RegulonDB

Gene
Name:	rpsO
Synonym(s):	ECK3154, EG10914, b3165, secC
Genome position(nucleotides):	3311415 <-- 3311684
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.85
External database links:

ASAP:	ABE-0010401
CGSC:	217
ECHOBASE:	EB0907
ECOLIHUB:	rpsO
OU-MICROARRAY:	b3165
STRING:	511145.b3165
COLOMBOS:	rpsO

Product

Name:

30S ribosomal subunit protein S15

Synonym(s):

RpsO, SecC

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol,ribosome

Molecular weight:

10.269

Isoelectric point:

11.052

Motif(s):

Type	Positions	Sequence	Comment
	1 -> 1	M
	2 -> 89	SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR	UniProt: 30S ribosomal protein S15.
	9 -> 88	AKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLR

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
		2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
		6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0005840 - ribosome GO:0022627 - cytosolic small ribosomal subunit
	molecular_function	GO:0003735 - structural constituent of ribosome GO:0003723 - RNA binding GO:0019843 - rRNA binding GO:0070181 - small ribosomal subunit rRNA binding GO:1903231 - mRNA binding translation repressor activity
	biological_process	GO:0006412 - translation GO:0006417 - regulation of translation GO:0016441 - posttranscriptional gene silencing GO:0000028 - ribosomal small subunit assembly GO:0002181 - cytoplasmic translation

Note(s):

Note(s): ...[more].

Reference(s):

[1] Abdurashidova GG., et al., 1985
[2] Abdurashidova GG., et al., 1985
[3] Adilakshmi T., et al., 2008
[4] Babkina GT., et al., 1984
[5] Babkina GT., et al., 1985
[6] Babkina GT., et al., 1986
[7] Bernabeu C., et al., 1979
[8] Brewer LA., et al., 1983
[9] Broude NE., et al., 1985
[10] Budker VG., et al., 1980
[11] Burton B., et al., 2012
[12] Champney WS. 1980
[13] Culver GM., et al., 1999
[14] Duval M., et al., 2013
[15] Dzionara M., et al., 1977
[16] Gimautdinova OI., et al., 1981
[17] Giri L., et al., 1978
[18] Gogia ZV., et al., 1979
[19] Gooch BD., et al., 2005
[20] Gorelic L. 1976
[21] Held WA., et al., 1973
[22] Isono K., et al., 1976
[23] Kakegawa T., et al., 1986
[24] Katayama A., et al., 2002
[25] Klostermeier D., et al., 2004
[26] Knopf UC., et al., 1975
[27] Lelong JC., et al., 1974
[28] Littlechild J., et al., 1987
[29] Lux B., et al., 1977
[30] Mandiyan V., et al., 1989
[31] Mizushima S., et al., 1970
[32] Morinaga T., et al., 1976
[33] Mueller F., et al., 1997
[34] Mulder AM., et al., 2010
[35] Muller R., et al., 1979
[36] Osterberg R., et al., 1978
[37] Plumbridge JA., et al., 1983
[38] Portier C. 1982
[39] Portier C., et al., 1984
[40] Ramakrishnan V., et al., 1984
[41] Ramakrishnan VR., et al., 1981
[42] Rinke J., et al., 1977
[43] Sands JF., et al., 1988
[44] Schendel PL., et al., 1976
[45] Schuwirth BS., et al., 2005
[46] Serdiuk IN., et al., 1984
[47] Spirin AS., et al., 1996
[48] Spirin AS., et al., 1979
[49] Spirin AS., et al., 1979
[50] Spitnik-Elson P., et al., 1979
[51] Spitnik-Elson P., et al., 1982
[52] Stoffler-Meilicke M., et al., 1987
[53] Takata R. 1978
[54] Takata R., et al., 1982
[55] Takata R., et al., 1976
[56] Takata R., et al., 1984
[57] Thurlow DL., et al., 1978
[58] Vasiliev VD., et al., 1977
[59] Walles-Granberg A., et al., 2001
[60] Wittmann-Liebold B. 1973
[61] Ying BW., et al., 2003
[62] Zhang W., et al., 2009
[63] Zhao Q., et al., 2004
[64] Zimmermann RA., et al., 1979
[65] Zwieb C. 1992

External database links:

ALPHAFOLD:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

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REFSEQ:

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SMR:

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UNIPROT:

Operon

Name:

metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp

Operon arrangement:

Transcription unit	Promoter
pnp	pnpp
rpsO	rpsOp
rpsO-pnp	rpsOp
infB	infBp
nusA-infB	nusAp
rimP-nusA-infB	rimPp
metY	metYp1
metY-yhbC-nusA-infB	metYp1
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp	metYp1
metY	metYp2
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp	metYp2

