All ribosomes are equal, but some ribosomes are more equal than others

There are many ways of regulating translation - different mRNA structures, modifications of the canonical set of translation factors, specialized factors and so on. Well, you can also have different ribosomes and they may have different functions.

Here is a review about different ribosomal flavors. Main points:

1. rRNA can be modified differently under different conditions, thus resulting in ribosomes with different properties, such as thermal stability, affinity between 30S and 50S, etc. Here it an example of ITC used for studying these rRNA-modified ribosomes.

2. Ribosomes can have different rRNA and proteins when produced under different conditions. The most striking example is Haloarcula marismortui with 3 rRNA operones, out of which one codes extremely divergent copy which is expressed at high temperatures. You mess with it and bug becomes temperature sensitive.

3. Profs of functional differences of these ribosomes - here we do not have much. Stability - yes, see above. But function...

Well, we do have a bunch of proteomics data showing that in Saccharomyces cerevisiae different paralogues of r-proteins localize differently and are specifically involved in translation of some mRNAs.

A quick reminder - Saccharomyces cerevisiae had a whole genome duplication (WGD), thus they generally have loads of paralogues and thus are used to study evolution of proteins after duplication. Apart from yeast, WGD has happend in many other lineages (bony fish, plants), and it would be interesting to see what happens to r-proteins during WGD...

Back to the functionality of different ribosomes. One interesting possible functional regulation is discussed. Knocking out non-essential ribosomal protein Rps25 makes ribosomes incapable of translating some IRESes, though no effect on normal cap-dependent translation. Is expression of Rps25 regulated during viral invasion? No evidence of that as yet.

4. There are two possible ways of using different ribosomes:

First it can be that when the cell changes its ribosomal set, changes one flavor for another, no mixing - a global rewiring of the translational machinery. This seems to be the case for rRNA modification in bacteria - appropriate enzyme is induced  under certain conditions and all the ribosomes are modified, viola. Same for different rRNA genes in archaea.

Alternative approach is to have many different ribosomes for different mRNAs. This is seemingly what we have in yeast (see above). Specific localization of different ribosomes and use of different mRNA-specific factors would then ensure proper coupling of appropriate ribosome with the right mRNA. Different localization of different paralogues of r-proteins in Saccharomyces cerevisiae is shown experimentally, and these proteins have different requirements for assembly into the 80S.

PS: what all the ribosomes have in common is their color. They all are yellow.

References:

1. Gilbert VW. Functional specialization of ribosomes? (2011) Trends. Biochem. Sci. 2011 PIMD 21242088

2. Lopez-Lopez at al. Intragenomic 16S rDNA divergence in Haloarcula marismortui is an adaptation to different temperatures. (2007) J. Mol. Evol. 65, 687–696

3. Esguerra J. et al. Functional importance of individual rRNA 20-O-ribose methylations revealed by high-resolution phenotyping. (2008) RNA 14, 649–656

4. Komilli at al. Functional specificity among ribosomal proteins regulates gene expression. (2007) Cell PIMD 17981122

4. Kellis at al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae (2007) Nature v. 131 pp 557-571