Molecule of the Month: Ribosome Diversity

The first atomic structures of ribosomes, determined in 2000, revealed the details of biological protein synthesis. The small ribosomal subunit manages messenger RNA, pairing it with the appropriate transfer RNA molecules and matching codons with anticodons. The large ribosomal subunit connects the amino acids carried by transfer RNAs into a new protein chain. In the 25 years since then, thousands of additional structures of ribosomes have been determined, elucidating many of the steps of protein synthesis. These structures also allow us to compare structures of ribosomes from different organisms.

Since all living organisms need to have functional ribosomes, ribosome structures are useful for studying molecular evolution, allowing us to compare and contrast them across all the kingdoms of life. The image included here shows the small ribosomal subunit from several different organisms. Bacteria have relatively simple structures. The bacterial small subunit (PDB ID 1fjg) includes one RNA strand 1522 nucleotides in length and 20 proteins. Similarly, the archaeal small subunit (PDB ID 6tmf) has a small RNA strand with 1485 nucleotides and 29 proteins. However, the human and plant small subunits (PDB ID 5a2q and 8auv) have evolved a more complex structure, with RNA strands with over 1800 nucleotides and more than 30 proteins.

Mitochondria and chloroplasts make their own ribosomes, which are different from the ribosomes in the cytoplasm of plants, animals, and fungi. Both organelles are believed to have evolved from bacteria that became symbiotic residents in the cytoplasms of the progenitors of modern eukaryotic cells. The structure of chloroplast ribosomes is one piece of evidence supporting this endosymbiotic hypothesis. The chloroplast small ribosomal subunit (PDB ID 5mmj) is similar to its bacterial counterpart, with a short RNA chain with 1491 nucleotides and 25 proteins. The structure of the mitochondrial small subunit (PDB ID 6rw4) shows that mitochondrial ribosomes have diverged significantly from their putative bacterial antecedent, with an even shorter RNA chain with only 955 nucleotides and more proteins than a typical bacterial ribosome.

The increased complexity of eukaryotes is also seen in the many proteins that assist ribosomes in the process of protein synthesis. For example, the two structures shown here (PDB ID 5lmv and 8oz0) show the proteins that orchestrate initiation of protein synthesis. Together, they help capture a messenger RNA and align an initiator transfer RNA at the start codon of translation. Bacterial cells only require three initiation factor proteins to accomplish this task, but eukaryotes require about 20.