Symbol L31 InterPro IPR016340 SCOP 1m90 | Pfam PF09784 PROSITE PDOC00880 SUPERFAMILY 1m90 | |
A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. A large part of the knowledge about these organic molecules has come from the study of E. coli ribosomes. All ribosomal proteins have been isolated and many specific antibodies have been produced. These, together with electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome. E.coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans. More recently, a near-complete (near)atomic picture of the ribosomal proteins is emerging from the latest high-resolution cryo-EM data (including PDB ID: 5AFI).
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Conservation of ribosomal proteins
Ribosomal proteins are among the most highly conserved proteins across all life forms. Among the 40 proteins found in various small ribosomal subunits, 15 subunits are universally conserved across prokaryotes and eukaryotes. However, 7 subunits are only found in bacteria (S21, S6, S16, S18, S20, S21, and THX), while 17 subunits are only found in archea and eukaryotes. Typically 22 proteins are found in bacterial 30S subunits and 32 in yeast, human and most likely most other eukaryotic species. Twenty-seven (out of 32) proteins of the eukaryotic small ribosomal subunit proteins are also present in archaea (no ribosomal subunit is exclusively found in archaea), confirming that they are more closely related to eukaryotes than to eubacteria.
Among the large ribosomal subunit, 18 proteins are universal, i.e. found in both bacteria, eukaryotes, and archea. 14 proteins are only found in bacteria, while 27 proteins are only found in archea and eukaryotes. Again, archea have no proteins unique to them
Essentiality
Despite their high conservation over billions of years of evolution, the absence of several ribosomal proteins in certain species shows that ribosomal subunits have been added and lost over the course of evolution. This is also reflected by the fact that several ribosomal proteins do not appear to be essential when deleted. For instance, in E. coli nine ribosomal proteins (L15, L21, L24, L27, L29, L30, L34, S9, and S17) are nonessential for survival when deleted. Taken together with previous results, 22 of the 54 E. coli ribosomal protein genes can be individually deleted from the genome. Similarly, 16 ribosomal proteins (L1, L9, L15, L22, L23, L28, L29, L32, L33.1, L33.2, L34, L35, L36, S6, S20, and S21) were successfully deleted in Bacillus subtilis. In conjunction with previous reports, 22 ribosomal proteins have been shown to be nonessential in B. subtilis, at least for cell proliferation.
Proteins in E. coli ribosomes
The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 33 proteins in the large subunit (somewhat counter-intuitively called L1 to L36). All of them are different with three exceptions: one protein is found in both subunits (S20 and L26), L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7/L12 and L10. In addition, L31 is known to exist in two forms, the full length at 7.9 kilodaltons (kDa) and fragmented at 7.0 kDa. This is why the number of proteins in a ribosome is of 56. Except for S1 (with a molecular weight of 61.2 kDa), the other proteins range in weight between 4.4 and 29.7 kDa.
Recent 'de novo' proteomics experiments where the authors characterized in vivo ribosome-assembly intermediates and associated assembly factors from wild-type Escherichia coli cells using a general quantitative mass spectrometry (qMS) approach have confirmed the presence of all the known small and large subunit components and have identified a total of 21 known and potentially new ribosome-assembly-factors that co-localise with various ribosomal particles.
Disposition in the small ribosomal subunit
In the small (30S) subunit of E. coli ribosomes, the proteins denoted S4, S7, S8, S15, S17, S20 bind independently to 16S rRNA. After assembly of these primary binding proteins, S5, S6, S9, S12, S13, S16, S18, and S19 bind to the growing ribosome. These proteins also potentiate the addition of S2, S3, S10, S11, S14, and S21. Protein binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure. Nearly all the proteins contain one or more globular domains. Moreover, nearly all contain long extensions that can contact the RNA in far-reaching regions [reference needed]. Additional stabilization results from the proteins' basic residues, as these neutralize the charge repulsion of the RNA backbone. Protein–protein interactions also exist to hold structure together by electrostatic and hydrogen bonding interactions. Theoretical investigations pointed to correlated effects of protein-binding onto binding affinities during the assembly process
Assembly of the ribosome in eukaryotes
Ribosomes, which synthesize the proteome of cells, are complex ribonucleoproteins that, in eukaryotes, contain 79–80 proteins and four ribosomal RNAs(rRNAs). General or specialized chaperones solubilize the ribosomal proteins and facilitate their import into the nucleus. Assembly of the eukaryotic ribosome appears to be driven by the ribosomal proteins in vivo when assembly is also aided by chaperones. Most ribosomal proteins assemble with rRNA co-transcriptionally, becoming associated more stably as assembly proceeds, and the active sites of both subunits are constructed last.