How Proteins Adapt and Evolve New Functions
In the microscopic world of bacteria, a relentless evolutionary arms race is taking place. As scientists develop new antibiotics, bacteria counter with sophisticated defense mechanisms. At the same time, ancient enzymes continuously evolve new capabilities to help organisms survive in changing environments.
A specialized protein that confers resistance to the antibiotic fusidic acid in harmful bacteria like Staphylococcus aureus.
An enzyme involved in histidine biosynthesis that reveals how new functions emerge over millennia.
Though they operate in different biological contexts, both proteins provide fascinating windows into the fundamental principles of structural adaptation and functional innovation at the molecular level.
Fusidic acid is an antibiotic that has been used clinically since the 1960s, primarily to treat Staphylococcus infections. It works by locking elongation factor G (EF-G)—a crucial bacterial protein—onto the ribosome after it has completed its job of protein synthesis. This effectively halts the production of new proteins, stalling bacterial growth.
However, some bacteria have acquired a secret weapon: the FusB protein. FusB provides resistance to fusidic acid, allowing bacteria to survive despite antibiotic treatment. This makes understanding FusB's structure and mechanism a pressing concern in the fight against antibiotic-resistant bacteria .
Through detailed structural studies using X-ray crystallography, scientists have determined that FusB is a two-domain protein with a unique architecture not seen in other known proteins . The N-terminal domain forms an elongated four-helix bundle, while the C-terminal domain has a more spherical alpha/beta structure stabilized by a zinc ion that forms a "treble-clef zinc finger" motif—a specific structural arrangement that helps coordinate metal ions .
| Domain | Structural Characteristics | Functional Significance |
|---|---|---|
| N-terminal domain | Four-helix bundle | Provides structural stability and interaction surfaces |
| C-terminal domain | Alpha/beta fold with zinc finger | Contains conserved basic residues critical for EF-G binding |
| Conserved basic patch | Lysine-rich region (residues 93-105) | Likely involved in molecular recognition and binding |
| Zinc binding site | Treble-clef motif | Stabilizes domain structure |
For years, scientists knew that FusB provided antibiotic resistance, but its precise mechanism remained mysterious until recent breakthroughs. In 2025, researchers used time-resolved cryo-electron microscopy—an advanced technique that captures snapshots of molecular structures at different time points—to unravel exactly how FusB rescues protein synthesis from fusidic acid inhibition 2 7 .
Fusidic acid locks EF-G onto the ribosome, halting protein synthesis.
12.7% of ribosomes have FA-locked EF-G complexes 2
FusB binds directly to EF-G while it's trapped on the ribosome.
FusB causes large-scale conformational changes in EF-G that break its interactions with the ribosome.
EF-G and fusidic acid are released, allowing protein synthesis to resume.
Only 2.7% of ribosomes remain inhibited after FusB action 2
Think of FusB as a specialized rescue team that pries a stuck piece of machinery loose from where it's jammed. Specifically, FusB's N-terminal domain wedges between domains of EF-G, while its C-terminal domain anchors to the ribosome, effectively pulling EF-G away from its stuck position 2 .
While FusB represents a relatively recent evolutionary adaptation, HisA showcases how proteins evolve over deep time. HisA is an enzyme involved in the histidine biosynthesis pathway, specifically catalyzing the fourth step in this essential process 9 .
What makes HisA particularly fascinating to evolutionary biologists is its TIM-barrel structure—a common protein fold consisting of eight alternating beta-strands and alpha-helices that form a barrel-like structure 5 .
HisA and a related enzyme, HisF, are believed to have evolved through a series of gene elongation and duplication events from a common ancestral half-barrel protein 5 . This evolutionary history makes HisA an excellent model for studying how enzymes acquire new functions.
To understand how HisA might evolve new capabilities, researchers at Uppsala University conducted clever experiments using the HisA enzyme from Salmonella enterica 9 . They investigated whether HisA could acquire the function of TrpF—an enzyme involved in tryptophan biosynthesis that catalyzes a similar chemical reaction but on a different substrate.
| Evolutionary Path | HisA Activity Retention | TrpF Activity Acquisition | Likely Evolutionary Outcome |
|---|---|---|---|
| Single mutations (3/16 variants) | Partial retention | Limited | Generalist enzyme (if trade-off weak) |
| Further evolved variants | Complete loss | Significant improvement | Specialization after gene duplication |
| Natural PriA enzyme | Full function | Full function | Rare generalist without trade-off |
These experiments demonstrated a strong trade-off between the original and new functions—a finding with important implications for how new enzymes evolve in nature. When such strong trade-offs exist, evolution typically favors gene duplication and divergence, where one copy maintains the original function while the other is free to specialize in the new function 9 .
The insights about FusB and HisA were made possible by sophisticated research tools and techniques. Here are some of the key methods used in structural and evolutionary biology:
| Tool/Method | Function/Application | Example in FusB/HisA Research |
|---|---|---|
| X-ray crystallography | Determines atomic-level protein structures by analyzing crystal diffraction patterns | Used to solve FusB structure at 1.6-2.3 Å resolution |
| Cryo-electron microscopy | Captures high-resolution images of frozen hydrated biomolecules in multiple states | Revealed time-resolved mechanism of FusB rescue from FA inhibition 2 7 |
| Error-prone PCR | Introduces random mutations into genes for directed evolution experiments | Used to generate HisA variants with new TrpF activity 9 |
| Site-directed mutagenesis | Creates specific, targeted changes in protein sequences | Identified FusB-EF-G binding determinants |
| Isothermal titration calorimetry | Measures binding affinities and thermodynamics of molecular interactions | Confirmed ribosome binding of FusB 3 |
| Growth rate assays | Uses bacterial growth as proxy for enzymatic activity in evolutionary experiments | Measured trade-offs between HisA and TrpF activities 9 |
Techniques like X-ray crystallography and cryo-EM reveal atomic details of protein structures.
Methods like PCR and mutagenesis allow controlled manipulation of genes and proteins.
Tools like calorimetry quantify molecular interactions and thermodynamic properties.
FusB demonstrates how evolution can craft highly specific solutions to modern challenges—in this case, antibiotic resistance—through structural innovation. The 2025 cryo-EM studies of FusB represent a triumph of modern structural biology, showing us precisely how this molecular machine operates at the atomic level 2 7 .
HisA, in contrast, takes us back to life's deep evolutionary history, showing how gene duplication and elongation events have shaped metabolic pathways over billions of years 5 . The experimental evolution studies with HisA give us a window into the fundamental trade-offs that constrain and direct protein evolution.
Together, these examples highlight why understanding protein structure and evolution is so crucial. As we face growing challenges like antibiotic resistance, the insights gained from studying proteins like FusB and HisA may help us develop smarter antibiotics and design novel enzymes for medicine and industry. The remarkable adaptability of proteins—whether occurring naturally over evolutionary timescales or being harnessed in laboratory settings—continues to inspire both basic scientific curiosity and practical innovation.
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