The other lives of ribosomal proteins.

Despite the fact that ribosomal proteins are the constituents of an organelle that is present in every cell, they show a surprising level of regulation, and several of them have also been shown to have other extra-ribosomal functions, such in replication, transcription, splicing or even ageing. This review provides a comprehensive summary of these important aspects.

Introduction

Protein synthesis requires accurate translation of the nucleotide sequence of messenger RNA (mRNA) to the amino acid sequence of a protein. This translation of mRNA to protein is carried out by the ribosome and transfer RNA (tRNA), along with other protein factors. In past years, studies on the structure of the ribosome have led us to understand this complex process of protein synthesis. The ribosome consists of two subunits, each of which is made up of ribosomal RNA (rRNA) and many ribosomal proteins. Structurally, ribosomes of prokaryotes and eukaryotes vary by the types of rRNA and protein molecules found in them. The prokaryotic 70S ribosome has a small 30S and a large 50S subunit. The 30S subunit consists of one 16S molecule of rRNA and about 21 proteins, while the 50S subunit consists of two rRNAs (5S and 23S) and 31 proteins. The eukaryotic 80S ribosome has a small 40S and a large 60S subunit. The 40S subunit consists of one 18S molecule of rRNA and about 33 proteins, whereas the 60S consists of three rRNAs (5S, 28S and 5.8S) and about 50 proteins [1].

During protein synthesis, the small ribosomal subunit plays a role in accurate codon-anticodon recognition between the mRNA and tRNA molecules, while the large subunit is mainly involved in the peptide bond formation of the growing amino acid chain. In addition, structural studies of the ribosome have now revealed that they are also involved in functions such as the translocation of tRNA and mRNA on the ribosome [2].

Apart from protein synthesis, many of the ribosomal proteins are shown to be involved in other cellular functions, independent of the ribosome [3]. Their first extra-ribosomal activity was observed for S1, as a replicase in the RNA phages, and numerous extra-ribosomal functions of these proteins have subsequently been discovered. This bifunctional tendency of ribosomal proteins can be explained by theories postulating the pre-existence of the ribosomal proteins as independent molecules before forming the components of the ribosome [3]. Another interesting functional aspect of the ribosomal proteins is their regulation. These proteins are shown to affect the mechanisms of development, apoptosis and ageing during their altered expression levels. In this review, information on the extra-ribosomal roles of these proteins is provided, along with information about their specific regulation in different cellular functions. Detailed lists of all functions and regulation are presented as Tables S1 (Table 4) and S2 (Table 5).

