Scientists uncover ‘superfamily’ of bacterial predator proteins

Scientists have identified a new type of protein in bacteria that could change our understanding of how these organisms interact with their environments.

A new study, published in Nature Communications, focuses on a protein called PopA, found in the bacterial predator Bdellovibrio bacteriovorus. The protein forms a unique fivefold structure, unlike the usual single or three-part structures seen in similar proteins.

Supported by the Wellcome Trust, BBSRC, ERC, MRC, and EPSRC an international research team, led by University of Birmingham scientists, used advanced imaging techniques to reveal that PopA has a bowl-like shape that can trap parts of the bacterial membrane inside it.

When PopA - an outer membrane protein (OMP) - is introduced into E. coli bacteria, it causes damage to their membranes. This suggests that PopA might play a role in how Bdellovibrio attacks and consumes other bacteria, whilst its ability to trap lipids (fats) suggests a new way bacteria might interact with their surroundings.

Structural analysis and AI-driven searches showed that PopA homologues - found across diverse bacterial species - form tetramers, hexamers, and even nonamers, all sharing the signature lipid‑trapping features. This suggests a widespread, previously unrecognised ‘superfamily’ of proteins.

Lead author Professor Andrew Lovering, from the University of Birmingham, commented: “Our discovery is significant because it challenges what scientists thought they knew about bacterial proteins. The unique structure and function of PopA suggest that bacteria have more complex ways of interacting with their environments than previously understood.

“This could open new possibilities for understanding how bacteria function and interact with their environments - leading to new ways to target harmful bacteria with important implications for medicine and biotechnology.”

The study also identified another new family of proteins that form ring-like structures, further expanding our knowledge of bacterial proteins and suggesting that the mechanism to combine into rings might be more common than previously thought.

Using a combination of X‑ray crystallography, cryo-electron microscopy, and molecular dynamics, the team demonstrated that PopA, previously known as Bd0427, forms a central lipid-trapping cavity which is unusual given that the textbook model of membrane protein formation is centred on excluding lipids.

OMPs perform a wide range of functions including signalling, host cell adhesion, catalysis of crucial reactions, and transport of solutes/nutrients into and out of organelles within the human body. Understanding the natural variability of OMPs may have benefits ranging from antibacterial development to synthetic biology.

ENDS

For more information, please contact Tony Moran, International Communications Manager t.moran@bham.ac.uk  tel: +44 (0)7827 832312.

Notes to editor:

• The University of Birmingham is ranked amongst the world’s top 100 institutions. Its work brings people from across the world to Birmingham, including researchers, teachers and more than 8,000 international students from over 150 countries.
• ‘A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily’ - Rebecca J. Parr, Yoann G. Santin, Giedrė Ratkevičiūte, Simon G. Caulton, Paul Radford, Dominik Gurvič, Matthew Jenkins, Matthew T. Doyle, Liam Mead, Augustinas Silale, Bert van den Berg, Timothy J. Knowles, R. Elizabeth Sockett, Phillip J. Stansfeld, Géraldine Laloux & Andrew L. Lovering is published in Nature Communications.
• Participating institutions: Universities of Birmingham, Nottingham and Warwick, UK; UCLouvain, Belgium; Newcastle University, UK; and WEL Research Institute.