Ribosomal protein
A ribosomal protein (r-protein or rProtein[1][2][3]) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. 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.[4] Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.[5]
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 PDB: 5AFI).
Conservation
[edit]
Ribosomal proteins are among the most highly conserved proteins across all life forms.[5] 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.[5] 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.[5]
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.[5]
Essentiality
[edit]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.[7] 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.[8] 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.[9]
Assembly
[edit] | This section is missing information about how (intermediates, etc.). (April 2019) |
In E. coli
[edit]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),[dubious – discuss] 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.[10]
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.[11]
Disposition in the small ribosomal subunit
[edit]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.[citation 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[12]
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.[13] 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.[13]
In eukaryotes
[edit]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.[5]
Table of ribosomal proteins
[edit]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.[5]
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).[5] Organelle-specific proteins use their own cross-domain prefixes, for example "mS33" for MRPS33[14]: Table S3, S4 and "cL37" for PSRP5.[15]: Table S2, S3 (See the two proceeding citations, also partially by Ban N, for the organelle nomenclatures.)
| Cross-domain name[a] | Pfam domain | Taxonomic range[b] | Bacteria name (E. coli UniProt) | Yeast name | Human name |
|---|---|---|---|---|---|
| bS1 | PF00575 | B | S1 P0AG67 | — | — |
| eS1 | PF01015 | A E | — | S1 | S3A |
| uS2 | PF00318, PF16122 | B A E | S2 P0A7V0 | S0 | SA |
| uS3 | PF00189, PF07650 | B A E | S3 P0A7V3 | S3 | S3 |
| uS4 | PF00163, PF01479 | B A E | S4 P0A7V8 | S9 | S9 |
| eS4 | PF00900, PF08071, PF16121 | A E | — | S4 | S4 (X, Y1, Y2) |
| uS5 | PF00333, PF03719 | B A E | S5 P0A7W1 | S2 | S2 |
| bS6 | PF01250 | B | S6 P02358 | — | — |
| eS6 | PF01092 | A E | — | S6 | S6 |
| uS7 | PF00177 | B A E | S7 P02359 | S5 | S5 |
| eS7 | PF01251 | E | — | S7 | S7 |
| uS8 | PF00410 | B A E | S8 P0A7W7 | S22 | S15A |
| eS8 | PF01201 | A E | — | S8 | S8 |
| uS9 | PF00380 | B A E | S9 P0A7X3 | S16 | S16 |
| uS10 | PF00338 | B A E | S10 P0A7R5 | S20 | S20 |
| eS10 | PF03501 | E | — | S10 | S10 |
| uS11 | PF00411 | B A E | S11 P0A7R9 | S14 | S14 |
| uS12 | PF00164 | B A E | S12 P0A7S3 | S23 | S23 |
| eS12 | PF01248 | E | — | S12 | S12 |
| uS13 | PF00416 | B A E | S13 P0A7S9 | S18 | S18 |
| uS14 | PF00253 | B A E | S14 P0AG59 | S29 | S29 |
| uS15 | PF00312 | B A E | S15 P0ADZ4 | S13 | S13 |
| bS16 | PF00886 | B | S16 P0A7T3 | — | — |
| uS17 | PF00366 | B A E | S17 P0AG63 | S11 | S11 |
| eS17 | PF00366 | A E | — | S17 | S17 |
| bS18 | PF01084 | B | S18 P0A7T7 | — | — |
| uS19 | PF00203 | B A E | S19 P0A7U3 | S15 | S15 |
| eS19 | PF01090 | A E | — | S19 | S19 |
| bS20 | PF01649 | B | S20 P0A7U7 | — | — |
| bS21 | PF01165 | B | S21 P68681 | — | — |
| bTHX | PF17070, PF17067 | B | THX (missing from E. coli) | — | — |
| eS21 | PF01249 | E | — | S21 | S21 |
