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 ribosomal subunit (PDB: 1FFK​).
A small ribosomal subunit (PDB: 1FKA​).
The two ribosomal subunits. Proteins are shown in blue and the RNA chains in brown and yellow.

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
A 2016 tree of life using 16 universally-conserved ribosomal protein sequences[6]

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

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

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.[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

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[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

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

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. cervisiae, 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.)

Small subunit ribosomal proteins[5]
Cross-domain name[lower-alpha 1] Pfam domain Taxonomic range[lower-alpha 2] 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
Large subunit ribosomal proteins[5]
Cross-domain name[lower-alpha 1] Pfam domains Taxonomic range[lower-alpha 2] 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)
  1. b = bacteria (+organelle); e = eukarya cytoplasm; u = universal. Older nomenclature often have the order reversed, so that "bS1" becomes S1b or S1p (for "prokaryote").
  2. B = bacteria (+organelle); A = archaea; E = eukarya cytoplasm

See also

References
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  13. 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.
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Further reading
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