Ribosomal protein

A ribosomal protein (r-protein or rProteinSalini Konikkat: Dynamic Remodeling Events Drive the Removal of the ITS2 Spacer Sequence During Assembly of 60S Ribosomal Subunits in S. cerevisiae. Carnegie Mellon University Dissertations, Feb. 2016.) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. Bacteria and archaea have a small ribosomal subunit (30S) and a large ribosomal subunit (50S). Eukaryotes have a small ribosomal subunit (40S), and a large ribosomal subunit (60S). Equivalent subunits are frequently numbered differently between bacteria, archaea, and eukaryotes.

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. More recently, a near-complete (near)atomic picture of the ribosomal proteins is emerging from the latest high-resolution cryo-EM data (including ).

Conservation

Ribosomal proteins are among the most highly conserved proteins across all life forms. Among the 40 proteins found in various small ribosomal subunits (RPSs), 15 subunits are universally conserved across prokaryotes and eukaryotes. However, 7 subunits are only found in bacteria (bS21, bS6, bS16, bS18, bS20, bS21, and bTHX), while 17 subunits are only found in archaea and eukaryotes. Typically 22 proteins are found in bacterial small 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 protein is exclusively found in archaea), confirming that they are more closely related to eukaryotes than to bacteria.

Among the large ribosomal subunit (RPLs), 18 proteins are universal, i.e. found in both bacteria, eukaryotes, and archaea. 14 proteins are only found in bacteria, while 27 proteins are only found in archaea and eukaryotes. Again, archaea 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 (uL15, bL21, uL24, bL27, uL29, uL30, bL34, uS9, and uS17) 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 (uL1, bL9, uL15, uL22, uL23, bL28, uL29, bL32, bL33.1, bL33.2, bL34, bL35, bL36, bS6, bS20, and bS21) 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.

Assembly

In E. coli 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 uS4, uS7, uS8, uS15, uS17, bS20 bind independently to 16S rRNA. After assembly of these primary binding proteins, uS5, bS6, uS9, uS12, uS13, bS16, bS18, and uS19 bind to the growing ribosome. These proteins also potentiate the addition of uS2, uS3, uS10, uS11, uS14, and bS21. 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. 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

In one study, the net charges (at pH 7.4) of the ribosomal proteins comprising the highly conserved S10-spc cluster were found to have an inverse relationship with the halophilicity/halotolerance levels in bacteria and archaea. In non-halophilic bacteria, the S10-spc proteins are generally basic, contrasting with the overall acidic whole proteomes of the extremely halophiles. The universal uL2 lying in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to.

In eukaryotes Ribosomes in eukaryotes contain 79–80 proteins and four ribosomal RNA (rRNA) molecules. 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.

Table of ribosomal proteins In the past, different nomenclatures were used for the same ribosomal protein in different organisms. Not only were the names not consistent across domains; the names also differed between organisms within a domain, such as humans and S. cerevisiae, both eukaryotes. This was due to researchers assigning names before the sequences were known, causing trouble for later research. The following tables use the unified nomenclature by Ban et al., 2014. The same nomenclature is used by UniProt's "family" curation.

In general, cellular ribosomal proteins are to be called simply using the cross domain name, e.g. "uL14" for what is currently called L23 in humans. A suffix is used for the organellar versions, so that "uL14m" refers to the human mitochondrial uL14 (MRPL14). Organelle-specific proteins use their own cross-domain prefixes, for example "mS33" for MRPS33 and "cL37" for PSRP5. (See the two proceeding citations, also partially by Ban N, for the organelle nomenclatures.)

+Small subunit ribosomal proteinsCross-domain namePfam domainTaxonomic rangeBacteria name (E. coli UniProt)Yeast nameHuman nameHuman mitoPlastidbS1BS1 eS1A ES1S3AuS2, B A ES2 S0SAuS3, B A ES3 S3S3uS4, B A ES4 S9S9eS4, , A ES4S4 (X, Y1, Y2)uS5, B A ES5 S2S2bS6BS6 eS6A ES6S6uS7B A ES7 S5S5eS7ES7S7uS8B A ES8 S22S15AeS8A ES8S8uS9B A ES9 S16S16uS10B A ES10 S20S20eS10ES10S10uS11B A ES11 S14S14uS12B A ES12 S23S23eS12ES12S12uS13B A ES13 S18S18uS14B A ES14 S29S29uS15B A ES15 S13S13bS16BS16 uS17B A ES17 S11S11eS17A ES17S17bS18BS18 uS19B A ES19 S15S15eS19A ES19S19bS20BS20 bS21BS21 bTHX, BTHX (missing from E. coli)eS21ES21S21eS24A ES24S24eS25A ES25S25eS26ES26S26eS27A ES27S27eS28A ES28S28eS30A ES30S30eS31A ES31S27ARACK1EAsc1RACK1 +Large subunit ribosomal proteinsCross-domain namePfam domainsTaxonomic rangeBacteria name (E. coli UniProt)Yeast nameHuman nameHuman mitoPlastiduL1B A EL1 L1L10AuL2, B A EL2 L2L8uL3B A EL3 L3L3uL4B A EL4 L4L4uL5, (b)B A EL5 L11L11uL6B A EL6 L9L9eL6, EL6L6eL8A EL8L7AbL9, BL9 uL10B A EL10 P0P0uL11, B A EL11 L12L12bL12, BL7/L12 uL13B A EL13 L16L13AeL13A EL13L13uL14B A EL14 L23L23eL14A EL14L14uL15B A EL15 L28L27AeL15A EL15L15uL16B A EL16 L10L10bL17BL17 uL18B A EL18 L5L5eL18A EL18L18bL19BL19 eL19A EL19L19bL20BL20 eL20EL20L18AbL21BL21 eL21A EL21L21uL22B A EL22 L17L17eL22EL22L22uL23, (e)B A EL23 L25L23AuL24 (b), (ae)B A EL24 L26L26eL24A EL24L24bL25BL25 bL27BL27 eL27EL27L27bL28BL28 eL28EL28uL29B A EL29 L35L35eL29EL29L29uL30B A EL30 L7L7eL30A EL30L30 (L7A)bL31BL31 eL31A EL31L31bL32BL32 eL32A EL32L32bL33BL33 eL33A EL33L35AbL34BL34 eL34A EL34L34bL35BL35 bL36BL36 eL36EL36L36eL37A EL37L37eL38A EL38L38eL39A EL39L39eL40A EL40L40eL41A EL41L41eL42A EL42L36AeL43A EL43L37AP1/P2A EP1/P2 (AB)P1/P2 (αβ)

See also Alpha operon ribosome binding site Ribosomal protein L20 leader Mitochondrial ribosome, for a list of its protein subunits

References

Ribosomal protein

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