Transcriptional Regulation
	Display Regulation
Activated by:	Fis
Repressed by:	CRP, ArgR

RNA cis-regulatory element

Cis-reg; leader	Ribosomal S15 leader

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_3451	3311249	reverse	nd	[RS-EPT-CBR]	[66]
promoter	TSS_3453	3312149	reverse	nd	[RS-EPT-CBR]	[66]
promoter	TSS_3454	3312155	reverse	nd	[RS-EPT-CBR]	[66]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Abdurashidova GG., Nargizian MG., Rudenko NV., Turchinskii MF., Budovskii EI., 1985, [Contacts of ribosomal proteins with tRNAPhe and 16S RNA in analogs of the 30S initiation complex]., Mol Biol (Mosk) 19(2):553-7
[2] Abdurashidova GG., Tsvetkova EA., Chernyi AA., Kaminir LB., Budowsky EI., 1985, Intersubunit RNA-protein contacts in pre- and post-translocated E. coli ribosome., FEBS Lett 185(2):291-4
[3] Adilakshmi T., Bellur DL., Woodson SA., 2008, Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly., Nature 455(7217):1268-72
[4] Babkina GT., Karpova GG., Matasova NB., 1984, [Affinity modification of Escherichia coli ribosomes near the acceptor tRNA-binding site]., Mol Biol (Mosk) 18(5):1287-96
[5] Babkina GT., Karpova GG., Matasova NB., Berzin' VM., Gren EIa., 1985, [Study of the mRNA-binding region of ribosomes at different steps of translation. II. Affinity modification of Escherichia coli ribosomes by benzylidene derivative of AUGU6 in the 70S initiation complex]., Mol Biol (Mosk) 19(4):1079-85
[6] Babkina GT., Veniaminova AG., Vladimirov SN., Karpova GG., Yamkovoy VI., Berzin VA., Gren EJ., Cielens IE., 1986, Affinity labelling of Escherichia coli ribosomes with a benzylidene derivative of AUGU6 within initiation and pretranslocational complexes., FEBS Lett 202(2):340-4
[7] Bernabeu C., Vazquez D., Conde FP., 1979, Comparative study between prokaryotes and eukaryotes by chemical iodination of ribosomal proteins., Biochim Biophys Acta 577(2):400-9
[8] Brewer LA., Noller HF., 1983, Ribonucleic acid-protein cross-linking within the intact Escherichia coli ribosome, utilizing ethylene glycol bis[3-(2-ketobutyraldehyde) ether], a reversible, bifunctional reagent: identification of 30S proteins., Biochemistry 22(18):4310-5
[9] Broude NE., Medvedeva NI., Kusova KS., Budovskii EI., 1985, [Ribosomal proteins directly interacting with fMet-tRNAfMet in the 30S initiation complex]., Mol Biol (Mosk) 19(5):1269-72
[10] Budker VG., Kobets ND., Kollektsionok IE., Karpova GG., Grineva NI., 1980, [Affinity labeling of ribosomes from Escherichia coli with 4-(N-2-chloroethyl, N-methylamino)-benzaldehyde actyl derivatives of oligouridylates]., Mol Biol (Mosk) 14(3):507-16
[11] Burton B., Zimmermann MT., Jernigan RL., Wang Y., 2012, A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly., PLoS Comput Biol 8(5):e1002530
[12] Champney WS., 1980, Protein synthesis defects in temperature-sensitive mutants of Escherichia coli with altered ribosomal proteins., Biochim Biophys Acta 609(3):464-74
[13] Culver GM., Noller HF., 1999, Efficient reconstitution of functional Escherichia coli 30S ribosomal subunits from a complete set of recombinant small subunit ribosomal proteins., RNA 5(6):832-43
[14] Duval M., Korepanov A., Fuchsbauer O., Fechter P., Haller A., Fabbretti A., Choulier L., Micura R., Klaholz BP., Romby P., Springer M., Marzi S., 2013, Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation., PLoS Biol 11(12):e1001731
[15] Dzionara M., Robinson SM., Wittmann-Liebold B., 1977, Secondary structures of proteins from the 30S subunit of the Escherichia coli ribosome., Hoppe Seylers Z Physiol Chem 358(8):1003-19
[16] Gimautdinova OI., Karpova GG., Knorre DG., Kobetz ND., 1981, The proteins of the messenger RNA binding site of Escherichia coli ribosomes., Nucleic Acids Res 9(14):3465-81
[17] Giri L., Franz A., 1978, The shape of proteins S15 and S18 from the small subunit of the Escherichia coli ribosome., FEBS Lett 87(1):31-6
[18] Gogia ZV., Venyaminov SY., Bushuev VN., Serdyuk IN., Lim VI., Spirin AS., 1979, Compact globular structure of protein S15 from Escherichia coli ribosomes., FEBS Lett 105(1):63-9