Table S1

Function and regulation of eukaryotic small subunit ribosomal proteins

Protein Name	Organism	Function	Reference	Find online at:
RPSA	Porcine	Candidate for binding and internalisation of externally added cellular prion protein in the gut	Knorr, C., Beuermann, C., Beck, J. and Brenig, B. (2007), 'Characterization of the porcine multicopy ribosomal protein SA/37-kDa laminin receptor gene family', Gene Vol. 395(1-2), pp. 135-143.	http://www.ncbi.nlm.nih.gov/pubmed/17434268
RPS3A	Human	Cell apoptosis regulation	Naora, H. (1999), 'Involvement of ribosomal proteins in regulating cell growth and apoptosis: Translational modulation or recruitment for extraribosomal activity?', Immunol. Cell Biol. Vol. 77, pp. 197-205.	http://www.ncbi.nlm.nih.gov/pubmed/10361251
RPS6	Drosophila homologue of human S6	Tumour suppressor in the haematopoietic system	Watson, K.L., Konrad, K.D., Woods, D.F. and Bryant, P.J. (1992), 'Drosophila homolog of the human S6 ribosomal protein is required for tumor suppression in the hematopoietic system. Proc. Natl. Acad. Sci. USA Vol. 89, pp. 11302-11306.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=50538
RPS7	Zebrafish	Mutations result in malignant peripheral nerve sheath tumour (zMPNST); RP genes may be 'haploinsufficient tumour suppressors' in zebrafish and cancer genes in humans	Amsterdam, A., Sadler, K.C., Lai, K., Farrington, S. et al. (2004), 'Many ribosomal protein genes are cancer genes in zebrafish', PLoS Biol. Vol. 2, p. E139.	http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0020139&ct=1
RPS8	Zebrafish	Mutations result in malignant peripheral nerve sheath tumour (zMPNST); RP genes may be 'haploinsufficient tumour suppressors' in zebrafish and cancer genes in humans	Amsterdam, A., Sadler, K.C., Lai, K., Farrington, S. et al. (2004), 'Many ribosomal protein genes are cancer genes in zebrafish', PLoS Biol. Vol. 2, p. E139.	http://biology.plosjournals.org/perlserv/?request=get-document &doi=10.1371%2Fjournal.pbio.0020139&ct=1
RPS9	Human	Involved in retinal formation	Uechi, T., Tanaka, T. and Kenmochi, N. (2001), 'Complete map of the human ribosomal protein genes: Assignment of 80 genes to the cytogenetic map and implications for human disorders', Genomics Vol. 72, pp. 223-230.	http://www.ncbi.nlm.nih.gov/pubmed/11401437
RPS10	Arabidopsis thaliana	Developmental regulation	Majewski, P., Wołoszyńska, M. and Janńska, H. (2009), 'Developmentally early and late onset of Rps10 silencing in Arabidopsis thaliana: Genetic and environmental regulation', J. Exp. Bot. Vol. 60, pp. 1163-1178.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2657537&tool=pmcentrez
RPS13	Human	Cell growth or proliferation regulation	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
RPS15	Drosophila	Overexpression of S15a suppresses a utation in the Saccharomyces cerevisiae cdc33 gene, which encodes the cap-binding subunit of eukaryotic initiation factor 4F (eIF-4F); mutations of cdc33 lead to arrest in the cell cycle at the G1 to S transition.	Saeboe-Larssen, S. and Lambertsson, A. (1996), 'A novel Drosophila Minute locus encodes ribosomal protein S13', Genetics Vol. 143, pp. 877-885.	http://www.genetics.org/cgi/reprint/143/2/877
	Human	Role in nuclear export of 40S subunit precursors	Gazda, H., Sheen, M.R., Vlachos, A., Choesmel, V. et al. (2008), 'Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients', Am. J. Hum. Genet. Vol. 83, pp. 769-780.	http://www.ncbi.nlm.nih.gov/pubmed/19061985
RPS15A	Zebrafish	Mutations result in malignant peripheral nerve sheath tumour (zMPNST); RP genes may be 'haploinsufficient tumour suppressors' in zebrafish and cancer genes in humans	Amsterdam, A., Sadler, K.C., Lai, K., Farrington, S. et al. (2004), 'Many ribosomal protein genes are cancer genes in zebrafish', PLoS Biol. Vol. 2, p. E139.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=406397
RPS18	Arabidopsis thaliana	Developmental regulation	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
	Arabidopsis thaliana	Mutation in S18 associated with growth retardation and abnormal leaf development	Naora, H. (1999), 'Involvement of ribosomal proteins in regulating cell growth and apoptosis: Translational modulation or recruitment for extraribosomal activity?', Immunol. Cell Biol. Vol. 77, pp. 197-205.	http://www.ncbi.nlm.nih.gov/pubmed/10361251
	Zebrafish	Mutations result in malignant peripheral nerve sheath tumour (zMPNST); RP genes may be 'haploinsufficient tumour suppressors' in zebrafish and cancer genes in humans	Amsterdam, A., Sadler, K.C., Lai, K., Farrington, S. et al. (2004), 'Many ribosomal protein genes are cancer genes in zebrafish', PLoS Biol. Vol. 2, p. E139.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=406397
