In the previous posting, I asked which state is more like the ancestral state – the eukaryotic system with its larger RNA molecule, Alu domain, and SRP9/14 proteins or the bacterial system with its smaller RNA molecule lacking an Alu domains and the SRP9/14 proteins?
Consider the secondary structure of the SRP RNA from mammals and E.coli*. Here is the complex mammalian RNA:
and here is the much simplified E. coli RNA, where the entire left half (the Alu domain) is missing:
So which is more like the ancestral state?
We can first look to protozoa, which constitute a diverse set of unicellular eukaryotes. The Alu domain is present in most protozoa that have been analyzed, albeit with some significant variations . The same theme holds true with fungi. The SRP9/14 proteins are found in algae, amoeba, and the protozoa that cause malaria, but missing in other protozoa. These data are consistent with the blind watchmaker gradually stringing together the process of elongation arrest during the evolution of eukaryotes. But they are also consistent with independent loss of these proteins. So let’s take a closer look at the prokaryotes, as a much more interesting picture emerges.
If we first consider Archaea, they have the ‘eukaryotic’ version of the large RNA, complete with an Alu domain that is strongly conserved in terms of size and structure!  Have a look at the archaeal SRP RNA (and compare it to the mammalian and E. coli versions above):
What is most interesting is that their Alu domain closely resembles that found in humans, where the entire RNA “can be folded into a series of helices that are virtually identical to the secondary structure of human SRP RNA.”  In other words, the human Alu domain looks more like the archaeal Alu domain than other protozoan Alu domains, even through the later organisms, being eukaryotes like humans, should be more closely related. Archaea are also completely missing the SRP9 and SRP14 proteins and it is not known if their ribosomes undergo elongation arrest. Yet it gets better.
While it is true that most bacteria lack the Alu domain, many gram positive bacteria do not. In fact, the RNA from the bacterium B. subtilis looks very much like that found in humans and archaea. Have a look at the SRP RNA from gram positive bacteria:
And while B. subtilis likewise does not contain the SRP9 and SRP14 proteins, unlike archaea, its Alu domain binds to a protein known as HBsu.  HBsu is a small protein that is very similar to proteins that normally bind DNA and it seems to be an important component in SRP function in B. subtilis. 
Since eukaryotes, archaea, and gram positive bacteria all have the same RNA component of the SRP system, this strongly suggests the larger version of RNA is ancestral and that the smaller version lacking the Alu domain was lost very early in most bacterial lineages through reductive evolution. This view is supported by the fact that chloroplasts, the highly simplified and extensively streamlined descendents of cyanobacteria, have completely lost their entire RNA component through reductive evolution.
If the RNA with the Alu domain is indeed ancestral, we have a fairly decent echo of front-loading. Clearly, this Alu domain is not needed for the bacterial way of life as seen by the majority of bacteria that lack it. Yet it is an essential component of elongation arrest in eukaryotes. If the first cells were front-loaded to evolve the eukaryotic cell plan, might the ancestral Alu domain have nudged into existence the necessary appearance of elongation arrest once eukaryotes arose? After all, the structure of the Alu domain is remarkably conserved in gram positive bacteria and archaea, indicating that it has hung around for vast spans of evolutionary time, despite being jettisoned by most bacteria. This means it could have served as the bait to fish out components that would interact with the Alu domain to elicit a full blown elongation arrest. Since SRP9, SRP14, and HBsu are all small, simple proteins, the baiting might work. In fact, what is striking is that even though these proteins are not related, and SRP9/14 need to work as a team to bind the Alu domain, while HBsu can do it alone, the three dimensional structures of Hbsu and the SRP9/14 complex show remarkable similarity . Apparently the conserved structure of the Alu domain fished out similarly shaped proteins in two different evolutionary lineages.
Oh, but it gets even better, as the nudging potential of the Alu domain may have reached much further into the future than the evolution of eukaryotic cell plan. Time to buckle those seat belts.