IU research shows how protein sequence changes drive species evolution

Study unravels mystery of cell shape diversity in bacteria

  • Jan. 19, 2014


BLOOMINGTON, Ind. -- Biologists from Indiana University have uncovered the evolutionary mechanisms by which a group of bacteria synthesize an appendage-like structure at a precise cellular position, analogous to the placement of limbs on an animal.  The new research demonstrates how evolutionary changes occurring at the molecular level can lead to dramatic variations in the shape of species.

The groundbreaking work led by IU professor of biology Yves Brun and graduate student Chao Jiang shows how stepwise evolution of a specific protein, the developmental regulator SpmX, led to a new function and localization of the protein. The changes in SpmX function and location led to a sequential transition in the positioning of the appendage-like structure, called a stalk, which is common in aquatic bacteria.

The discovery is the first of its kind in bacteria.

“The evolutionary mechanisms we uncovered could serve as the foundation to explain how what Darwin called the ‘endless forms most beautiful and wonderful’ came into being,” said Jiang, lead author on the paper. “Mechanistically, our findings are potentially relevant in animals, plants, fungi, as well, that is, from the microscopic to the macroscopic world.”

The team investigated the functional evolution of the SpmX protein by artificially creating chimeric proteins -- new proteins created by fusing domains of SpmX from different species -- and then teasing out the function of the individual domains.

The study used three rod-shaped bacteria, each with stalks in a different cellular location: In Caulobacter crescentus, the stalk is positioned at a single cell pole; in Asticcacaulis excentricus, the stalk is synthesized at a subpolar position off-center from the cell pole; and in Asticcacaulis biprosthecum, two stalks are positioned bilaterally midway in the cell body.

“The unique sub-cellular organization of the stalk in each species enabled us to devise a creative strategy to identify SpmX as the protein that determines the position of stalk synthesis,” said co-author Pamela Brown, a former postdoctoral researcher in the Brun lab who is now assistant professor at the University of Missouri.

“The first time I saw these distinct shapes in closely related species, now 20 years ago, I thought maybe we can use them to determine how bacterial shapes evolve," Brun said. "But we had to wait for the development of technology, from genome sequencing to the ability to follow single proteins inside cells, to enable our studies.”

The researchers thought it made sense that stalk positioning evolved from a single ancestral polar stalk, to a single subpolar stalk, and then subsequently to more complex bilateral stalks. But to prove it, they needed to sequence the genomes and perform rigorous phylogenetic analysis of the species.

“We sequenced five selected species, and each consisted of 5 million bases of data,” Brun said. “And from these data, we were able to infer the evolutionary history of the stalk, including approximately dating that the morphological transition events happened hundreds of millions of years ago.”

It was co-author Adrien Ducret, a post-doctoral researcher in the Brun lab, who devised the software tailored for analyzing, at the sub-micron scale, the localization of SpmX within the microbial cell bodies.

“We were able to track the localization of the SpmX protein at a sub-pixel level within the cell bodies with an automated process that handled thousands of cells in seconds, which was critical for the interpretation of our results,” Ducret said.

In the end, the researchers concluded that evolution of a specific region of the SpmX protein was responsible for its ability to drive stalk synthesis from polar to subpolar to bilateral positions in the different bacteria.

“We also see that changes in just the amount of SpmX are able to alter the number of stalks in one of the species, suggesting that simple changes in the regulation of protein expression can potentially drive the evolution of a species with several subpolar stalks,” Jiang said.

Hypothetically, he added, synthetic biology tools could be used to localize SpmX in a new position, in turn changing cell shape at that position and then generating an optimal cell shape needed for a specific process.

“Understanding the molecular mechanisms of generating different morphologies in bacteria is strongly tied to pressing needs in medicine, as the inhibition of such mechanisms can fight diseases,” Brun noted. Bacterial shapes are known to play a critical role in the infectivity and pathogenesis of bacteria in human- and animal-contracted diseases.

For example, the spiral shape of Helicobacter and Campylobacter bacteria is important for their initial invasion of the mucosal membrane in the gastrointestinal system, which can then result in acute infection, cause inflammatory diarrhea with fever, or even gastric carcinoma and lymphoma, and, if left untreated, eventually death.

“Sequential evolution of bacterial morphology by co-option of a developmental regulator,” published online Sunday in the journal Nature, was authored by Jiang, Ducret, Brown and Brun.

Funding for this work was provided by the National Institutes of Health, the National Science Foundation and the IU Metabolomics and Cytomics Initiative.

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Electron micrographs of, from left, Caulobacter crescentus, Asticcacaulis excentricus and Asticcacaulis biprosthecum. The tube-like structures emanating from the cell bodies at distinct positions are the stalks, cell envelope extensions that improve nutrient uptake by the bacterial cells.

Electron micrographs of, from left, Caulobacter crescentus, Asticcacaulis excentricus and Asticcacaulis biprosthecum. The tube-like structures emanating from the cell bodies at distinct positions are the stalks, cell envelope extensions that improve nutrient uptake by the bacterial cells. | Photo by Chao Jiang

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