A recent research article nicely illustrates how front-loading is an increasingly plausible perspective on evolution. The article is Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestorby Bridgham et al.
The researchers analyzed the superfamily of nuclear receptor transcription factors. As they note, these proteins represent “a diverse superfamily of transcriptional regulators that play key roles in animal development, physiology, and reproduction.” I briefly described one such receptor earlier – the retinoic acid receptor – as it appears the Alu elements are front-loaded to generate DNA binding sites for these proteins.
This class of receptors share common features:
a modular domain structure, including a highly conserved DNA-binding domain (DBD) and a moderately conserved ligand-binding domain (LBD)—which in most receptors contains a ligand-regulated transcriptional activation function—along with extremely variable hinge and N-terminal domains.
To recognize why this study is relevant to front-loading, pay close attention to this paragraph.
It is widely believed that the NR superfamily evolved from a ligand-independent transcriptional activator, with binding of different ligands gained independently in numerous NR lineages ,. The alternate view—that NRs evolved from a liganded ancestor, with ligand-dependence lost in the lineages leading to the ligand-independent receptors—has received little attention. These two hypotheses exemplify opposite views on the general nature of molecular evolution and the origin of complex functions. The hypothesis that the ancestral NR was ligand-independent implies that a complex molecular function—allosteric regulation of transcription by binding a ligand—evolved de novo many independent times, requiring evolution to repeatedly create novelty and complexity ,. In contrast, the hypothesis of a ligand-activated ancestor implies that evolution produced new functions primarily by subtle tinkering with a conserved ancestral mechanism ,, which allowed receptors to accommodate new molecular partners or lose dependence on those partners because of mutations that modified or degraded existing functions.
Okay, so there are two hypotheses concerning the evolutionary expansion of this family of receptors.
The first view is the most widely shared view and begins with a DNA binding protein that later acquires the ability to bind other molecules that in turn will regulate its DNA binding. This view envisions a “simple beginning” that is gradually made more complex with the addition of evolutionary innovations.
The second view has been neglected and begins with a protein that is much like extant nuclear receptor transcription factors, in that both the ability to bind DNA and another ligand are present and subsequent evolution simply tinkers around with the basic theme.
Those familiar with my hypothesis of front-loading will recognize that it would predict the second view to be more accurate. New functions coming about by subtle tinkering with a conserved ancestral mechanism better connects the past to the future, where subsequent evolution can be nudged, than de novo evolution repeatedly creating novelty and complexity.
And what did the authors find?
Our findings indicate that NR LBDs evolved their functional diversity by tinkering with a ligand-dependent transcriptional activator. Ligand-regulated NRs are thermodynamically tuned so that in the appropriate contexts the active conformation is favored in the presence of activating ligand but not its absence. The most common functional shift during NR evolution was modification of ligand specificity due to subtle changes in the shape and surface properties of the ancestral ligand pocket. Both historical and contemporary studies indicate that such shifts in ligand preference can evolve through a relatively small number of mutations that subtly alter the ligand cavity (e.g., –).
In other words, the second, front-loading-friendly, view was discovered to be most likely. The expansion of this family of control proteins that play key roles in animal development, physiology, and reproduction did not involve the de novo generation of evolutionary innovations. Instead, it began with a more complex, modern-like state that was expanded by gene duplication and shaped by loss and convergent evolution. The core “information” wasn’t added; it was there at the base. In fact, the authors make a very interesting conclusion:
Most gene families, like the NRs, have some common conserved core function—some catalytic activity, for example, or the capacity to interact with DNA. Functional diversity within such families is conferred by members’ binding to and carrying out that function on different partners. Our observations in the NRs underscore the capacity of evolution to produce dramatic functional diversity by tinkering with a common ancestral template over long periods of time. The varied and subtle nature of these tinkering events is revealed only when densely sampled structural and functional data are analyzed in a phylogenetic context. We predict that, when sufficient data are gathered to allow detailed evolutionary reconstructions, it will become apparent that most protein superfamilies diversified by subtle modification and partial degradation of ancient, deeply homologous functions. Invoking the evolution of wholesale “novelty” will seldom be necessary.
Let’s make sure you did not miss that:
We predict that, when sufficient data are gathered to allow detailed evolutionary reconstructions, it will become apparent that most protein superfamilies diversified by subtle modification and partial degradation of ancient, deeply homologous functions. Invoking the evolution of wholesale “novelty” will seldom be necessary.
Whoa. That’s what we would expect from front-loading. Now couple this with the recent finding that new gene families stopped appearing long before the Cambrian explosion,and we can begin to see that evolution has occurred within a fairly structured context.
Yet there does seem to be one significant problem:
NRs appear to be a metazoan innovation, because they are absent from the genomes of choanoflagellates, fungi, plants, and prokaryotes.
Let’s deal with that in the next posting.