RPS19	Ascaris lumbricoides	Developmental regulation	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
	Human	Tumour progression, invasion, metastasis, differentiation'	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
	Human	Degeneration of retina	Uechi, T., Tanaka, T. and Kenmochi, N. (2001), 'Complete map of the human ribosomal protein genes: Assignment of 80 genes to the cytogenetic map and implications for human disorders', Genomics Vol. 72, pp. 223-230.	http://www.ncbi.nlm.nih.gov/pubmed/11401437
	Human	Dimer acts as a monocyte chemotactic factor in phagocytic clearance of apoptotic cells	Naora, H. (1999), 'Involvement of ribosomal proteins in regulating cell growth and apoptosis: Translational modulation or recruitment for extraribosomal activity?', Immunol. Cell Biol. Vol. 77, pp. 197-205.	http://www.ncbi.nlm.nih.gov/pubmed/10361251
	Zebrafish	Haematopoietic and developmental abnormalities	Danilova, N., Sakamoto, K.M. and Lin, S. et al. (2008), 'Ribosomal protein S19 deficiency in zebrafish leads to developmental abnormalities and defective erythropoiesis through activation of p53 protein family', Blood Vol. 112, pp. 5228-5537.	http://www.ncbi.nlm.nih.gov/pubmed/18515656
RPS20	Yeast	Overexpression of S20 suppresses temperature-sensitive RNA pol III (but no specificity?)	Hermann-Le Denmat, S., Sipiczki, M. and Thuriaux, P. (1994), 'Suppression of yeast RNA polymerase III mutations by the URP2 gene encoding a protein homologous to the mammalian ribosomal protein S20', J. Mol. Biol. Vol. 240, pp. 1-7.	http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45PV6 2P-1S&_user=4887109&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000062864&_version=1&_urlVersion=0&_userid=4887109&md5=88a77e1986 f7765e9374d649cc9b23a8
	Human	mRNA downregulated in onset of apoptosis in leukaemic cells	Naora, H. (1999), 'Involvement of ribosomal proteins in regulating cell growth and apoptosis: Translational modulation or recruitment for extraribosomal activity?', Immunol. Cell Biol. Vol. 77, pp. 197-205.	http://www.ncbi.nlm.nih.gov/pubmed/10361251
RPS21	Drosophila	Acts as a translation initiation factor rather than as a core ribosomal protein	Török, I., Herrmann-Horle, D., Kiss, I., Tick, G. et al. (1999), 'Down-regulation of RpS21, a putative translation initiation factor interacting with P40, produces viable minute imagos and larval lethality with overgrown hematopoietic organs and imaginal discs', Mol. Cell Biol. Vol. 19, pp. 2308-2321.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=84023&tool=pmcentrez
RPS27A	Human	Cell growth or proliferation regulation	Ye, J.L. and Zhang, Y.Z. (2007), 'The connection between tumor and ubiquitin-ribosomal protein S27a, ubiquitin and ribosomal protein', Sheng Wu Gong Cheng Xue Bao Vol. 23, pp. 982-988. [Article in Chinese]	http://www.ncbi.nlm.nih.gov/pubmed/18257223?ordinalpos=5&itool=EntrezSystem2.PEntrez. Pubmed.Pubmed_Results Panel.Pubmed_DefaultReport Panel.Pubmed_RVDocSum
	Human	Cell growth or proliferation regulation	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
	Human	Cell malignant transformation	Ye, J.L. and Zhang, Y.Z. (2007), 'The connection between tumor and ubiquitin-ribosomal protein S27a, ubiquitin and ribosomal protein', Sheng Wu Gong Cheng Xue Bao Vol. 23, pp. 982-988. [Article in Chinese]	http://www.ncbi.nlm.nih.gov/pubmed/18257223?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
RPS28	Yeast	Binds to the 3' UTR of its mRNA to stimulate its deadenylation and degradation	Badis, G., Saveanua, C., Fromont-Racinea, M. and Jacquie, A. (2004), 'Targeted mRNA degradation by deadenylation-independent decapping', Mol. Cell Vol. 15, pp. 5-15.	http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSR-4CRXKG3-3&_user=4887109&_rdoc=1&_fmt=&_orig=search &_sort=d&view=c&_acct=C000062864&_version=1&_urlVersion=0&_userid=4887109&md5=9b5ba025da819e725850644ba547d47c
RPS29	Human	Tumour suppression gene regulation	Lai, M.D. and Xu, J. (2007), 'Ribosomal proteins and colorectal cancer', Curr. Genomics Vol. 8, pp. 43-49.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474683
	Human	Increases tumour supporessor activity of Krev-1'	Naora, H. (1999), 'Involvement of ribosomal proteins in regulating cell growth and apoptosis: Translational modulation or recruitment for extraribosomal activity?', Immunol. Cell Biol. Vol. 77, pp. 197-205.	http://www.ncbi.nlm.nih.gov/pubmed/10361251
	Zebrafish	Mutations result in malignant peripheral nerve sheath tumour (zMPNST); RP genes may be 'haploinsufficient tumour suppressors' in zebrafish and cancer genes in humans	Amsterdam, A., Sadler, K.C., Lai, K., Farrington, S. et al. (2004), 'Many ribosomal protein genes are cancer genes in zebrafish', PLoS Biol. Vol. 2, p. E139.	http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=406397

