Ribosomal protein


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 atomic picture of the ribosomal proteins is emerging from the latest high-resolution cryo-EM data.

Conservation

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, while 17 subunits are only found in archea 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 proteins of the eukaryotic small ribosomal subunit proteins are also present 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 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 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 and 33 proteins in the large subunit. All of them are different with three exceptions: one protein is found in both subunits, 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 and fragmented at 7.0 kDa. This is why the number of proteins in a ribosome is of 56. Except for S1, 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 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 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. 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 eukaryotes

Ribosomes, which synthesize the proteome of cells, are complex ribonucleoproteins that, in eukaryotes, contain 79–80 proteins and four ribosomal RNAs.
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

''E.coli'' small 30S subunit

Subunit No.Subunit nameE.coli proteinPfam family with E.coli proteinUniprot accession of E.coli protein
1S1RS1_ECOLIPF00575
2S2RS2_ECOLIPF00318
3S3RS3_ECOLIPF00189, PF07650
4S4RS4_ECOLIPF00163, PF01479
5S5RS5_ECOLIPF00333, PF03719
6S6RS6_ECOLIPF01250
7S7RS7_ECOLIPF00177
8S8RS8_ECOLIPF00410
9S9RS9_ECOLIPF00380
10S10RS10_ECOLIPF00338
11S11RS11_ECOLIPF00411
12S12RS12_ECOLIPF00164
13S13RS13_ECOLIPF00416
14S14RS14_ECOLIPF00253
15S15RS15_ECOLIPF00312
16S16RS16_ECOLIPF00886
27S17RS17_ECOLIPF00366
28S18RS18_ECOLIPF01084
29S19RS19_ECOLIPF00203
20S20RS20_ECOLIPF01649
21S21RS21_ECOLIPF01165
22S22RS22_ECOLIPF08136

