Question

I need to elaborate a general comparison between "Group I-Group II introns" and "nuclear introns". Please could you help with the main features? Thank you!

Answer 1

Ans: Well, first of all, you have to know what is Splicing? Splicing is a mechanism by which the introns (carried by pre- mRNA) gets deleted from pre-mRNA to form mature mRNA by the help of spliceosome (which have only exon or the coding sequence).

Now, I will first discuss the Nuclear pre-mRNA splicing and after that group I & group II intron splicing.

Nuclear pre-mRNA splicing: There are five types of RNAs (UI, U2, U4, U5, U6) which are collectively called small nuclear RNAs (snRNAs) and all of these are complexed with several proteins. These RNA-protein complexes are called small nuclear ribonuclear proteins (snRNPs). It has 3 roles in it:

a) It recognizes the 5' splice site and the branch site

b) it brings those sites together

c) and it catalyzes the RNA cleavage and joining reactions.

Now, first of all, 5' splice site is recognizes by U1 snRNPs. One sub-unit of U2AF binds to the Py tract and the other to the 3' splice site. The former subunit interacts with BBP and helps it to bind to the branch site. This whole arrangement of protein and RNA are called early complex.

Then U2snRNP binds to the branch site replacing BBP with the help of U2AF. This is called A complex. Next step is to bring all three splice sites and this is achieved by incorporation of U4, U6, U5 snRNPs and finally it forms B complex from A complex. Now, U1 leaves the complex, and U6 replaces it at the 5' splice site. This requires that the base pairing between the U1 snRNA and the pre-mRNA be broken, allowing the U6 RNA to anneal with the same region. U4 is released from the complex allowing U6 to interact with U2. This arrangement, called the C complex, produces the active site. Formation of the active site juxtaposes the 50 splice site of the pre-mRNA
and the branch site, facilitating the first transesterification reaction. The second reaction, between the 5' and 3' splice sites, is aided by the U5 snRNP, which helps to bring the two exons together. The final step involves the release of the mRNA product and the snRNPs. The snRNPs are initially still bound to the lariat, but they get recycled after rapid degradation of that piece of RNA.

-Another term you have to understand, that is Self-splicing. It means, that these introns can remove itself from RNAs in absence of any other proteins or RNA molecules.

Group-I introns: Group I introns splice by a different pathway. Rather than a branchpoint A residue, they use a free G nucleotide or nucleoside. This G species is bound by the RNA, and it's 3'-OH group is presented to the 5' splice site. The same type of transesterification reaction that leads to the lariat formation in the earlier examples here fuses the G to the 5' end of the intron. The second reaction now proceeds like the last process and the freed 3' end of the exon attacks the 3' splice site. This fuses the two exons and releases the intron. Although, in this case,
the intron is linear rather than a lariat structure.

Group II Introns: In the case of group II introns, the chemistry of splicing and the RNA intermediates produced are the same as those for nuclear pre-mRNAs, The intron uses an A residue within the branch site to attack the phosphodiester bond at the boundary between its 5' end and the end of the 5' exon—that is, at the 5' splice site. This reaction produces the branched lariat and is followed by a second reaction in which the newly freed 3'-OH of the exon attacks the 3' splice site, releasing the intron as a lariat and fusing the 3' and 5' exons.

I have uploaded a picture demonstrating these 3 types of splicing mechanism ina concise manner. I hope this will help you.