Date last accessed for all websites is 17th June, 2010

Table S2

Function and regulation of eukaryotic large subunit ribosomal proteins

Protein Name	Organism	Function	Reference	Find online at
RPL4	Rat	Required for rapid neurite regeneration	Twiss, J.L., Smith, D.S., Chang, B. and Shooter, E.M. (2000), 'Translational control of ribosomal protein L4 mRNA is required for rapid neurite regeneration', Neurobiol. Dis. Vol. 7, pp. 416-428.	http://www.ncbi.nlm.nih.gov/pubmed/10964612
	S. cerevisiae	Binds to single-stranded RNA/DNA	Cusick, M.E. (1994), 'Purification and identification of two major single-stranded binding proteins of yeast Saccharomyces cerevisiae as ribosomal protein L4 and histone H2B', Biochim. Biophys. Acta. Vol. 1217, pp. 31-40.	http://www.ncbi.nlm.nih.gov/pubmed/8286414
RPL7A	Human	Part of chimeric protein encoded by trk-2h oncogene	Ziemiecki, A., Müller, R.G., Fu, X.C., Hynes, N.E. et al. (1990), 'Oncogenic activation of the human trk proto-oncogene by recombination with the ribosomal large subunit protein L7a', EMBO J. Vol. 9, pp. 191-196.	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC551645/
	Zebrafish	Categorised as an ocular gene; downregulated in eyeless masterblind zebrafish.	Wang, H., Kesinger, J.W., Zhou, Q., Wren, J.D. et al. (2008), 'Identification and characterization of zebrafish ocular formation genes', Genome Vol. 51, pp. 222-235.	http://www.ncbi.nlm.nih.gov/pubmed/18356958
RPL7	Human	Coregulator of vitamin D receptor-retinoid X receptor-mediated transactivation of genes	Berghöfer-Hochheimer, Y., Zurek, C., Wölfl, S., Hemmerich, P. et al. (1998), 'L7 protein is a coregulator of vitamin D receptor-retinoid X receptor-mediated transactivation', J. Cell. Biochem. Vol. 69, pp. 1-12.	http://www.ncbi.nlm.nih.gov/pubmed/9513041
	Rana sylvatica	Upregulated under freezing conditions	Wu, S., De Croos, J.N. and Storey, K.B. (2008), 'Cold acclimation-induced up-regulation of the ribosomal protein L7 gene in the freeze tolerant wood frog, Rana sylvatica', Gene Vol. 424, pp. 48-55.	http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-4T3DCV0-1&_user=4887109&_coverDate=11%2F15%2F2008&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1246451135&_rerunOrigin=google&_acct=C000062864&_version=1&_urlVersion=0&_userid=4887109&md5=4e11f74a6e6a29fe16aa172087195d0d
RPL10	Arabidopsis	A component of the NIK-mediated antiviral signaling	Rocha, C.S., Santos, A.A., Machado, J.P. and Fontes, E.P. (2008), 'The ribosomal protein L10/QM-like protein is a component of the NIK-mediated antiviral signaling', Virology Vol. 380, pp. 165-169.	http://www.ncbi.nlm.nih.gov/pubmed/18789471
RPL13	Hamster cells	Upregulated in response to DNA damage	Kobayashi, T., Sasaki, Y., Oshima, Y., Yamamoto, H. et al. (2006), 'Activation of the ribosomal protein L13 gene in human gastrointestinal cancer', Int. J. Mol. Med. Vol. 18, pp. 161-170.	http://www.ncbi.nlm.nih.gov/pubmed/16786168
RPL22	Mammals	Identical to heparin-binding protein, HBp15	Fujita, Y., Okamoto, T., Noshiro, M., McKeehan, W.L. et al. (1994), 'A novel heparin-binding protein, HBp15, is identified as mammalian ribosomal protein L22', Biochem. Biophys. Res. Commun. Vol. 199, pp. 706-713.	http://www.ncbi.nlm.nih.gov/pubmed/8135813
	Drosophila	Interacts with casein kinase II	Zhao, W., Bidwai, A.P. and Glover, C.V. (2002), 'Interaction of casein kinase II with ribosomal protein L22 of Drosophila melanogaster', Biochem. Biophys. Res. Commun. Vol. 298, pp. 60-66.	http://www.ncbi.nlm.nih.gov/pubmed/12379220
	Human	Binds Epstein-Barr virus (EBV)-encoded RNA (EBER) in EBV-infected cells	Le, S., Sternglanz, R. and Greider, C.W. (2000), 'Identification of two RNA-binding proteins associated with human telomerase RNA', Mol. Biol. Cell Vol. 11, pp. 999-1010.	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC14826/
	Human	Binds human telomerase RNA	Le, S., Sternglanz, R. and Greider, C.W. (2000), 'Identification of two RNA-binding proteins associated with human telomerase RNA', Mol. Biol. Cell Vol. 11, pp. 999-1010.	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC14826/
RPL23A	Human	May play a role in growth inhibition	Jiang, H., Lin, J.J., Tao, J. and Fisher, P.B. (1997), 'Suppression of human ribosomal protein L23A expression during cell growth inhibition by interferon-beta', Oncogene Vol. 14, pp. 473-480.	http://www.nature.com/onc/journal/v14/n4/abs/1200858a.html
RPL24	Arabidopsis	Gynoecium development	Nishimura, T., Wada, T. and Okada, K. (2004), 'A key factor of translation reinitiation, ribosomal protein L24, is involved in gynoecium development in Arabidopsis', Biochem. Soc. Trans. Vol. 32, pp. 611-613.	http://www.ncbi.nlm.nih.gov/pubmed/15270688?dopt=Abstract
	Marine shrimp	Differential expression in gonads	Zhang, Z., Wang, Y., Jiang, Y., Lin, P. et al. (2007), 'Ribosomal protein L24 is differentially expressed in ovary and testis of the marine shrimp Marsupenaeus japonicus', Comp. Biochem. Physiol. B Biochem. Mol. Biol. Vol. 147, pp. 466-474.	http://www.ncbi.nlm.nih.gov/pubmed/17462931
RPL35A	Human	Cell death inhibition	Lopez, C.D., Martinovsky, G. and Naumovski, L. (2002), 'Inhibition of cell death by ribosomal protein L35a', Cancer Lett. Vol. 180, pp. 195-202.	http://www.ncbi.nlm.nih.gov/pubmed/12175552
RPP0	Human	Interacts with GCIP, and over-expression in breast and liver cancer results in cell proliferation	Chang, T.W., Chen, C.C., Chen, K.Y., Su, J.H. et al. (2008), 'Ribosomal phosphoprotein P0 interacts with GCIP and overexpression of P0 is associated with cellular proliferation in breast and liver carcinoma cells', Oncogene Vol. 27, pp. 332-338.	http://www.ncbi.nlm.nih.gov/pubmed/17621266
RPLP1	Mouse	Over-expression leads to cell proliferation of mouse embryonic fibroblasts	Artero-Castro, A., Kondoh, H., Fernández-Marcos, P.J., Serrano, M. et al. (2009), 'Rplp1 bypasses replicative senescence and contributes to transformation', Exp. Cell Res. Vol. 315, pp. 1372-1383.	http://www.ncbi.nlm.nih.gov/pubmed/19233166
MRPL41	Human and mice	Suppresses cell growth	Yoo, Y.A., Kim, M.J., Park, J.K., Chung, Y.M. et al. (2005), 'Mitochondrial ribosomal protein L41 suppresses cell growth in association with p53 and p27Kip1', Mol. Cell. Biol. Vol. 25, pp. 6603-6616.	http://www.ncbi.nlm.nih.gov/pubmed/16024796