[19] Gooch BD., Krishnamurthy M., Shadid M., Beal PA., 2005, Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex., Chembiochem 6(12):2247-54
[20] Gorelic L., 1976, Photoinduced cross-linkage, in situ, of Escherichia coli 30S ribosomal proteins to 16S rRNA: identification of cross-linked proteins and relationships between reactivity and ribosome structure., Biochemistry 15(16):3579-90
[21] Held WA., Mizushima S., Nomura M., 1973, Reconstitution of Escherichia coli 30 S ribosomal subunits from purified molecular components., J Biol Chem 248(16):5720-30
[22] Isono K., Krauss J., Hirota Y., 1976, Isolation and characterization of temperature-sensitive mutants of Escherichia coli with altered ribosomal proteins., Mol Gen Genet 149(3):297-302
[23] Kakegawa T., Sato E., Hirose S., Igarashi K., 1986, Polyamine binding sites on Escherichia coli ribosomes., Arch Biochem Biophys 251(2):413-20
[24] Katayama A., Tsujii A., Wada A., Nishino T., Ishihama A., 2002, Systematic search for zinc-binding proteins in Escherichia coli., Eur J Biochem 269(9):2403-13
[25] Klostermeier D., Sears P., Wong CH., Millar DP., Williamson JR., 2004, A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly., Nucleic Acids Res 32(9):2707-15
[26] Knopf UC., Sommer A., Kenny J., Traut RR., 1975, A new two-dimensional gel electrophoresis system for the analysis of complex protein mixtures: application to the ribosome of E. coli., Mol Biol Rep 2(1):35-40
[27] Lelong JC., Gros D., Gros F., Bollen A., Maschler R., Stoffler G., 1974, Function of individual 30S subunit proteins of Escherichia coli. Effect of specific immunoglobulin fragments (Fab) on activities of ribosomal decoding sites., Proc Natl Acad Sci U S A 71(2):248-52
[28] Littlechild J., Malcolm A., Paterakis K., Ackermann I., Dijk J., 1987, The tertiary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by proton magnetic resonance spectroscopy and limited proteolysis experiments., Biochim Biophys Acta 913(2):245-55
[29] Lux B., Gerard D., Laustriat G., 1977, Tyrosine fluorescence of S8 and S15 Escherichia coli ribosomal proteins., FEBS Lett 80(1):66-70
[30] Mandiyan V., Tumminia S., Wall JS., Hainfeld JF., Boublik M., 1989, Protein-induced conformational changes in 16 S ribosomal RNA during the initial assembly steps of the Escherichia coli 30 S ribosomal subunit., J Mol Biol 210(2):323-36
[31] Mizushima S., Nomura M., 1970, Assembly mapping of 30S ribosomal proteins from E. coli., Nature 226(5252):1214
[32] Morinaga T., Funatsu G., Funatsu M., Wittman HG., 1976, Primary structure of the 16S rRNA binding protein S15 from Escherichia coli ribosomes., FEBS Lett 64(2):307-9
[33] Mueller F., Brimacombe R., 1997, A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. II. The RNA-protein interaction data., J Mol Biol 271(4):545-65
[34] Mulder AM., Yoshioka C., Beck AH., Bunner AE., Milligan RA., Potter CS., Carragher B., Williamson JR., 2010, Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit., Science 330(6004):673-7
[35] Muller R., Garrett RA., Noller HF., 1979, The structure of the RNA binding site of ribosomal proteins S8 and S15., J Biol Chem 254(10):3873-8
[36] Osterberg R., Sjoberg B., 1978, Small-angle X-ray scattering study of the proteins S1, S8, S15, S16, S20 from Escherichia coli ribosomes., FEBS Lett 93(1):115-9
[37] Plumbridge JA., Springer M., 1983, Organization of the Escherichia coli chromosome around the genes for translation initiation factor IF2 (infB) and a transcription termination factor (nusA)., J Mol Biol 167(2):227-43
[38] Portier C., 1982, Physical localisation and direction of transcription of the structural gene for Escherichia coli ribosomal protein S15., Gene 18(3):261-6
[39] Portier C., Regnier P., 1984, Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions., Nucleic Acids Res 12(15):6091-102
[40] Ramakrishnan V., Capel M., Kjeldgaard M., Engelman DM., Moore PB., 1984, Positions of proteins S14, S18 and S20 in the 30 S ribosomal subunit of Escherichia coli., J Mol Biol 174(2):265-84
