Atomic techniques reveal the evolution of a bacterial protein

Atomic techniques reveal the evolution of a bacterial protein

Using a synergistic approach, the collaborative KAUST team analyzed the reaction of different H-NS proteins (shown above) at temperature and salinity at an atomistic level. Credit: KAUST; Vladlena Kharchenko

The researchers show how bacteria have adapted a detection mechanism that allows them to live in different environments.

A combination of a number of techniques at the atomic level has allowed researchers to show how changes in an environmentally sensitive protein allow bacteria to survive in different habitats, from the human gut to deep-sea hydrothermal vents.

“The study provides us with unprecedented information at the atomic level on how bacteria adapt to changing conditions,” says Stefan Arold, professor of bioscience at KAUST. “To gain this insights, we pushed the limits of three different research methods and combined their results into a unified picture.”

Histone-like nucleoid structuring protein (H-NS) enables bacteria to detect changes in their environment, such as changes in temperature and salinity. Previously, the team had shown how the intestinal pathogen Salmonella typhimurium uses H-NS to control its gene expression profile, allowing it to optimally live inside its warm-blooded host or outside in the ground.

The H-NS protein is also found in bacteria that do not experience massive fluctuations in temperature, such as plant pathogens, insect symbionts, and free-living microbes that inhabit deep-sea hydrothermal vents. However, it remains puzzling how different bacteria have adapted the same detection mechanism to suit a variety of lifestyles.

No analysis technique has been able to unravel the inner workings of this mechanism, and therefore, to gain a more integrated view, Arold assembled a diverse team from KAUST and international collaborators. Arold and Lukasz Jaremko, a molecular biochemist at KAUST, collaborated with Jianing Li of the University of Vermont to combine several methods: proton-free nuclear magnetic resonance spectroscopy, all-atom molecular dynamics simulations, and biophysical techniques. This synergistic approach allowed the researchers to analyze the reaction of different H-NS proteins to temperature and salinity at the atomistic level.

All H-NS proteins showed the same ancestral detection mechanism, whereby temperature and salinity promoted the fusion of one of the two H-NS dimerization domains, releasing its control over DNA.

However, amino acid substitutions at specific sites, mainly at residues involved in salt bridges, produced a variety of static and dynamic characteristics. These effects dampen or amplify the protein’s response to adapt to the lifestyle of the bacteria.

“Although the sequences of these proteins are largely conserved, small specific changes lead to big differences in their behavior,” says KAUST research scientist Umar Farook Shahul Hameed.

Therefore, the H-NS protein of the apple pathogen Erwinia amylovoral lost its sensitivity to heat, which is consistent with the pathogen’s lifestyle in stable temperate climates. And only a few amino acid changes made Buchnera aphidicola’s H-NS nearly insensitive to the environment, in line with its role as an obligate endosymbiont of aphids.

“If you tickle in the right positions, the behavior changes very easily,” says Arold. “Approaches that interfere with this detection mechanism may find applications in areas ranging from mitigating climate change to fighting antibiotic resistance.”

Raising the pressure on pathogenic bacteria

More information:
Xiaochuan Zhao et al. Molecular basis for the adaptive evolution of the detection of the environment by H-NS proteins, eLife (2021). DOI: 10.7554 / eLife.57467

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Provided by King Abdullah University of Science and Technology

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