Date last accessed for all websites is 17th June, 2010

Extra-ribosomal properties of the ribosomal proteins

Ribosomal proteins and gene expression

Temporal regulation of gene expression is critical for cell survival and function. Chromatin modification, transcription, translation, RNA processing and post-translational modification are the major checkpoints for a cell to regulate gene expression. Many of the prokaryotic and eukaryotic ribosomal proteins are involved in the regulation of their own expression or expression of other genes at different levels of gene regulation (Table 1).

Table 1

Ribosomal proteins involved in gene regulation mechanisms

Gene regulation level	Ribosomal protein (RP)	Organism	Function	Reference
Chromatin	S2	Escherichia coli	Negative regulator of rpsB and tsf expression	4
	S3	Homo sapiens	Becomes a part of nuclear factor-κB complex that interacts with specific sites in the genome, on tumour necrosis factor stimulation	6
	S4	Bacillus subtilis	Autoregulates rpsD gene expression	5
	L13a	H. sapiens	Inflammatory gene expression	7
Transcription	S1	E. coli	Transcription anti-termination and stimulates transcriptional activity of RNA polymerase	8,9
	S4	E. coli	Transcription anti-termination	10
	S10	E. coli	Transcription anti-termination	11
	L3	E. coli	Transcription anti-termination	10
	L4	E. coli	Inhibits transcription of S10 operon mRNA and transcription anti-termination	3,10
	S14	H. sapiens	Self-regulation at both transcriptional and translational levels	3,12
	S20	Saccharomyces cerevisiae	Transcription anti-termination	3
	S0 and S21 (in association with each other)	S. cerevisiae	Promote maturation of 3' end of 18S rRNA	13
	L11	Rattus rattus	Inhibits the transcriptional activity of peroxisome proliferator-activated receptor-alpha, a nuclear receptor	14
	L13	E. coli	Transcription anti-termination	10
Post-transcription	S14	S. cerevisiae	Post-transcriptional repression of RPS14B [CRY2] expression	15
RNA processing and splicing	S12	E. coli	Acts as RNA chaperone in the folding process of T4 phage intron RNA	16
	S12	H. sapiens	RNA splicing and modification	12
	S13	S. cerevisiae and H. sapiens	Binds to the first intron of its transcript to inhibit splicing.Overproduction of RPS13 interferes with splicing of its own pre-mRNA by a feedback mechanism.Negatively controls splicing of its own pre-mRNA	17,18
	S14	H. sapiens	Required for 18S pre-RNA processing and 40S subunit formation	19
	L4	Mus musculus	Interacts with Gu(alpha) which is involved in rRNA processing	20
Translation	S4	E. coli	Translational repressor of α operon (operon genes; S13, S11, S4, L17)	21
	S8	E. coli	Translational repressor of spc operon	22
	S15	E. coli	Self-translation regulation	23
	L1	E. coli	Self-translation regulation	12
	L4	E. coli	Suppresses translation of S10 operon mRNA.Self-translation regulation	3,12
	L10	E. coli	Self-translation regulation	12
	S26	H. sapiens	Self-translation regulation	12
	S30	S. cerevisiae	Self-translation regulation	12
	L13a	H. sapiens	Silence translation of ceruloplasmin (Cp) mRNA	24
Post-translation	S20	E. coli	Post-translational inhibition of ornithine and arginine decarboxylase enzymes	25

Ribosomal proteins and nucleic acid replication

During viral infection, viruses recruit some of the host machinery in order to produce new viral particles. The synthesis of new viral particles requires the replication of the viral genome, and in most of the DNA viruses the duplication of their genome is carried out by the host replication system. Ribosomal proteins are shown to take part in the genome replication in both DNA and RNA viruses. The ribosomal protein L14 helps Rep helicase to unwind the DNA during replication of the bacteriophage genome[12], and S1 is a subunit of Qβ replicase that replicates the genome of RNA coliphage Qβ [3]. In yeast, L3 helps in replication or maintenance of the double-stranded RNA genome [26].

