EMBL supports the ‘impossible’: Mapping the ribosome

Cells use large molecular ‘machines’ – assemblies of molecules called ribosomes – to turn their genetic code into protein.

This process of translation is essential for life and is present in all organisms. While their basic working mechanisms are similar, ribosomes in bacteria (prokaryotes) and higher organisms (eukaryotes) have different structures. These differences present an important opportunity: around half of the antibiotics currently in use selectively target the prokaryotic ribosome to disrupt protein synthesis and stop microbial attack. Understanding the structure and mechanism of the translational machinery can provide key information for research on new antibiotics and on antibiotic resistance – an issue of critical importance that is threatening effective prevention and treatment of infectious diseases.

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Molecular structure of the ribosome (pale yellow and blue) as imaged by EMBL Group Leader Julia Mahamid in 2020. Credit: Liang Xue, Julia Mahamid/EMBL

Ribosomes were first described as cellular organelles in the 1950s. Over the next decade, scientists managed to work out the central role that ribosomes play in all living cells, but they were unable to determine their structure or precise mechanism. In the 1970s, studies using classical electron microscopy provided the first views of the ribosomal architecture, albeit at fairly low resolution. To improve on the 'blobby' electron microscope image, the researchers would need to use X-ray crystallography. This technique requires the large molecular assembly of the ribosome to be arranged into a regular order -- a crystal -- a feat that seemed well beyond the achievable at the time.

In the late 1970s, Israeli crystallographer Ada Yonath decided to tackle ribosomal crystallography, more than a decade before others entered the field. Throughout the 1980s and early 1990s, Yonath worked to coax ribosomes into more ordered lattices and tested the resulting crystals using powerful X-rays. This is where scientists at EMBL Hamburg and EMBL Grenoble were able to help Yonath to tackle this seemingly impossible task.

Scientific breakthroughs are often made possible only by technological innovation. Using beamlines at synchrotrons, such as the EMBL beamline at the German Electron Synchrotron Radiation Facility (DESY) in Hamburg, Yonath not only showed success in growing ribosomal crystals, but also developed a method for freezing biological crystals that allowed them to survive the intense beams for longer. The technique, termed cryo-crystallography, enabled Yonath to obtain crystallographic data on ribosomes -- and has since become routine in structural studies of macromolecules.

The breakthrough occurred in 2000 and 2001, when the hard work of Yonath and other groups paid off: together, they revealed the structure of ribosomal particles at atomic resolution. In recognition of this achievement, Yonath was awarded the 2009 Nobel Prize in Chemistry alongside two other crystallographers. Yonath worked on the EMBL beamlines during her time as head of a unit of the Max Planck Institute for the Structure and Dynamics of Matter at DESY from 1986 to 2004. She highlighted the crucial contribution of EMBL in providing experimental equipment for her studies:

EMBL provided the equipment needed for our biochemical preparations and storage.

Yonath continues to conduct research on ribosomes. Today, she focuses on how structural changes in the ribosome, as a result of mutations in the bacterial genome, make them resistant to antibiotics. This knowledge is paving the way for the design of new and improved antibiotics.

The following year after being awarded the Nobel Prize, with the basic structure in hand, Yonath was able to solve the structures of five antibiotics bound to the ribosome. The structures demonstrated how these drugs stop translation – and thereby kill the organism.

Ada Yonath
Ada Yonath gives Jentschke Lecture. Credit: Marta Mayer/DESY

EMBL researchers are also addressing the issue of antibiotic resistance. For example, a group led by Orsolya Barabas at EMBL Heidelberg reported the first crystal structure of a protein-DNA machine that inserts transposons into the bacterial genome. In this way, transposons can transfer antibiotic resistance genes between bacteria, a key mechanism by which resistance spreads. The group then designed ways to help control the spread: based on the crystal structure, Barabas and colleagues developed molecules and provided proof of principle for how they could block the transposons' movement.

EMBL’s experimental services deliver substantial value to Europe by delivering scientific services and thereby enabling researchers to conduct novel and demanding experiments that could not be easily achieved at a purely national level, an independent review found.

The global consultancy Technopolis Group, specialising in research and innovation policy, conducted a survey and analysis of external (non-EMBL) users of EMBL’s experimental services. The survey aimed to identify whether users perceived scientific, technological, societal and economic benefits as a result of utilising the experimental services at EMBL Barcelona, Grenoble, Hamburg, Heidelberg, and Rome.