Switches and latches on the ribosome

Call me a geek, but I'm a big fan of translational GTPases (trGTPases). They're essential factors for translation by the ribosome, highly conserved in all life and they're ancient. Really ancient. There were at least three (EF-Tu, IF2 and EF-G) in the ancestor of all life on earth. These have subsequently diversified through gene duplication and subfunctionalisation into the multiple trGTPase subfamilies that are known today.

Since a lot of my research is on trGTPase evolution,  I was really interested to see this paper today in Nature Structural and Molecular Biology: A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases. 

In this paper, Wang et al have identified a universally conserved residue, Pro22 of ribosomal protein L11 that switches conformation upon trGTPase EF-G binding, controlling the L11 and L12 protein interactions required for each peptide elongation cycle. They find that EF-G carries peptidyl-prolyl cis-trans isomerase (PPIase) activity, driving conformational switching of two adjacent prolines (PS22) from a trans to cis orientation. 

Most exciting for me is their claim that all known universal trGTPases contain an active PPIase center,  and therefore that the cis-trans isomerization of PS22 is a universal event required for efficient turnover of trGTPases throughout the translation process. This is pretty cool. Hang on though... structures show that the potential PPIase motif is located in the cleft between domains G and V of EF-G, but the other trGTPases they mention in the paper (IF2, EF-Tu, EF-G, EF4 (LepA) and RF3) don't carry a domain homologous to EF-G's C-terminal domain V, so how does that work? Their structural figures of RF3, EF-Tu and LepA show their predictions of where the PPIase centre might be in these proteins. In each case, the centre is formed by residues of the GTPase (G) domain that correspond to the EF-G PPIase sites, plus nearby residues in the non-homologous C-terminal domains of these various trGTPases. So we would predict that if this is a universal mechanism, at least those residues of the G domain that are involved should be universally conserved. Unfortunately, an alignment of this region isn't presented in the paper, but fortunately I have one up my sleeve:

The region of the G domain containing sites proposed to be acting as a PPIase (yellow highlighting). These are just upstream of the G4 nucleotide binding motif (highlighted in turquoise). These are consensus sequences: the residue shown for each trGTPase in each position is the most common amino acid found there across all sequences of the subfamily. In essence, each sequence is an average of hundreds of sequences.

The G domain is generally very well conserved across its length, with patches of universal conservation. However, the potential PPIase sites (yellow) are not universally conserved. The variability of these sites contrasts sharply with the nearby conserved G4 motif (one of the five motifs of the trGTPases - and in fact all GTPases - that coordinate the GTP/GDP nucleotides). It's disappointing, but this pattern of conservation doesn't really bear the hallmark of a universal mechanism. Indeed, Wang et al find that mutating the PPIase motif of EF-G has only a modest effect: a single turn of GTP hydrolysis was unaffected, but the multiple- turnover rates were inhibited by 15–40%. Similarly, mutation of PS22 did not completely abolish translation.

In fact, L11 is actually one of the few ribosomal proteins that is not essential for life, which makes L11 knock out strains useful molecular biological tools (for example this paper). Therefore, the mechanistic details of this protein's role in translation, although very interesting of course, do not translate to an understanding of the core principles of how trGTPase work on the ribosome.  

Are we really looking at something as concrete as a conserved "switch-and-latch" mechanism, or is PS22 just a trGTPase binding site with integral flexibility? Anyway, it's all interesting additional details of how trGTPases interact with the ribosome, and another plus: it got me blogging again after a long hiatus!

Reference:

Wang L, Yang F, Zhang D, Chen Z, Xu RM, Nierhaus KH, Gong W, & Qin Y (2012). A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases. Nature Structural & Molecular Biology PMID: 22407015