Ribosomal proteins and DNA repair

Any damage to DNA disrupts the genome's integrity and thus proves fatal to the cell. The causes of such DNA damage are either metabolic processes within the cell or environmental factors like radiation/mutagens. Several DNA repair mechanisms exist within the cell to correct DNA damage. The type of mechanism employed is determined, in turn, by the type of damage. Ribosomal proteins are shown to function in DNA repair mechanisms in both prokaryotes and eukaryotes (Table 2).

Table 2

Ribosomal proteins in DNA repair mechanisms

Ribosomal protein	Organism	Function	Reference
S9	E. coli	Involved in SOS repair mechanism by participating with polymerase UmuC	3
S3	Drosophila spp.	DNA repair endonuclease. Corrects damage resulting from oxidative and ionising radiation	27
	H. sapiens	Knockdown of S3 protects human cells from genotoxic stress.This is the converse of the situation in Drosophila S3	28
P0/LP0 (constituent of ribosomal stalk structure)	Drosophila, H. sapiens	Apurinic/apyrimidinic endonuclease activity	29

Regulation of ribosomal proteins

Ribosomal proteins and the cell cycle

The cell undergoes different phases of growth and division during the cell cycle. The progression of a cell through these phases is controlled by cyclin/cyclin-dependent kinases (Cdk) and regulatory molecules of cell cycle checkpoints. Ribosomal proteins have been shown to alter the cell cycle fate by interacting with these molecules as an extra-ribosomal function. Human L34 inhibits the cell cycling proteins Cdk4 and Cdk5 [30]. L26 binds to the 5' untranslated region (UTR) of p53 mRNA upon DNA damage and increases translation of p53, a key player in cell cycle regulation and apoptosis [31].

Many of the other ribosomal proteins function to control the cell cycle and apoptosis through their expression levels. Abnormal expression levels of L7[32] and L13a[33] in humans interfere with cell cycle progression by arresting the cell cycle and inducing apoptosis. The involvement of ribosomal proteins in apoptosis is further evidenced by their interaction with Mdm2, a ubiquitin ligase that keeps a check on P53 levels under normal cellular conditions. The mammalian ribosomal protein L26 interacts with Mdm2 and thus regulates p53 levels [34]. Many more eukaryotic ribosomal proteins (S7, S19, S20, S27L, L5, L22 and L23) function in p53-mediated apoptosis [35-38]. In humans, the ribosomal protein S3 is shown to induce caspase-dependent apoptosis [12]. Also, some of the ribosomal proteins involved in apoptosis are over-expressed in cancers (Table 3).

Table 3

Expression pattern of ribosomal proteins in cancers

Ribosomal protein	Expression pattern	Cancer type	Reference
S2	Over-expressed	Prostate cancer, head and neck carcinomas	39,40
S3, S6, S8, S12	Over-expressed	Colon cancer	40
S3A, S4, S17	Over-expressed	Feline leukaemia virus-induced lymphomas	40
S11	Over-expressed	Colorectal cancer	41
L7A	Over-expressed	Colorectal cancer	42
	Under-expressed	Osteosarcoma	43
L13	Over-expressed	Gastrointestinal cancer	44
L15	Over-expressed	Oesophageal cancer	45
	Over-expressed	Gastric cancer	46
L19	Over-expressed	Human breast cancer Used as marker for human prostate cancer	47,48
L23A, L27, L30	Over-expressed	Hepatocellular carcinoma	49
L30	Over-expressed	Medulloblastoma	50

Ribosomal proteins and disease

Any defects in ribosomal proteins affect the synthesis of proteins that are required by a cell for carrying out vital cellular functions. Apart from protein synthesis, some of the ribosomal proteins are implicated in disease conditions owing to abnormal expression levels or expression of mutated genes. A mutation in ribosomal protein S19 was initially characterised as the cause of Diamond-Blackfan anaemia (DBA), a congenital erythroid aplasia [51]. Subsequently, ribosomal proteins S17, S15, S24, S7, L5 and L11 were also found to be involved in DBA [52]. It also has been shown that ribosomal proteins S3A (mouse) and S19 (zebrafish) function in erythropoiesis [18,53]. The function of these ribosomal proteins in erythropoiesis and DBA might give some clues as to how defects in the ribosomal proteins lead to the low red blood cell count in DBA patients.

In some disease conditions, the expression levels of the ribosomal proteins play an important role, as in Turner syndrome and human cataracts. Turner syndrome has been linked to a deficiency in human ribosomal proteins 4X and 4Y (isoforms of rps4)[54], and expression of L7A, L15 and L21 is downregulated in human cataracts [55]. A similar syndrome, named Noonan's syndrome, has been linked to ribosomal protein gene rpl6. This gene was found to be located in the same chromosome locus as Noonan's syndrome [56]. Other ribosomal proteins, such as S14, L24 and S26, are associated with 5q syndrome, mouse Bst and diabetes, respectively [19,57,58].

