New study unravels mystery of cell shape diversity in bacteria

Electron micrographs of the three species of rod-shaped bacteria that display different stalk positions. From left, Caulobacter crescentus with a polar stalk; Asticcacaulis excentricus with a subpolar stalk; and A. biprosthecum with bilateral stalks. (Photo by Chao Jiang)
Pamela Brown, assistant professor of biological sciences, co-authored the paper.
Indiana University Bloomington Newsroom
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Biological Sciences

Bacteria come in a dazzling array of shapes and sizes—from spherical to star shaped. The evolutionary mechanisms that give rise to the morphological diversity of bacteria are the focus of a new study co-authored by MU biologist Pamela Brown and published in Nature.

Bacterial shapes are known to play a critical role in the infectivity and pathogenesis of bacteria in human- and animal-contracted diseases. “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,” said Yves Brun, who is a professor of biology at Indiana University where the research was carried out.

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.

In this study, the investigators demonstrate 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 have led to a sequential transition in the positioning of an appendage-like structure, called a stalk, which is common in aquatic bacteria.

This discovery is the first of its kind in bacteria.

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 different cellular locations. In Caulobacter crescentus, the stalk is positioned at a single cell pole; in Asticcacaulis excentricus, the stalk is located at a subpolar position off-center from the cell pole; and in A. 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 Brown, who completed the research while a postdoctoral researcher in the Brun lab and who is now assistant professor of biological sciences at MU.

The researchers hypothesized 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 five 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.”

Co-author Adrien Ducret, a post-doctoral researcher in the Brun lab, devised 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 is 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,” said lead author Chao Jiang.

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 in the end generating an optimal cell shape needed for a specific process.

The study, titled “Sequential evolution of bacterial morphology by co-option of a developmental regulator,” was released January 19th as an advance online publication and will appear in an upcoming issue of Nature.

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

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