| eS24 | PF01282 | A E | — | S24 | S24 |
| eS25 | PF03297 | A E | — | S25 | S25 |
| eS26 | PF01283 | E | — | S26 | S26 |
| eS27 | PF01667 | A E | — | S27 | S27 |
| eS28 | PF01200 | A E | — | S28 | S28 |
| eS30 | PF04758 | A E | — | S30 | S30 |
| eS31 | PF01599 | A E | — | S31 | S27A |
| RACK1 | PF00400 | E | — | Asc1 | RACK1 |
| Cross-domain name[a] | Pfam domains | Taxonomic range[b] | Bacteria name (E. coli UniProt) | Yeast name | Human name |
|---|---|---|---|---|---|
| uL1 | PF00687 | B A E | L1 P0A7L0 | L1 | L10A |
| uL2 | PF03947, PF00181 | B A E | L2 P60422 | L2 | L8 |
| uL3 | PF00297 | B A E | L3 P60438 | L3 | L3 |
| uL4 | PF00573 | B A E | L4 P60723 | L4 | L4 |
| uL5 | PF00281, PF00673 (b) | B A E | L5 P62399 | L11 | L11 |
| uL6 | PF00347 | B A E | L6 P0AG55 | L9 | L9 |
| eL6 | PF01159, PF03868 | E | — | L6 | L6 |
| eL8 | PF01248 | A E | — | L8 | L7A |
| bL9 | PF01281, PF03948 | B | L9 P0A7R1 | — | — |
| uL10 | PF00466 | B A E | L10 P0A7J3 | P0 | P0 |
| uL11 | PF03946, PF00298 | B A E | L11 P0A7J7 | L12 | L12 |
| bL12 | PF16320, PF00542 | B | L7/L12 P0A7K2 | — | — |
| uL13 | PF00572 | B A E | L13 P0AA10 | L16 | L13A |
| eL13 | PF01294 | A E | — | L13 | L13 |
| uL14 | PF00238 | B A E | L14 P0ADY3 | L23 | L23 |
| eL14 | PF01929 | A E | — | L14 | L14 |
| uL15 | PF00828 | B A E | L15 P02413 | L28 | L27A |
| eL15 | PF00827 | A E | — | L15 | L15 |
| uL16 | PF00252 | B A E | L16 P0ADY7 | L10 | L10 |
| bL17 | PF01196 | B | L17 P0AG44 | — | — |
| uL18 | PF00861 | B A E | L18 P0C018 | L5 | L5 |
| eL18 | PF00828 | A E | — | L18 | L18 |
| bL19 | PF01245 | B | L19 B1LPB3 | — | — |
| eL19 | PF01280 | A E | — | L19 | L19 |
| bL20 | PF00453 | B | L20 P0A7L3 | — | — |
| eL20 | PF01775 | E | — | L20 | L18A |
| bL21 | PF00829 | B | L21 P0AG48 | — | — |
| eL21 | PF01157 | A E | — | L21 | L21 |
| uL22 | PF00237 | B A E | L22 P61175 | L17 | L17 |
| eL22 | PF01776 | E | — | L22 | L22 |
| uL23 | PF00276, PF03939 (e) | B A E | L23 P0ADZ0 | L25 | L23A |
| uL24 | PF00467 (b), PF16906 (ae) | B A E | L24 P60624 | L26 | L26 |
| eL24 | PF01246 | A E | — | L24 | L24 |
| bL25 | PF01386 | B | L25 P68919 | — | — |
| bL27 | PF01016 | B | L27 P0A7M0 | — | — |
| eL27 | PF01777 | E | — | L27 | L27 |
| bL28 | PF00830 | B | L28 P0A7M2 | — | — |
| eL28 | PF01778 | E | — | — | L28 |
| uL29 | PF00831 | B A E | L29 P0A7M6 | L35 | L35 |
| eL29 | PF01779 | E | — | L29 | L29 |
| uL30 | PF00327 | B A E | L30 P0AG51 | L7 | L7 |
| eL30 | PF01248 | A E | — | L30 | L30 |
| bL31 | PF01197 | B | L31 P0A7M9 | — | — |
| eL31 | PF01198 | A E | — | L31 | L31 |
| bL32 | PF01783 | B | L32 C4ZS29 | — | — |
| eL32 | PF01655 | A E | — | L32 | L32 |
| bL33 | PF00471 | B | L33 P0A7N9 | — | — |
| eL33 | PF01247 | A E | — | L33 | L35A |
| bL34 | PF00468 | B | L34 P0A7P6 | — | — |
| eL34 | PF01199 | A E | — | L34 | L34 |
| bL35 | PF01632 | B | L35 P0A7Q2 | — | — |
| bL36 | PF00444 | B | L36 P0A7Q7 | — | — |
| eL36 | PF01158 | E | — | L36 | L36 |
| eL37 | PF01907 | A E | — | L37 | L37 |
| eL38 | PF01781 | A E | — | L38 | L38 |
| eL39 | PF00832 | A E | — | L39 | L39 |
| eL40 | PF01020 | A E | — | L40 | L40 |
| eL41 | PF05162 | A E | — | L41 | L41 |
| eL42 | PF00935 | A E | — | L42 | L36A |
| eL43 | PF01780 | A E | — | L43 | L37A |
| P1/P2 | PF00428 | A E | — | P1/P2 (AB) | P1/P2 (αβ) |
See also
[edit]- Alpha operon ribosome binding site
- Ribosomal protein L20 leader
- Mitochondrial ribosome, for a list of its protein subunits
References
[edit]- ^ Salini 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.