''E.coli'' large 50S subunit

Human small 40S subunit

Subunit No.Subunit nameHuman proteinPfam family with Human protein
240S ribosomal protein S2RS2_HUMANPF03719 Ribosomal protein S5, C-terminal domain
240S ribosomal protein S2RS2_HUMANPF00333 Ribosomal protein S5, N-terminal domain
340S ribosomal protein S3RS3_HUMANPF00189 Ribosomal protein S3, C-terminal domain
3A40S ribosomal protein S3aRS3A_HUMANPF01015 Ribosomal S3Ae family
440S ribosomal protein S4, X isoformRS4X_HUMANPF08071 RS4NT domain
440S ribosomal protein S4, X isoformRS4X_HUMANPF01479 S4 domain
440S ribosomal protein S4, X isoformRS4X_HUMANPF00900 Ribosomal family S4e
440S ribosomal protein S4, X isoformRS4X_HUMANPF16121 40S ribosomal protein S4 C-terminus
440S ribosomal protein S4, Y isoform 1RS4Y1_HUMANPF08071 RS4NT domain
440S ribosomal protein S4, Y isoform 1RS4Y1_HUMANPF00900 Ribosomal family S4e
440S ribosomal protein S4, Y isoform 1RS4Y1_HUMANPF16121 40S ribosomal protein S4 C-terminus
440S ribosomal protein S4, Y isoform 2RS4Y2_HUMANPF08071 RS4NT domain
440S ribosomal protein S4, Y isoform 2RS4Y2_HUMANPF00900 Ribosomal family S4e
440S ribosomal protein S4, Y isoform 2RS4Y2_HUMANPF16121 40S ribosomal protein S4 C-terminus
540S ribosomal protein S5RS5_HUMANPF00177 Ribosomal protein S7p/S5e
640S ribosomal protein S6RS6_HUMANPF01092 Ribosomal protein S6e
740S ribosomal protein S7RS7_HUMANPF01251 Ribosomal protein S7e
840S ribosomal protein S8RS8_HUMANPF01201 Ribosomal protein S8e
940S ribosomal protein S9RS9_HUMANPF01479 S4 domain
940S ribosomal protein S9RS9_HUMANPF00163 Ribosomal protein S4/S9 N-terminal domain
1040S ribosomal protein S10RS10_HUMANPF03501 Plectin/S10 domain
1140S ribosomal protein S11RS11_HUMANPF16205 Ribosomal_S17 N-terminal
1140S ribosomal protein S11RS11_HUMANPF00366 Ribosomal protein S17
1240S ribosomal protein S12RS12_HUMANPF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
1340S ribosomal protein S13RS13_HUMANPF08069 Ribosomal S13/S15 N-terminal domain
1340S ribosomal protein S13RS13_HUMANPF00312 Ribosomal protein S15
1440S ribosomal protein S14RS14_HUMANPF00411 Ribosomal protein S11
1540S ribosomal protein S15RS15_HUMANPF00203 Ribosomal protein S19
15A40S ribosomal protein S15aRS15A_HUMANPF00410 Ribosomal protein S8
1640S ribosomal protein S16RS16_HUMANPF00380 Ribosomal protein S9/S16
1740S ribosomal protein S17RS17_HUMANPF00833 Ribosomal S17
1840S ribosomal protein S18RS18_HUMANPF00416 Ribosomal protein S13/S18
1940S ribosomal protein S19RS19_HUMANPF01090 Ribosomal protein S19e
2040S ribosomal protein S20RS20_HUMANPF00338 Ribosomal protein S10p/S20e
2140S ribosomal protein S21RS21_HUMANPF01249 Ribosomal protein S21e
2340S ribosomal protein S23RS23_HUMANPF00164 Ribosomal protein S12/S23
2440S ribosomal protein S24RS24_HUMANPF01282 Ribosomal protein S24e
2540S ribosomal protein S25RS25_HUMANPF03297 S25 ribosomal protein
2640S ribosomal protein S26RS26_HUMANPF01283 Ribosomal protein S26e
2740S ribosomal protein S27RS27_HUMANPF01667 Ribosomal protein S27
2840S ribosomal protein S28RS28_HUMANPF01200 Ribosomal protein S28e
2940S ribosomal protein S29RS29_HUMANPF00253 Ribosomal protein S14p/S29e
3040S ribosomal protein S30RS30_HUMANPF04758 Ribosomal protein S30
A40S ribosomal protein SARSSA_HUMANPF16122 40S ribosomal protein SA C-terminus
A40S ribosomal protein SARSSA_HUMANPF00318 Ribosomal protein S2
RACK1/GNB2L1RACK1_HUMANPF00400 Receptor for activated C kinase 1

