Making Protein

Ribosomes in action
01 November 2017

The human genome codes for 20-25,000 proteins. The lab workhorse bacterium, E.coli, codes for around 2,300. Every single one of those proteins is produced by the huge molecular machine shown on our 2017 calendar image for November.

This molecular machine, called the ribosome, is formed of two parts, termed the “large” and “small” subunits. Each subunit contains several RNA molecules and tens of different proteins. The two subunits come together to form the whole ribosome, but only when they associate with the messenger RNA (mRNA), which carries the genetic instructions from the DNA. It is this message, encoding the sequence of amino acids in a protein, that is read by the ribosome. When fully assembled, the ribosome begins making protein - a process called translation, because the mRNA sequence is being translated into protein sequence.

It’s all about that base

Three consecutive bases in the mRNA sequence specify one amino acid in the protein to be produced. Together, these three bases are termed a codon. Another form of RNA called a transfer RNA (tRNA) delivers amino acids to the ribosome for them to be added to the newly forming protein. There are specific tRNAs for each codon and each has a certain amino acid bound. These tRNAs only bind the mRNA in the ribosome when the three bases in their anti-codon loop match up with the three bases of the codon in the mRNA. Thus, the codons in the mRNA are read and subsequently translated to the correct amino acid in the new protein. Once the tRNA has brought in the right amino acid, a chemical reaction links it to the preceding amino acid in the growing protein chain. This is done by cleaving the link to the previous tRNA and attaching the amino acid on the newly arrived tRNA. By repetition of this mechanism for each amino acid the whole protein is constructed in a process called elongation.

While the protein components of the ribosome are essential in stabilising it and fine-tuning its performance, they don’t actually perform the catalytic step. The structure of the ribosome published in Science in 2000 (PDB entry 1ffk) confirmed what had been suspected - that this chemistry is carried out by the ribosomal RNAs themselves. The ribosome is therefore a ribozyme, raising a number of interesting evolutionary questions- but that's a story for another day!

Many ways to kill a ribosome

Ribosomes in both humans and bacteria are similar, however there are sufficient differences that enable antibiotics to stop the bacterial ones working, while leaving the human ones functioning. This is critical to ensure they can cure a disease without killing the patient! Around half of antibiotics in use today target the ribosome, stopping them from functioning in several different ways. Neomycin, for instance, prevents the two ribosomal subunits from coming together to begin translation, while tetracycline blocks tRNAs from binding. Chloramphenicol sits right at the centre of the ribosome (For example, in PDB entry 4v7w) and prevents the chemical reaction which makes a bond between the peptide chain and the new amino acid. Finally, the less commonly known antibiotic troleandomycin blocks the exit tunnel in the ribosome through which the newly formed protein emerges, stopping protein synthesis in that way, as shown in the image below.

Surface of the ribosome with troleandomycin bound

Troleandomycin (grey and red ball-and-stick representation) bound in the peptide exit tunnel of the ribosome, PDB entry 3i56.

Of course, substances which inhibit human ribosomes are highly toxic to us. Ricin, famously used in the 1978 assassination of Georgi Markov, targets the ribosome. Human ribosome inhibitors can work in our favour - the compound cycloheximide inhibits elongation and is widely used in in vitro research. Ribosome inhibitors could also be used as anti-cancer drugs.

Still more work to be done

The first structures of the ribosomes and their subunits were solved around the turn of the millennium, for which Venki Ramakrishnan, Tom Steitz and Ada Yonath were awarded the Nobel Prize in 2009. But the story is far from over and structures of the ribosome continue to be deposited in the PDB. For such large, complex and vital machines there is still much to learn about their mechanism, regulation and crucially their inhibition.

About the image

The image on our calendar first graced the cover of the EMBL-EBI Annual Scientific Report in 2014, designed by Spencer Phillips, EMBL-EBI’s senior graphic designer. Based on PDB entry 4v5h, it shows the ribosome (in red) in action actively translating mRNA (cyan) and making protein (green).