Ribosomal proteins and developmental regulation

During the development of an organism, the cells undergo growth and differentiation to give rise to tissues and organs. These processes are regulated by spatial and temporal control of gene expression. The ribosomal proteins that are involved in protein synthesis are also found to regulate development in many species. In Arabidopsis, some of the ribosomal protein genes are termed embryo defective, as mutated forms of these genes are lethal to embryo development [59]. A similar study in zebrafish has shown that ribosomal protein L11 affects embryological development in this species [60]. In animals, ribosomal proteins are involved in processes such as oogenesis and gonad development. The ribosomal protein S2 in Drosophila melanogaster and S15A in sea urchins play a role in oogenesis, while S4 in human is involved in gonad development [3]. Developmental defects in genes such as Drosophila minutes, mouse Bst (belly spot and tail), which encodes rpL24, and Dsk (dark skin mutants), which encodes rpS19, are also the result of defective ribosomal proteins. Organisms with these conditions exhibit various growth defects and have reduced adult size.

Since protein synthesis is the essential process that needs to be regulated during development, expression levels of ribosomal proteins are also regulated during the different developmental stages (Figure 1). Any change in this expression profile thus affects the protein machinery that is necessary for the normal development of an organism.

Figure 1

(. (b) rp///transcription profile during zebrafish development. See the Array Express Archive from the European Bioinformatics Institute: http://www.ebi.ac.uk/;http://www.ebi.ac.uk/microarray-as/ae/(accessed 23rd March, 2010).

Ribosomal proteins and lifespan regulation

Many recent studies have come up with different mechanisms by which an organism regulates its life span. The insulin/insulin-like growth factor 1 signalling (IIS) pathway and caloric restriction (CR) has been the major players of lifespan regulation in many species [61]. In the insulin signalling pathway, the components of this pathway, such as abnormal DAuer Formation (DAF)-2 or the downstream factor DAF-16, regulate the expression of various genes involved in metabolism, the stress response and other processes that shorten life span [61,62]. In CR, the life span of an organism is increased by decreasing the caloric intake. There is not much evidence of the mechanism by which CR affects the life span but some genes have been identified in Caenorhabditis elegans that influence life span regulation through CR [61]. It is further observed that the genes involved in CR mechanism are also linked to the IIS pathway [63,64]. Another player of longevity is the nutrient-responsive pathway mammalian target of rapamycin (mTOR) [65]. Both IIS and mTOR have a common downstream factor, ribosomal protein S6 kinase 1, which functions in regulating the mammalian life span [66]. Thus, these different pathways interact with each other to regulate longevity.

Also, many of the genes essential for growth and development are shown to extend the life span of a wide range of organisms. Among these genes are those involved in protein synthesis. The inactivation of translation initiation factors and ribosomal proteins S3, S8 and S11 was observed to increase the mean life span in Caenorhabditis elegans [61]. This indicates that the cell conserves its energy by keeping a check on protein synthesis.

Clearly, ribosomal proteins have additional functions outside the ribosome which are also regulated. One would expect that this would not be the case for such 'housekeeping' factors (indeed, several ribosomal protein genes are used as controls to normalise for gene regulation). Why does such regulation exist, and is it important? One answer could be that differential regulation might slow or speed up the process of protein synthesis. In the case of life span extension, it seems that downregulation of protein synthesis is involved. Another interesting aspect is how these extra-ribosomal functions have evolved; one possibility is via gene duplication, something that has been suggested for plant development and also in yeast [38,59]. These properties provide an important evolutionary paradigm in which nature uses existing genes for diversification.

