Bacterial protein structures bridge the gap between host and pathogen

Bacteria have evolved to thrive in the host environments they occupy. Counteracting these pathogens requires understanding how they interact with hosts, from a global health perspective right down to the molecular exchanges that govern these interactions.

St. Jude researchers are studying the protein complexes that allow bacteria to interact with their hosts. These range from tiny assemblies hidden within membranes to multi-component molecular machines that inject payloads directly into neighboring host cells. In this pursuit, Susan Lea, DPhil, FMedSci, FRS, Department of Structural Biology, brings a wealth of knowledge on the inner workings of these processes, collectively called bacterial secretion.

“As a medical student, I was fascinated by structural biology, particularly human virus receptors, which control how viruses get into host cells,” said Lea. “This eventually led me into the world of bacteria that hijack and modify those mechanisms, where I was particularly drawn to processes concerned with the secretion of proteins across membranes. In this regard, bacteria use several very different systems to achieve what is essentially the same function.”

In fact, there are at least nine distinct secretion pathways in bacteria, many with multi-step processes. This transmembrane medley emphasizes how important their functions are to bacteria, invading mammalian hosts, causing tissue damage and evading immune responses.

Bacterial nanomachines and assemblies

Like a mechanic taking apart an engine, Lea has disassembled and reassembled the structural architecture of several bacterial secretion pathways to understand how they work. Type-III secretion, for example, involves an enormous protein assembly called the injectisome. This nanomachine not only contributes to host interactions but is also the core component of the bacterial flagellum, the tail-like structure that helps bacteria move.

Lea’s team has uncovered the structural basis for many components of the injectisome, including:

• A protein ring central to its export apparatus in a 2012 Nature Structural & Molecular Biology study.
• The architecture of an export gate in the bacterial membrane, published in 2018 in Nature Structural & Molecular Biology and in a follow-up 2019 study in mBio.
• A substrate specificity switch that interacts with the export gate, published in 2020 in Nature Communications.
• The system that drives bacterial flagellum rotation, published in 2020 in Nature Microbiology.
• The flagellar base, which encompasses the rotor and shaft, published in 2021 in Nature Microbiology.
• The protein systems within the flagellum that allow bacteria to change direction, published in 2024 in Nature Microbiology.

Type-III secretion delivers bacterial proteins into host cells by working as a protein threading machine, capable of exporting only unfolded proteins. To secrete folded proteins, bacteria rely on a much smaller three-protein team called the twin arginine translocation (Tat) system. “I was intrigued by the contrast between the huge type-III machinery, which seemed to do the simpler job, and this tiny set of proteins that did this comparably much more complex task,” Lea explained.

The Tat system thins the inner membrane to secrete proteins

Many bacteria have an outer and inner membrane. The space between these two partitions is called the periplasm, a gel-like holding area responsible for a variety of processes such as protein oxidation, folding and quality control. The Tat system moves proteins from the inner cytoplasm to the periplasm for processing and secretion via a separate apparatus. While efforts have been made to figure out the mechanism behind the Tat system and how its three components — TatA, TatB and TatC — are arranged, the consensus in the field was that something was missing.

In a 2026 paper published in Nature Microbiology, co-corresponding author Lea and her team realized that researchers had been looking at the system the wrong way — literally. Traditional membrane proteins involved in trafficking sit perpendicular to the plane of the membrane, creating a pore through which proteins can travel. Instead, cryo-electron microscopy structures revealed that the core components of the Tat system sit within the membrane with an unusual 45-degree tilt.

This revelation offered a clue to the Tat system’s mechanism. The researchers noticed that these strangely oriented proteins were having a dramatic effect on the membrane bilayer.

“It was thought that TatB and TatC formed the assembly that interacts with substrates and then recruits TatA. But we found that this core is composed of all three proteins and the full assembly works to thin the membrane,” explained co-first author Owain Bryant, PhD, Department of Structural Biology. “We think that substrate binding further weakens the membrane to render the barrier so thin that substrates can pass straight through.”

The findings reframe a decades-long research pursuit for Lea. As she has come to realize, sometimes the answer comes from a new perspective. “In the absence of information, the field had settled on a very different assembly than what we uncovered,” Lea said. “Molecular dynamics simulations had always sat our previous structures straight up in the membrane. The structures themselves are very similar; they’re just not sitting in relation to the membrane how we thought they were.”

Structures complement the big picture with the intricate details

When host-pathogen research so often focuses on the macroscopic level — drug resistance evolution, symptom tracking and population vulnerability — a fresh perspective is exactly what Lea’s structural approach aims to provide. The molecular insights offered by her research establish key process mechanisms, shed light on unknown vulnerabilities and ultimately open new therapeutic pathways.

“I want to uncover the basic mechanisms of processes fundamental to the bacterial lifestyle,” Lea said. “Understanding them at a genetic and phenotypic level is vital, but I’m driven by molecular and atomistic understanding. I want to know why particular systems have the impact they do. And that’s exactly what we think structural biology brings to the host-pathogen party.”