Human large 60S subunit

Subunit No.Subunit nameHuman proteinPfam family with Human protein
360S ribosomal protein L3RL3_HUMANPF00297 Ribosomal protein L3
460S ribosomal protein L4RL4_HUMANPF00573 Ribosomal protein L4/L1 family
460S ribosomal protein L4RL4_HUMANPF14374 60S ribosomal protein L4
560S ribosomal protein L5RL5_HUMANPF00861 Ribosomal L18p/L5e family
560S ribosomal protein L5RL5_HUMANPF14204 Ribosomal L18 C-terminal region
660S ribosomal protein L6RL6_HUMANPF01159 Ribosomal protein L6e
660S ribosomal protein L6RL6_HUMANPF03868 Ribosomal protein L6, N-terminal
7A60S ribosomal protein L7aRL7A_HUMANPF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
760S ribosomal protein L7RL7_HUMANPF00327 Ribosomal protein L30p/L7e
760S ribosomal protein L7RL7_HUMANPF08079 Ribosomal L30 N-terminal domain
860S ribosomal protein L8RL8_HUMANPF00181 Ribosomal Proteins L2, RNA-binding domain
860S ribosomal protein L8RL8_HUMANPF03947 Ribosomal Proteins L2, C-terminal
960S ribosomal protein L9RL9_HUMANPF00347 Ribosomal protein L6
960S ribosomal protein L9RL9_HUMANPF00347 Ribosomal protein L6
10A60S ribosomal protein L10aRL10A_HUMANPF00687 Ribosomal protein L1p/L10e family
1060S ribosomal protein L10RL10_HUMANPF00252 Ribosomal protein L16p/L10e
1160S ribosomal protein L11RL11_HUMANPF00281 Ribosomal protein L5
1160S ribosomal protein L11RL11_HUMANPF00673 ribosomal L5P family C-terminus
1260S ribosomal protein L12RL12_HUMANPF00298 Ribosomal protein L11, RNA-binding domain
1260S ribosomal protein L12RL12_HUMANPF03946 Ribosomal protein L11, N-terminal
13A60S ribosomal protein L13aRL13A_HUMANPF00572 Ribosomal protein L13
1360S ribosomal protein L13RL13_HUMANPF01294 Ribosomal protein L13e
1460S ribosomal protein L14RL14_HUMANPF01929 Ribosomal protein L14
1560S ribosomal protein L15RL15_HUMANPF00827 Ribosomal L15
1760S ribosomal protein L17RL17_HUMANPF00237 Ribosomal protein L22p/L17e
18A60S ribosomal protein L18aRL18A_HUMANPF01775 Ribosomal L18ae/LX protein domain
1860S ribosomal protein L18RL18_HUMANPF00828 Ribosomal_L18e
1960S ribosomal protein L19RL19_HUMANPF01280 Ribosomal protein L19e
2160S ribosomal protein L21RL21_HUMANPF01157 Ribosomal protein L21e
2260S ribosomal protein L22RL22_HUMANPF01776 Ribosomal L22e protein family
23A60S ribosomal protein L23aRL23A_HUMANPF00276 Ribosomal protein L23
23A60S ribosomal protein L23aRL23A_HUMANPF03939 Ribosomal protein L23, N-terminal
2360S ribosomal protein L23RL23_HUMANPF00238 Ribosomal protein L14p/L23e
2460S ribosomal protein L24RL24_HUMANPF01246 Ribosomal protein L24e
2660S ribosomal protein L26RL26_HUMANPF16906 Ribosomal proteins L26 eukaryotic, L24P archaeal
27A60S ribosomal protein L27aRL27A_HUMANPF00828 Ribosomal protein L18e/L15
2760S ribosomal protein L27RL27_HUMANPF01777 Ribosomal L27e protein family
2860S ribosomal protein L28RL28_HUMANPF01778 Ribosomal L28e protein family
2960S ribosomal protein L29RL29_HUMANPF01779 Ribosomal L29e protein family
3060S ribosomal protein L30RL30_HUMANPF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
3160S ribosomal protein L31RL31_HUMANPF01198 Ribosomal protein L31e
3260S ribosomal protein L32RL32_HUMANPF01655 Ribosomal protein L32
3460S ribosomal protein L34RL34_HUMANPF01199 Ribosomal protein L34e
35A60S ribosomal protein L35aRL35A_HUMANPF01247 Ribosomal protein L35Ae
3560S ribosomal protein L35RL35_HUMANPF00831 Ribosomal L29 protein
36A60S ribosomal protein L36aRL36A_HUMANPF00935 Ribosomal protein L44
3660S ribosomal protein L36RL36_HUMANPF01158 Ribosomal protein L36e
37A60S ribosomal protein L37aRL37A_HUMANPF01780 Ribosomal L37ae protein family
3760S ribosomal protein L37RL37_HUMANPF01907 Ribosomal protein L37e
3860S ribosomal protein L38RL38_HUMANPF01781 Ribosomal L38e protein family
3960S ribosomal protein L39RL39_HUMANPF00832 Ribosomal L39 proteiin
40Ubiquitin-60S ribosomal protein L40RL40_HUMANPF01020 Ribosomal L40e family
4160S ribosomal protein L41RL41_HUMANPF05162 Ribosomal protein L41
P060S acidic ribosomal protein P0RLA0_HUMANPF00466 Ribosomal protein L10
P060S acidic ribosomal protein P0RLA0_HUMANPF00428 60s Acidic ribosomal protein
P160S acidic ribosomal protein P1RLA1_HUMANPF00428 60s Acidic ribosomal protein
P260S acidic ribosomal protein P2RLA2_HUMANPF00428 60s Acidic ribosomal protein