Nature: For the first time, scientists have looked at how antibiotics work in pathogenic bacteria in atomic detail

It is well known that cells are the basic structures and functions that make up an organism; Proteins are like the "soul" of the cell, and every living cell depends on proteins to function
.
The process of protein synthesis (translation) is essential
for the survival of cells.
Ribosomes are present in all biological cells, from bacteria to humans, and these oldest macromolecular machines (which may have existed before the advent of cells) are molecular factories
for protein synthesis.
Ribosomes are also one of the most important targets for
antibiotics.
Past methods have identified many antibiotics to delay translation through intermediates in the stabilization process, but a detailed structural description of the translation process in the native cellular environment is currently lacking
.
On September 29, Beijing time, in a new study published in Nature, an international research team led by the European Molecular Biology Laboratory (EMBL) observed for the first time how antibiotics affect the protein production process
within bacterial cells from atomic details.
The study marks the first time scientists have looked directly inside cells at atomic-level structural changes
in active translation mechanisms.
Importantly, the study also revealed how translation mechanisms respond
to different antibiotic disturbances at the single-cell level.
Mycoplasma is the smallest prokaryotic microorganism with no cell wall and is filamentous or branched
.
They are widespread in nature
.
There are 5 known pathogenic mycoplasma, of which Mycoplasma pneumoniae (M.
pneumoniae) can cause pneumonia
.
Although less than a thousandth of a millimeter tall, this extremely small bacterium has a well-functioning protein synthesis mechanism
.
As a result, mycoplasmas are widely used as model cells
in systems biology and synthetic biology research.
Today, the birth of Cryo ET (cryo-electron tomography) technology has revolutionized the resolution in the life sciences
.
The technique allows researchers to perform continuous imaging of fast-frozen biological samples using electron microscopy and combine the resulting images into a three-dimensional view
of cells.
It's like a miniature version of a magnetic resonance imaging (MRI) machine
.
Previously, scientists have observed actively translated ribosomes within cells through Cryo ET, but the resulting images are limited to nanoscale resolution
.
In this new study, the team developed an image processing algorithm
for frozen ET.
Using large-scale frozen ET data from raw preserved cells, they captured high-resolution snapshots of molecular machines in different states and synthesized images
.
When frozen ET images of Mycoplasma pneumoniae cells are presented in front of the eyes, one of the most prominent structures is the tiny black spots, which are ribosomes
.
This new method not only allows researchers to discover and count ribosomes inside bacteria, but also to observe their structure
at atomic-level resolution.
By studying the large number of ribosomes that "freeze" at different stages of the active cycle, the researchers deciphered how ribosomal structures change during protein synthesis
.
Not only that, but they also localized ribosomes in a three-dimensional space within the cell to determine how the translation process was spatially organized
.
Within living cells, ribosomes operate as highly interconnected systems, rather than as individual molecular machines
.
The study revealed new features of ribosomes and different pathways
of translational reactions in cells.
On top of that, using cryo-ET, researchers can observe what
happens when antibiotics enter cells and bind to ribosomes.
They identified two broad-spectrum antibiotics, chloramphenicol and spectinomycin, binding to different sites on ribosomes and disrupting different steps
of the protein synthesis process.
Previous studies of isolated ribosomes have predicted this, but have never been observed inside actual bacterial cells
.
The researchers observed that ribosomes in cells treated with antibiotics underwent fundamental changes
in function, structure, and space.
The interaction between ribosomes and other complexes within the cell changes with the action of the drug, suggesting that the effect of antibiotics may extend far beyond specific complexes bound to ribosomes
.
These findings help scientists understand the non-targeted effects of antibiotics while providing a basis
for designing more effective combinations of antibiotics.
Together, this new method establishes a framework to analyze the structural dynamics of future cellular processes, helping to build functional cell models
in atomic detail.
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