacent monomers (Collins et al. 2001;Törö et al. 2002). The maximum number of distinct Sm proteins found in archaeal species is currently three. At present, there are only four archaeal species known (Pyrobaculum aerophilum, Sulfolobus acidocaldarius, Sulfolobus solfataricus, and Sulfolobus tokodaii) that contain all three Sm-type proteins. The Sm1-type is most abundant among Reprint requests to: Dietrich Suck, Structural and Computational Biology Programme, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; e-mail: suck@embl.de; fax: 49-6221-387306.Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi

Similar Modes of Interaction Enable Trailer Hitch and EDC3 To Associate with DCP1 and Me31B in Distinct Protein Complexes

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The Small β-Barrel Domain: A Survey-Based Structural Analysis

“…The SBB module also appears to enable oligomeric plasticity, including for various paralogs that form heteromeric assemblies or even for the very same protein (homomeric assemblies). As a striking example, the SBB of the Archaeoglobus fulgidus SmAP2 protein forms both hexamers and heptamers depending on solution-state conditions (a hexamer at low pH, without RNA, but a heptamer in the presence of U-rich RNA; Kilic et al, 2006). In terms of SBB structure, the mechanistic basis of such plasticity remains murky; recent molecular simulations suggest a role for both residue-level conformational dynamics and rigid-body structural rearrangements (McAnany and C.M, unpublished data).…”

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