Sandbox 502: Difference between revisions

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 processing of [http://en.wikipedia.org/wiki/Pre-mRNA pre-mRNA] takes place through the use of a large dynamic machine known as the spliceosome, through which [http://en.wikipedia.org/wiki/Intron introns] are removed and [http://en.wikipedia.org/wiki/Exon exons] are spliced together to create a mature [http://en.wikipedia.org/wiki/MRNA mRNA]<ref name ="architecture of"/><ref name ="structure and function">PMID:19000813</ref>.  The spliceosome is comprised of five [http://en.wikipedia.org/wiki/SnRNA snRNA] molecules (snRNAs U1, U2, U4, U5, and U6) and over one hundred associated proteins<ref name ="architecture of"/><ref name ="structure and function"/>.  Assembly of the spliceosome is thought to take place in a stepwise manner around the pre-mRNA transcript<ref name ="architecture of"/><ref name ="structure and function"/>.  The first step involves recognition of the 5’ splice site by U1 snRNP, followed by recognition of the branch point sequence by U2 snRNP<ref name ="architecture of"/><ref name ="structure and function"/>.  From this point the remaining snRNPs U4, U5, and U6 join as a preformed tri-snNRP<ref name ="architecture of"/><ref name ="structure and function"/>.  Together the five snRNPs form the precatalytic spliceosome which must undergo a series of changes before it can actively splice<ref name ="structural evidence">PMID:19525970</ref><ref name ="structure and function"/><ref name ="common design">PMID:19525970</ref><ref name ="architecture of">PMID:22471593</ref>.

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.   

In yeast degradation of mRNA takes place by first shortening the poly(A) tail then the removing the 5’cap by [[4a53|Dcp1]], a decapping protein <ref name ="pannone"/>.  The major exoribonuclease in mRNA decay ([[2y35|Xrn1]]) then quickly degrades the decapped mRNA <ref name ="pannone"/>.  Interestingly, when the Lsm 1-7 complex is purified Xrn1, Dcp1, Mrt1 (an additional protein associated with mRNA decapping), and mRNA co-immunopercipitate <ref name ="pannone"/>.  However, it is not only Lsm 1 that plays a role in mRNA decay.  Lsm mutants of the 2-7 proteins have increased amounts of capped, deadenylated mRNAs <ref name ="pannone"/>.  There are two postulated functions of the Lsm1-7 complex in mRNA decay.  The first suggests that the Lsm ring binds to the mRNA first then recruits the Dcp1, the second function may be to facilitate rearrangements of the mRNP complex to allow decapping enzymes access to the 5’cap <ref name ="he"/>.  Lsm proteins therefore do not only appear to play a role in creating functional mRNA, but also in degradation of mature mRNA.   

Sm and Lsm proteins both exhibit the Sm motif, which consist of an <scene name='Sandbox_502/Splsm3_alpha/2'>N-terminal</scene> [http://en.wikipedia.org/wiki/Alpha_helix α-helix] proceeded by a twisted <scene name='Sandbox_502/Splsm3_beta/2'>five stranded </scene>[http://en.wikipedia.org/wiki/Beta_sheet β-sheet] <ref name ="wu"/><ref name ="naidoo"/>).  Loop L4, located between stands β3 and β4 of the β sheet, varies between 3 to 30 residues in length across the different Lsm proteins <ref name ="naidoo"/>.  The β-sheet encloses a set of hydrophobic residues <ref name ="naidoo"/>.  When the Lsm ring is assembled the hydrophobic region spreads into the now adjacent Lsm protein monomers <ref name ="naidoo"/>.  When assembled into the ring between each subunit there are hydrogen bonds formed between β4 of one subunit and β5 of the neighboring subunit <ref name ="naidoo"/>.  These interactions provided the Lsm ring with enough contacts to make a very stable structure <ref name ="naidoo"/>.  There are two sides to the ring, the helix face and the loop face, found on opposite sides of the ring <ref name ="wu"/>.  It has been postulated that a U-rich RNA may bind to the inner portion of the helix face, and take part in hydrogen bonding interactions with residues located on loops 3 and 5, as well as potentially pass through the pore itself <ref name ="naidoo"/>.