Sandbox 502: Difference between revisions

Sm-like ([http://en.wikipedia.org/wiki/LSm Lsm]) proteins most closely resemble Sm proteins, both of which are found in the three domains of life <ref name ="wu">PMID:22615807</ref>.  Sm proteins play a large role in [http://en.wikipedia.org/wiki/Spliceosome spliceosome] biogenesis through mediating U1, U2, U4, U5, and U6 [http://en.wikipedia.org/wiki/SnRNP snRNP assembly]<ref name ="he">PMID:10801455</ref>.  The <scene name='Sandbox_502/U1_sm_ring/2'>Sm ring</scene> of proteins can be broken down into seven specific proteins (SmB, SmD1, SmD2, SmD3, SmE, SmF, and SmG in humans) all of which share a conserved Sm motif which is also found in the Lsm proteins<ref name ="he"/><ref name ="naidoo"/>. Eukaryotes have 16 or more Lsm proteins encoded in their genome, in contrast archaeal species have only one to three <ref name ="naidoo">PMID:18329667</ref>.  A total of nine specific Lsm proteins are found in yeast (Lsm1-Lsm9).  The Lsm proteins 2-7 most closely resemble Sm proteins D1-G, where Lsm 1 and 8 most closely resemble the SmB proteins <ref name ="he"/>.  Lsm9 does not appear to resemble any of the Sm proteins, although there have been some related structures found in the archaeal genome <ref name ="he"/>.  Several studies have shown that the Sm proteins form into seven membered rings which bind to the Sm binding site, a U rich sequence found in all but U6 snRNA<ref name ="he"/>.  Lsm proteins can form homomeric rings of heptamers, hexamers, or octamers<ref name ="wu"/>.  In addition they have been found to predominately associate into three complexes: Lsm2-8, Lsm1-7, and Lsm2-7 <ref name ="wu"/>.  The exact functionality of these complexes is in either [http://en.wikipedia.org/wiki/RNA_splicing pre-mRNA splicing], [http://en.wikipedia.org/wiki/Messenger_RNA#Degradation mRNA decay] or other roles, and is dictated by their composition, structure, and cellular location <ref name ="wu"/><ref name ="he"/>.  

Evidence suggests that there are two distinct Lsm complexes, Lsm1-7 which is associated with mRNA decay, and Lsm 2-8 which is associated with pre-mRNA splicing<ref name ="wu"/><ref name ="he"/>.  The first piece of evidence to suggest different roles is the cellular localization of the different Lsm complexes<ref name ="wu"/>.  For example, Lsm1 is predominantly cytoplasmic (where mRNA degradation takes place), as is the Lsm1-7 complex<ref name ="wu"/>.  The Lsm complex 2-8 is most likely nuclear because that is the location of U6 snRNP assembly <ref name ="pannone">PMID:10898971</ref>.  In addition, mutation experiments have shown that while Lsm2 to Lsm7 mutants have altered mRNA decay and splicing function, Lsm1 and Lsm8 mutants only have altered mRNA decay and pre-mRNA splicing function respectively <ref name ="he"/>.  Further evidence is found in [http://en.wikipedia.org/wiki/Immunoprecipitation immunopercipitation] experiments.  For example, while Lsm2 to Lsm7 co-immunopercipitate with both U6 snRNA and with mRNA decay factors, Lsm1 and Lsm8 only co-immunopercipitate mRNA degradation factors and U6 snRNA respectively <ref name ="he"/>.  Due to the difference in functionality of either Lsm1 or Lsm8 it is interesting to note that Lsm1 and Lsm8 are both closely related to the SmB protein<ref name ="he"/>.   

The Lsm complex 2-8 is involved in pre-mRNA splicing through association with the 3’terminal poly(U) tract of U6 snRNA <ref name="pannone"/>.  U6 snRNP is different from the other snRNPs because it is completely assembled in the [http://en.wikipedia.org/wiki/Cell_nucleus nucleus], whereas the other snRNAs first travel to the [http://en.wikipedia.org/wiki/Cytoplasm cytoplasm] <ref name ="pannone"/><ref name ="architecture of"/>.  While the exact mechanism by which the Lsm2-8 complex acts is unclear, it is thought that it provides stability and function to the U6 snRNP<ref name ="he"/>.  For example, several experiments using mutants with point mutations in the Lsm proteins 2-8 have shown defects in splicing that correlate with low levels of U6 snRNA <ref name ="he"/>.  It may also play a role in the various rearrangements that are necessary throughout the splicing cycle, and has been shown to be important in the assembly of U4-U6 di snRNP and U4-U5/U6 tri snRNP <ref name ="he"/>.  An interesting difference between the Sm and Lsm proteins is that in order to assemble the Sm ring RNA must be present, yet this is not a requirement in Lsm ring assembly <ref name ="pannone"/>.  Overall, there is significant evidence to suggest that the Lsm proteins 2-8 play a key role in spliceosome biogenesis and architecture. Lsm 1 has not been shown to associate with snRNA, rather it has been suggested to play a role in mRNA decay. 

As in ScLsm3, SpLsm3 exhibits the sm motif containing an N-terminal α-helix (residues 10-17) and a curved β-sheet (residues 19-89).  However rather than forming an octomeric ring structure it formed a heptameric ring structure in crystallization experiments.  SpLsm3 monomers interact through the same β4-β5 pairing as in ScLsm3.  The overall ring is 61.5Å wide, 31Å thick, where the pore is approximately 20.7Å wide.  In this crystal structure loop four is distorted  (Fig.4)<ref name ="wu"/>.  

With respect to the role of Lsm proteins binding to RNA substrates, the pore of the Lsm657-657 ring is positively charged, which would confer to interactions with negatively charged RNA.  The Sm ring of Archaeoglobus fulgidus in complex with polyU RNA shows that each of the Sm proteins interacts with one base of RNA through residues in loops 3 and 5, and that the RNA is passed through the pore.  Due to the fact that the residues between the Sm and Lsm proteins are fairly conserved it is possible that the Lsm proteins act through a similar mechanism.  Two main differences can be seen however. There should be a canonical arginine or lysine in loop five of Lsm5 that forms a hydrogen bond to a base in the RNA, yet there is an asparagine present.  In addition, a canonical aromatic residue that provides stacking interactions with an RNA base should be found in loop three of Lsm7, however there is a leucine present instead.  While these differences prevent one from applying the RNA-protein interactions of Sm proteins to Lsm proteins future studies may elucidate the exact mechanism <ref name ="mund">PMID:22001694</ref>.