From function to structure take the archaeal TRAM.
In the course of evolution, interactions between objects create new relationships and this creates functions. In turn, functions capture pre existing structures and both act and evolve together. Shaping RNA is sensitive to cold. Archaea have found a way that differs from that of Bacteria to help proper RNA folding in the cold, thus illustrating how life could solve a general physico chemical hurdle. In a stroke of genius Carl Woese, back in 1977, named archaebacteria a group of prokaryotes that appeared to form a third domain of life (Woese and Fox, 1977) The name was important because it suggested implicitly that these organisms were ancient. It is notorious that the general public and scientists as well are nominalists: 'stat rosa pristina nomine, nomina nuda tenemus' as the late Umberto Eco highlighted in his famous book, The Name of the Rose. Associated to a name, a good many hidden memories are attached. If organisms spring from archaic organisms, near the origin of life, we will implicitly assume that they must witness harsh conditions. Despite the fact that one of the organisms studied by Woese was a mesophile, this assumption will consolidate the misleading notion that Archaea all but thrive in extreme environments that they are the only organisms able to colonize especially hot springs in volcanos above or below the sea level. Woese also implied that the origin of prokaryotes and of what he named 'ukaryotes' corresponded to organisms (progenotes) that were simpler than the extant ones. While this introduced an interesting possible origin of cells as predating eukaryotes, this added another misconception that constrained reflection for decades and is still pregnant, that ancient organisms must be small and simple. This is despite the repeated observation, in other circumstances (human engineering of computers for example) that, once emerging, first contraptions are generally very large, whereas miniaturization is a sign of advanced evolution. Prokaryotes are certainly as evolved as are eukaryotes. Because they form the third domain of life, quite distinct from Bacteria and Eukarya, Archaea, which epitomise the ability of minute organisms to sustain harsh conditions [an archaeon holds the record high temperature for growth 1138C (Stetter, 2013) ought to be the subject of intense studies. They should also become considerably more familiar to us: do not they contribute to the widely advertised negative input of the bovine livestock to climate change, via production of methane? Indeed they are highly evolved ordinary commensals of polygastric cattle where they form communities associated with a huge number of bacteria and a wealth of poorly known protists (Wallace et al. 2015) They are also frequently reported from soil where they form an important community of ammonium oxidizers (Sterngren et al. 2015) This makes them denizens of medium range temperature environments, but methanogens (always belonging to Archaea) are also present in cold or very cold habitats, far from the scalding temperatures the general public tends to associate to them. In a nutshell, organisms of this domain of life are present everywhere, or, rather, in all environmental niches poor in oxygen or anoxic, although some archaeal extreme halophiles grow aerobically. Part of the reason for the relative lack of knowledge about these remarkable organisms stems from the fact that they are generally difficult to grow and that many grow very slowly. To be sure, setting up laboratory facilities for growth in the absence of oxygen is tedious. However, these organisms are of considerable interest to understand the deep nature of biological functions. Indeed, contrary to a widely spread belief, more often than not, the structure does not tell the function. In the same way as when to avoid soiling our hands we use a large leaf, a pair of chopsticks or a fork, biological functions may be implemented in structures from completely foreign descents. Within the realm of prokaryotes, Archaea differ considerably from Bacteria, and their study allows investigators to better understand important functions via the study of conserved, yet genetically remote, functions. Received 7 March, 2016; accepted 12 March, 2016. *For correspondence. E mail antoine.danchin@normalesup.org; Tel. 1331 42 17 79 81; Fax 1331 42 17 84 73.
Environmental microbiology