Bacterial Acid Trips

The side chain of this artificial amino acid possesses an alkyl diazirine group that can crosslink to proteins in acidic conditions when exposed to light.

When you get food poisoning, the bacteria causing havoc in your intestines have first navigated a rather treacherous journey through your acidic stomach. The molecular mechanisms by which a pathogen survives this acid environment have long kept researchers guessing, but now a team of biochemists led by Peng R. Chen at Peking University in China have developed a new technique to study the bacterial coping mechanism (Nature Chem. Biol., DOI: 10.1038/NChemBio.644).

In addition to helping researchers better understand pathogen survival, the new technique, which permits protein-protein interactions to be studied at low pH, will likely find application in probing a wide range of biology that occurs in acidic conditions. To date, studying protein-protein interactions at low pH has been a challenge because most current techniques don't work in strong acidic environments, Chen explains.

To study how Escherichia coli survives our stomach, Chen's group, in collaboration with Zengyi Chang, also at Peking University, focused on the bacteria's chaperone proteins, which keep cellular proteins from unfolding in harmful environments. They engineered the gene for an essential chaperone protein called HdeA to incorporate an artificial amino acid at the site that binds client proteins. The artificial amino acid has a side chain that possesses an alkyl diazirine moiety that can crosslink to other proteins when irradiated.

The team exposed this engineered E. coli to acid so HdeA would start protecting proteins from denaturation. Then they hit the bacterium with light to trap HdeA with its client proteins and used mass spectrometry to identify these clients.

Among the dozens of client proteins protected by HdeA, the team detected two other chaperone proteins. This suggests that HdeA is a mother chaperone protein in a large acid-resistance network, note the authors. They also found that HdeA could protect E. coli cells without the help of adenosine triphosphate, the common chemical energy currency in cells.

It's "a very clever and elegant method," says John Foster, a microbiologist who studies pathogen acid resistance at the University of South Alabama. "The real value of this work is in the methodology, which could be used to probe many other chaperone-client interactions in bacteria, archaea, and eukaryotes."

Indeed, Chen says he's currently using the approach to examine protein-protein interactions in the lysosome, the organelle in eukaryotes whose acidic interior is responsible for breaking down waste proteins and other cellular molecules.

Chemical & Engineering News

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