Species-specific ribosomal protein comparison coming soon!
A rapidly dividing cell of bacterium Escherichia coli contains about ~70,000 ribosomes, and ~7,000 of ribosomes are present in cells during the stationary phase of growth. Each of E. coli ribosomes contains 54 different proteins and three large rRNA molecules – 5S (~120 bases), 16S (~1600 bases) and 23S rRNAs (~2400 bases) and has a molecular weight of ~2.4MDa. Apart from rRNA and proteins, ribosomes also absorb a substantial proportion of magnesium ions – a few tens percent of the total cellular pool of magnesium ions. As is the case of many other organisms, the content of E. coli ribosomes is sensitive to the environment and may differ due to such factors as: (i) post-translational modifications in ribosomal proteins, (ii) presence of alternative isoforms of 5S rRNA in E. coli genome, with some isoforms produced in response to stress or drugs, (iii) processing of 16S rRNA by nucleases in response to stress, (iv) presence of alternative isoforms of ribosomal proteins (as, for instance, Zn-coordinating versus Zn-free isoforms of protein L31), (v) substoichiometric binding of ribosomal protein S21 to the active site of the small ribosomal subunit – the mRNA channel, etc.
A rapidly dividing yeast cell carries ~200,000 ribosomes, with each ribosome comprising ~5,500 nucleotides and 81 different proteins with an impressive total molecular weight of ~3.3 MDa. One unique feature of S. cerevisiae ribosomes is the presence of two alternative isoforms of ribosomal proteins in the ribosome structure. Because ~30 of the ribosomal protein genes are present as non-identical copies in yeast genome, yeast ribosomes have slightly different composition between each other, caused by the presence of isoform A and B of several ribosomal proteins. This phenomenon provoked speculations that variants of ribosomal proteins in yeast may carry different functions, although this hypothesis still lacks experimental proof. The most prominent protein features that distinguish yeast ribosomes from ribosomes from other species are several extensions in ribosomal proteins A, B, and C, some described to have a tremendous impact on protein synthesis with canonical mode of translation initiation.
On average, a human cell contains about one million of ribosomes, with each ribosome being made of 82 different proteins and 4 large rRNAs, with a total molecular weight of 4.5MDa. Human ribosomes are so large compared to most other cellular components that the first microscopic snapshots of the cell suggested that ribosomes are small organelles. One hallmark feature that distinguishes human ribosomes from their counterparts from lower eukaryotes, are impressively large rRNA extensions – 5 long additional helices in 28S rRNA that surround the ribosome particle like long and flexible tails. Although these RNA extensions correspond to ~13% of total cellular RNA content, their physiological role remains unknown.
With the optimal growth temperature of 160F (~72C), bacterium Thermus thermophilus represents a group of microorganisms that thrive at conditions which are deadly for most other species. How the ribosome structure adapts to high temperatures? Comparison of T. thermophilus and E. coli shows that the major adaptation occurs via changes of protein and rRNA sequence: proteins contain a higher proportion of positively charged residues at the interface with rRNA, and the rRNA contains a higher proportion of G and C bases. Apart from these differences, ribosomes in T. thermophilus are overall similar to those in other bacteria. They carry only one additional protein, Thx, which helps stabilize folding of ribosomal RNA. This protein is buried deep in the interior of the small ribosomal subunit where it provides additional stabilization for the highly compact folding of 16S rRNA. And only a few protein in T. thermophilus ribosomes – such as ribosomal proteins bL25 and uL15) – evolve more elongated extensions compared to those in proteins from mesophilic species.
Microsporidia are parasites which body consists of a single cell, and this cell is the smallest eukaryotic cell known in nature. Unusually for eukaryotes, Microsporidia lack fully functional mitochondria and Golgi apparatus, and retain their highly degenerated equivalents. Microsporidia size is comparable with the size of E. coli, while their genome contains only 2,000 genes – which is ~10 times less than in humans, ~3 times less than in yeasts, and even ~2 times less than in bacteria E. coli. The miniature size of Microsporidia cells and genomes reflect the fact that these species are not capable to live in a free environment, and instead they live and proliferate inside of the cytosol of another eukaryotic cells causing a number of chronic disorders in animals, including humans. Our analysis of Microsporidian genomes indicates that these parasites have a highly distinct, functionally specialized machinery of protein synthesis with unprecedented changes in the functional centers of its central components – molecules of tRNAs, aminoacyl-tRNA synthetases, protein factors of protein synthesis and ribosomes. Our study also show that Microsporidian parasites have degenerated sites for binding many drugs targeting machinery of protein synthesis and, at time, are hypersensitive to stresses and toxicity caused by imbalanced supply of a host cell with small metabolites.
Microsporidian parasites carry the smallest known cytosolic ribosomes in nature
Pyrococcus furiosus is an extremophilic species of Archaea that grow best in a boiling water, at 212F (100C)! As is the case of many other archeal species, P. furiosus represent a curious hybrid between bacteria- and eukaryote-type of ribosomes. Thus, like bacterial ribosomes, P. furiosus ribosomes carry the anti-Shine-Dalgarno sequence that helps ribosomes to properly read the genetic code in archaeal messenger RNAs. However the protein composition of P. furiosus is similar to those of eukaryotic ribosomes.
Haloarcula marismortui is archaeal species of a halophilic microorganism – the organism that requires extremely salty conditions to grow. Typically, Haloarcula species requires at least 1.5 M NaCl for growth, but grow optimally in 2.0 to 4.5 M NaCl! Structural analysis of the large ribosomal subunit from H. marismortui showed that – like many proteins from halophilic species, – H. marismortui ribosomal proteins have a high negative charge on their surface that apparently stabilizes the fold of these proteins in a highly saline media of H. marismortui cells. H. marismortui ribosomeslack ~10 ribosomal proteins found in other archaeal species.