Study of protein structures reveals key events in evolutionary history

March 10, 2009

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).

Lead author Gustavo Caetano-Anollés, a professor of bioinformatics in the department of crop sciences at the University of Illinois and 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.

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.

"The history of the protein repertoire should match the history of the entire organism because the organism is made up of all those pieces," Caetano-Anollés said.

He 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.
-end-
Editor's note: To reach Gustavo Caetano-Anollés, please call: 217-333-8172; e-mail: gca@illinois.edu.

To view or subscribe to the RSS feed for Science News at Illinois, go to: http://webtools.uiuc.edu/rssManager/608/rss.xml.

University of Illinois at Urbana-Champaign

Related Proteins Articles from Brightsurf:

New understanding of how proteins operate
A ground-breaking discovery by Centenary Institute scientists has provided new understanding as to the nature of proteins and how they exist and operate in the human body.

Finding a handle to bag the right proteins
A method that lights up tags attached to selected proteins can help to purify the proteins from a mixed protein pool.

Designing vaccines from artificial proteins
EPFL scientists have developed a new computational approach to create artificial proteins, which showed promising results in vivo as functional vaccines.

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.

Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.

Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.

Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.

Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.

Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.

Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.

Read More: Proteins News and Proteins Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.