- ^ Weiler EW, Nover L (2008). Allgemeine und molekulare Botanik (in German). Stuttgart: Georg Thieme Verlag. p. 532. ISBN 978-3-13-152791-2.
- ^ de la Cruz J, Karbstein K, Woolford JL (2015). "Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo". Annual Review of Biochemistry (in German). 84: 93–129. doi:10.1146/annurev-biochem-060614-033917. PMC 4772166. PMID 25706898.
- ^ Rodnina MV, Wintermeyer W (April 2011). "The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation". Biochemical Society Transactions. 39 (2): 658–62. doi:10.1042/BST0390658. PMID 21428957.
- ^ a b c d e f g h i j Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, et al. (February 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology. 24: 165–9. doi:10.1016/j.sbi.2014.01.002. PMC 4358319. PMID 24524803.
- ^ Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. (April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
- ^ Gao F, Luo H, Zhang CT, Zhang R (2015). "Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes". Gene Essentiality. Methods in Molecular Biology. Vol. 1279. pp. 219–33. doi:10.1007/978-1-4939-2398-4_14. ISBN 978-1-4939-2397-7. PMID 25636622.
- ^ Shoji S, Dambacher CM, Shajani Z, Williamson JR, Schultz PG (November 2011). "Systematic chromosomal deletion of bacterial ribosomal protein genes". Journal of Molecular Biology. 413 (4): 751–61. doi:10.1016/j.jmb.2011.09.004. PMC 3694390. PMID 21945294.
- ^ Akanuma G, Nanamiya H, Natori Y, Yano K, Suzuki S, Omata S, et al. (November 2012). "Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation". Journal of Bacteriology. 194 (22): 6282–91. doi:10.1128/JB.01544-12. PMC 3486396. PMID 23002217.
- ^ Arnold RJ, Reilly JP (April 1999). "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry". Analytical Biochemistry. 269 (1): 105–12. doi:10.1006/abio.1998.3077. PMID 10094780.
- ^ Chen SS, Williamson JR (February 2013). "Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry". Journal of Molecular Biology. 425 (4): 767–79. doi:10.1016/j.jmb.2012.11.040. PMC 3568210. PMID 23228329.
- ^ Hamacher K, Trylska J, McCammon JA (February 2006). "Dependency map of proteins in the small ribosomal subunit". PLOS Computational Biology. 2 (2): e10. Bibcode:2006PLSCB...2...10H. doi:10.1371/journal.pcbi.0020010. PMC 1364506. PMID 16485038.
- ^ a b Tirumalai MR, Anane-Bediakoh D, Rajesh R, Fox GE (November 2021). "Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance". Microbiol. Spectr. 9 (3): e0178221. doi:10.1128/spectrum.01782-21. PMC 8672879. PMID 34908470.
- ^ Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N (April 2015). "Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome". Science. 348 (6232): 303–8. doi:10.1126/science.aaa3872. hdl:20.500.11850/100390. PMID 25837512. S2CID 206634178.
- ^ Bieri, P; Leibundgut, M; Saurer, M; Boehringer, D; Ban, N (15 February 2017). "The complete structure of the chloroplast 70S ribosome in complex with translation factor pY". The EMBO Journal. 36 (4): 475–486. doi:10.15252/embj.201695959. PMC 5694952. PMID 28007896.
Further reading
[edit]- Korobeinikova AV, Garber MB, Gongadze GM (June 2012). "Ribosomal proteins: structure, function, and evolution". Biochemistry. Biokhimiia. 77 (6): 562–74. doi:10.1134/S0006297912060028. PMID 22817455. S2CID 12608006.
- Armache JP, Anger AM, Márquez V, Franckenberg S, Fröhlich T, Villa E, et al. (January 2013). "Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution". Nucleic Acids Research. 41 (2): 1284–93. doi:10.1093/nar/gks1259. PMC 3553981. PMID 23222135.
- Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, et al. (February 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology. 24: 165–9. doi:10.1016/j.sbi.2014.01.002. PMC 4358319. PMID 24524803.
External links
[edit]- 30S Ribosomal proteins at biochem.umd.edu
- Ribosomal+Protein at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
- Ribosomal protein nomenclature visualization from Ban et al., with annotated structures of cellular and organellar ribosomes