Sandbox WWC7: Difference between revisions

In the ''Zea mays'' plastid, PPR10 binds specifically to the ssRNA oligonucleotides atpH (17 nucleotides: 5'-GUAUUCUUUAAUUAUUUC-3') and <scene name='69/696301/Atph/1'>spaJ</scene> (18 nucleotides: 5'-GUAUUCUUUAAUUAUUUC-3') where it has been shown to prevent degradation of sequences both upstream and downstream of its binding sites. In addition to stabilizing these RNA sequences, PPR10 increases the rate at which they are translated.<ref name = "translation"/>

The primary factor in the ability of PPR10 to bind RNA bases in a modular fashion lies in the identities of the residue at position 6 on a repeat and the residue at position 1 on the next repeat (designated 1'). For example, in the structure to the right, <scene name='69/696301/G1binding/1'>threonine residue 178 (blue) forms a hydrogen bond to G1 (green) of psaJ.</scene> Through van der Waals interactions, Val210 and Arg175 (both orange) also contribute to the specific binding of guanine in this example. These residues force G1 into a conformation where it forms a hydrogen bond to Thr178. The example of PPR10 binding G1 of spaJ exemplifies the general rules by which PPR proteins bind specific nucleotides: firstly, a residue at the 6 position of one repeat (Thr178 in the previous example) forms a hydrogen bond with the base. The identity of this residue determines whether the repeat will bind a purine (adenine and guanine) or pyrimidine (cytosine and uracil). It appears that serine and threonine at position 6 are specific for purines, and asparagine at position 6 is specific for pyrimidines.<ref name = "barkan">doi:10.1371/journal.pgen.1002910</ref> Secondly, a residue at position 1' (Val210 in the previous example) completes the specificity of the interaction. Through van der Waals interactions, this residue determines between A/G and C/U. Other amino acids further contribute to this mechanism, but the previously described rules always apply when PPR proteins bind RNA sequences with modularity.<ref name = "engineering">DOI:10.1111/tpj.12377</ref>

This image shows the general code by which PPR proteins recognize and bind RNA in a modular fashion<ref name = "barkan"/>

The mechanism by which PPR10 increases the rate of translation is still unknown. However, it is predicted that PPR10 binds to sequences near the ribosome binding site of the RNA transcript. By doing so, PPR10 prevents the ~20 nucleotides to which it is bound from base pairing to the ribosome binding site and impairing translation. Considering the bacterial origins of the chloroplast, it is interesting to note that the RNA stabilizing and translation enhancing properties of PPR10 in the platid mirror the some of the functions of small RNAs (smRNA) in bacteria. In bacterial cells, smRNAs similarly bind regions near ribosome binding sites of mRNA, preventing degradation by nucleases and increasing translation by preventing base-pairing to ribosome binding sites.<ref name = "translation"/>