Chemical & Engineering News.
Surviving an acidic journey
Nature Chemical Biology, September 5, 2011
A cooperative group of proteins that work together to protect cells from acid stress has been found in bacteria that transit through the human digestive tract, as reported online this week in Nature Chemical Biology.
When proteins encounter highly acidic environments, their normally stable structure can fall apart; if enough proteins lose their structure, the cell cannot operate normally and will die. Chaperones are a family of proteins that protect other proteins from losing their structure or help the proteins to regain their structure once lost.
Zengyi Chang, Peng Chen and colleagues look for ‘clients’ – or preferred protein substrates – of one of these chaperones by using a newly-designed non-natural amino acid to link the chaperone and its client together, allowing them to be identified as interacting. Among the clients, the authors discovered two more chaperones that subsequent tests demonstrated were working together with the initial chaperone to help other proteins more quickly regain their shape. This cooperative mechanism explains how bacteria might recover from their acidic travels.
September 7, 2011
Bacterial Acid Trips
Chemical Biology: New technique reveals how pathogens endure our acidic stomachs
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.