Homomeric Ring Assemblies of Eukaryotic Sm Proteins Have Affinity for Both RNA and DNA

Abstract

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) singlestranded DNA.

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

“…Canonical (L)Sm proteins multimerize in a head-to-tail fashion via an antiparallel arrangement of the ␤-strands ␤4 and ␤5. This leads to six-or seven-membered homo-or heteromeric rings with a continuous inner ␤-sheet (10,25,27,38,44,48,49). Similar multimerization properties were therefore predicted for the LSm domain of Tral and EDC3 (2).…”

“…These proteins have the Sm fold, which comprises an N-terminal ␣-helix stacked on top of a five-stranded ␤-barrel-like structure (10,25,38,44,48,49). Sm domains often oligomerize to form hexameric or heptameric rings that stably or transiently associate with singlestranded RNA.…”

A Protein Interaction Framework for Human mRNA Degradation

“…As observed with the yeast proteins (FromontRacine et al 2000), each human Lsm protein was capable of interacting with multiple other Lsm proteins (Table 1). Indeed, in vitro, Lsm3 can form homo-oligomeric ring structures (Collins et al 2003). However, these interactions conflict with evidence that in yeast each Lsm complex contains seven Lsm proteins (SalgadoGarrido et al 1999).…”

A Divergent Sm Fold in EDC3 Proteins Mediates DCP1 Binding and P-Body Targeting

“…The major contacts between the subunits of the ring are mediated by antiparallel interactions between the backbones of strand ␤4 of one subunit and strand ␤5 of the adjacent subunit. RNA binding is mediated mainly by residues in loops between strands ␤2 and ␤3 and between strands ␤4 and ␤5 (loops L3 and L5, respectively), which face the lumen of the ring (7,20,26,33,40,41).The eubacterial and archaeal genomes encode from one to three (L)Sm paralogs that form homohexameric or homoheptameric rings, while eukaryotes encode more than eighteen (L)Sm paralogs that assemble into heteroheptameric rings of different composition and function (reviewed in references 1, 2, 21, and 46).Seven of the eukaryotic proteins (SmB, SmD1, SmD2, SmD3, SmE, SmF, and SmG) form a ring that stably associates with RNA polymerase II-transcribed uridine-rich small nuclear RNAs (i.e., U1, U2, U4, and U5), and functions in uridine-rich snRNP biogenesis and mRNA splicing (18,21,34,46). In addition to the Sm ring, at least two LSm rings have been described (1,2,18,21,34,46).…”

“…The major contacts between the subunits of the ring are mediated by antiparallel interactions between the backbones of strand ␤4 of one subunit and strand ␤5 of the adjacent subunit. RNA binding is mediated mainly by residues in loops between strands ␤2 and ␤3 and between strands ␤4 and ␤5 (loops L3 and L5, respectively), which face the lumen of the ring (7,20,26,33,40,41).…”