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| Protein Structures May Reveal Key Evolutionary Events |
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| SciMed - Biology | |||
| TS-Si News Service | |||
| Sunday, 15 March 2009 16:00 | |||
 Urbana, IL, USA. A new study of proteins, the molecular machines that drive all life, also sheds light on the history of living organisms. The study, in the journal Structure, reveals that after eons of gradual  evolution, proteins suddenly experienced a "big bang" of innovation. The active regions of many proteins, called domains, combined with each other or split apart to produce a host of structures that had never been seen before.This explosion of new forms coincided with the rapidly increasing diversity of the three superkingdoms of life (bacteria; the microbes known as archaea; and eucarya, the group that includes animals, plants, fungi and many other organisms).
All proteins contain domains that can be identified by their structural and functional similarities to one another. These domains are the gears and motors that allow the protein machinery to work. Every protein has one or more of them, and very different proteins can contain the same, or similar, domains.
By conducting a census of all the domains that appear in different groups of organisms and comparing the protein repertoires of hundreds of different groups, the researchers were able to construct a timeline of protein evolution that relates directly to the history of life.
 Gustavo Caetano-Anollés, a professor of bioinformatics in the department of crop sciences at the University of Illinois, with postdoctoral researcher Minglei Wang, see evolution in the history of protein structures. Photo by L. Brian Stauffer, University of Illinois News Bureau.Lead author Caetano-Anollés, an affiliate of the Institute for Genomic Biology, has spent years studying protein structures – he calls them "architectures" – which he suggests offer a reliable record of evolutionary events.
"The history of the protein repertoire should match the history of the entire organism because the organism is made up of all those pieces," he says.
Caetano-Anollés and his co-author, postdoctoral researcher Minglei Wang, were interested in tracing how proteins make use of their domains, or groups of domains, to accomplish various tasks. These domains or domain clusters can be thought of as "modules" which fit together in various ways to achieve different ends.
Unlike the sequence of amino acids in a protein, which is highly susceptible to change, the protein modules found today in living organisms have endured because they perform critical tasks that are beneficial to the organisms that host them, Caetano-Anollés said.
"These modules are resistant to change, they are highly integrated and they are used in different contexts," he said.
By tracing the history of the modules, the researchers were able to build a rough timeline of protein evolution. It revealed that before the three superkingdoms began to emerge, most proteins contained only single domains that performed a lot of tasks.
"As time progressed, these domains started to combine with others and they became very specialized," Caetano-Anollés said. This eventually led to the big bang of protein architectures.
"Exactly at the time of the big bang," he said, many of the combined domains began to split apart, creating numerous single-domain modules again. But these new modules were much more efficient and specialized than their ancient predecessors had been.
"This makes a lot of sense," Caetano-Anollés said. "As you become more complex, you would want to fine-tune things, to do things in a more tailored way."
The protein modules of the three superkingdoms also began to diverge more dramatically from one another, with the eucarya (the group that includes plants and animals) hosting the greatest diversity of modules.
"This explosion of diversity allowed the eucarya to do things with their proteins that other organisms could not do," Caetano-Anollés said.
CitationThe Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World. Minglei Wang, Gustavo Caetano-Anollés. Structure 17(1): 66-78.
Summary Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements. In order to study their evolution, we reconstructed genome-based phylogenetic trees of architectures from a census of domain structure and organization conducted at protein fold and fold-superfamily levels in hundreds of fully sequenced genomes. These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages, the dominance of domain fusion processes throughout evolution, and the late appearance of a new class of multifunctional modules in Eukarya by fission of domain combinations. Our study provides a detailed account of the history and diversification of a molecular interactome and shows how the interplay of domain fusions and fissions defines an evolutionary mechanics of domain organization that is fundamentally responsible for the complexity of the protein world.  The TS-Si News Service is a collaborative effort by TS-Si.org editors, contributors, and corresponding institutions. Sources can include the cited individuals and organizations, as well as TS-Si.org staff contributions. Articles and news reports do not necessarily convey official positions of TS-Si, its partners, or affiliates. We welcome your comments. Use the form below to leave a public comment or send private correspondence via the TS-Si Contact Page. We will not divulge any personal details or place you on a mailing list without your permission.TS-Si is dedicated to the acceptance, medical treatment, and legal protection of individuals correcting the misalignment of their brains and their anatomical sex, while supporting their transition into society as hormonally reconstituted and surgically corrected citizens.
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