Table S3

Function and regulation of prokaryotic small subunit ribosomal proteins

Protein Name	Organism	Function	Reference	Find online at
RPS1	E. coli	Stimulates the T4 endo-ribonuclease Reg B	Aliprandi et al., S1 Ribosomal Protein Functions in Translation Initiation and Ribonuclease RegB Activation are mediated by similar RNA-Protein Interactions. (2008). The Journal of Biological Chemistry 283(19):13289-13301.	http://www.ncbi.nlm.nih.gov/pubmed/18211890
		Poly (A) binding protein in E. coli	Kalapos MP, Paulus H, Sarkar N. (1997). Identification of ribosomal protein S1 as a poly(A) binding protein in Escherichia coli. Biochimie 79(8):493-502.	http://www.ncbi.nlm.nih.gov/pubmed/9451450
		Interact with non-coding RNA DsrA and with rpoS mRNA and has a small role in altering the structures of these RNAs	Rositsa I. Koleva, Christina A. Austin, Jeffrey M. Kowaleski, Daniel S. Neems, Leyi Wang, Calvin P.H. Vary, Paula Jean Schlax. (2006). Interactions of ribosomal protein S1 with DsrA and rpoS mRNA. Biochemical and Biophysical Research Communications 348: 662-668.	http://www.ncbi.nlm.nih.gov/pubmed/16890206
		Binds to tmRNA, which tags truncated/trans-translated proteins for degradation	Matthieu Saguy, Reynald Gillet, Patricia Skorski, Sylvie Hermann-Le Denmat and Brice Felden. (2007). Ribosomal protein S1 influences trans-translation in vitro and in vivo. Nucleic Acids Research 35(7): 2368-2376.	http://nar.oxfordjournals.org/cgi/content/abstract/gkm100v1
		Over expression results in protection of mRNA degradation by PNPase	Briani et al.; (2008). Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli. RNA 4(11):2417-2429.	http://rnajournal.cshlp.org/content/14/11/2417.abstract
RPS3	E. coli	Identical to H-protein in E. coli (Binds DNA and is associated with E. coli nucleoid)	Robert C.Bruckner and Michael M.Cox. (1989). The histone-like H protein of Escherichia coli is ribosomal protein S3. Nucleic Acids Research 17(8).	http://nar.oxfordjournals.org/cgi/content/abstract/17/8/3145
RPS4	E. coli	Overproduction of S4 stimulate rRNA synthesis	Takabe, Y., Miura, A., Bedwell, D., Tam, M. and Nomura, M. (1985). Increased expression of ribosomal genes during inhibition of ribosome assembly in Escherichia coli. Journal of Molecular Biology 184: 23-30.	http://www.ncbi.nlm.nih.gov/pubmed/3897554
RPS6	Myxococcus xanthus	Heat inducible protein	Maria De Angelis, Raffaella Di Cagno, Claude Huet, Carmine Crecchio, Patrick F. Fox, and Marco Gobbetti. (2004). Heat Shock Response in Lactobacillus plantarum. Applied and Environmental Microbiology 70 (3): 1336-1346.	http://aem.asm.org/cgi/content/abstract/70/3/1336
RPS16	E. coli	Acts as an endonuclease	Jacques Oberto, Eliette Elisabeth Mouray, Olivier Pellegrini, P. Mikael Wikstrom and Josette Rouviere-Yaniv. (1996). The Escherichia coli ribosomal protein S16 is an Endonuclease. Molecular Microbiology 19(6): 1319-1330.	http://www3.interscience. wiley.com/journal/119219619/abstract

Table S4

Function and regulation of prokaryotic large subunit ribosomal proteins

Protein Name	Organism	Function	Reference	Find online at
RPL2	E. coli	Zinc-binding protein	Katayama A, Tsujii A, Wada A, Nishino T, Ishihama A. Systematic search for zinc-binding proteins in Escherichia coli Eur. J. Biochem. 269(9):2403-2413.	http://www.ncbi.nlm.nih.gov/pubmed/11985624?ordinalpos=2&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel. Pubmed_DefaultReportPanel.Pubmed_RVDocSum
RPL4	E. coli	Allosterically regulates RNase E-dependent RNA degradation 'inhibiting RNase E-specific cleavage in vitro, stabilising mRNAs targeted by RNase E in vivo, and controlling plasmid DNA replication by stabilizing an antisense regulatory RNA normally attacked by RNase E' also upregulated in stress, which accompanies inactivation of RNase E and increased half-life of stress-responsive transcripts	Singh D, Chang SJ, Lin PH, Averina OV, Kaberdin VR, Lin-Chao S. (2009), Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proc. Natl. Acad. Sci. USA. 106(3):864-869. Epub 2009 Jan 14.	http://www.ncbi.nlm.nih.gov/pubmed/19144914?ordinalpos=1&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel. Pubmed_DefaultReportPanel.Pubmed_RVDocSum
RPL11	E. coli	Involved in regulating the activity of (p)ppGpp synthetase I	Yang X, Ishiguro EE. (2001), Involvement of the N terminus of ribosomal protein L11 in regulation of the RelA protein of Escherichia coli. J. Bacteriol. 183(22):6532-6537.	http://www.ncbi.nlm.nih.gov/pubmed/11673421?ordinalpos=7&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel. Pubmed_DefaultReportPanel.Pubmed_RVDocSum
RPL13	E. coli	Zinc binding protein	Katayama A, Tsujii A, Wada A, Nishino T, Ishihama A. Systematic search for zinc-binding proteins in Escherichia coli. Eur. J. Biochem. 269(9):2403-2413.	http://www.ncbi.nlm.nih.gov/pubmed/11985624?ordinalpos=2&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel. Pubmed_DefaultReportPanel.Pubmed_RVDocSum
RPL25	E. coli/Bacillus subtilis	General stress protein Ctc: might be required for accurate translation under stress conditions	Schmalisch M, Langbein I, Stülke J. (2002), The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4(5):495-501.	http://www.ncbi.nlm.nih.gov/pubmed/12432960?ordinalpos=1&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel. Pubmed_DiscoveryPanel. Pubmed_Discovery_RA&linkpos=2& log$=relatedarticles&logdbfrom=pubmed