[41] Ramakrishnan VR., Yabuki S., Sillers IY., Schindler DG., Engelman DM., Moore PB., 1981, Positions of proteins S6, S11 and S15 in the 30 S ribosomal subunit of Escherichia coli., J Mol Biol 153(3):739-60
[42] Rinke J., Ross A., Brimacombe R., 1977, Characterisation of RNA fragments obtained by mild nuclease digestion of 30-S ribosomal subunits from Escherichia coli., Eur J Biochem 76(1):189-96
[43] Sands JF., Regnier P., Cummings HS., Grunberg-Manago M., Hershey JW., 1988, The existence of two genes between infB and rpsO in the Escherichia coli genome: DNA sequencing and S1 nuclease mapping., Nucleic Acids Res 16(22):10803-16
[44] Schendel PL., Craven GR., 1976, Studies on the ability of partially iodinated 16S RNA to participate in 30S ribosome assembly., Nucleic Acids Res 3(11):3001-14
[45] Schuwirth BS., Borovinskaya MA., Hau CW., Zhang W., Vila-Sanjurjo A., Holton JM., Cate JH., 2005, Structures of the bacterial ribosome at 3.5 A resolution., Science 310(5749):827-34
[46] Serdiuk IN., Agalarov SCh., Gongadze GM., Gudkov AT., Sedel'nikova SE., 1984, [Structure and density of ribosomal RNA and its complexes with proteins in a solution]., Mol Biol (Mosk) 18(1):244-61
[47] Spirin AS., Agafonov DE., Kolb VA., Kommer A., 1996, [Topography of ribosomal proteins: reconsideration of of protein map of small ribosomal subunit]., Biokhimiia 61(11):1928-30
[48] Spirin AS., Serdiuk IN., Shpungin IL., Vasil'ev VD., 1979, [Quaternary structure of the ribosomal 30S subparticle: the model and its experimental verification]., Mol Biol (Mosk) 13(6):1384-96
[49] Spirin AS., Serdyuk IN., Shpungin JL., Vasiliev VD., 1979, Quaternary structure of the ribosomal 30S subunit: model and its experimental testing., Proc Natl Acad Sci U S A 76(10):4867-71
[50] Spitnik-Elson P., Elson D., Abramowitz R., 1979, A purified nucleoprotein fragment of the 30 S ribosomal subunit of Escherichia coli., Biochim Biophys Acta 561(2):435-44
[51] Spitnik-Elson P., Elson D., Avital S., Abramowitz R., 1982, A ribonucleoprotein fragment of the 30 S ribosome of E. coli containing two contiguous domains of the 16 S RNA., Nucleic Acids Res 10(15):4483-92
[52] Stoffler-Meilicke M., Stoffler G., 1987, The topography of ribosomal proteins on the surface of the 30S subunit of Escherichia coli., Biochimie 69(10):1049-64
[53] Takata R., 1978, Genetic studies of the ribosomal proteins in Escherichia coli. XI. Mapping of the genes for L21, L27, S15 and S21 by using hybrid bacteria and over-production of these proteins in the merodiploid strains., Mol Gen Genet 160(2):151-5
[54] Takata R., Aoyagi M., Mukai T., 1982, Cloning of rpsO, the gene for ribosomal protein S15 of Escherichia coli., Mol Gen Genet 188(2):334-7
[55] Takata R., Kobata K., 1976, Genetic studies of the ribosomal proteins in Escherichia coli. X. Mapping of the ribosomal proteins, L21 and S15, by intergeneric mating experiments between Serratia marcescens and Escherichia coli K12., Mol Gen Genet 149(2):159-65
[56] Takata R., Mukai T., Aoyagi M., Hori K., 1984, Nucleotide sequence of the gene for Escherichia coli ribosomal protein S15 (rpsO)., Mol Gen Genet 197(2):225-9
[57] Thurlow DL., Zimmermann RA., 1978, Conservation of ribosomal protein binding sites in prokaryotic 16S RNAs., Proc Natl Acad Sci U S A 75(6):2859-63
[58] Vasiliev VD., Koteliansky VE., Rezapkin GV., 1977, The complex of 16 S RNA with proteins S4, S7, S8, S15 retains the main morphological features of the 30 S ribosomal subparticle., FEBS Lett 79(1):170-4
[59] Walles-Granberg A., Schnell R., Isaksson LA., Ryden-Aulin M., 2001, Ribosomes with large synthetic N-terminal extensions of protein S15 are active in vivo., Biochim Biophys Acta 1544(1-2):378-85
[60] Wittmann-Liebold B., 1973, Studies on the primary structure of 20 proteins from Escherichia coli ribosomes by means of an improved protein sequenator., FEBS Lett 36(3):247-9
[61] Ying BW., Suzuki T., Shimizu Y., Ueda T., 2003, A novel screening system for self-mRNA targeting proteins., J Biochem 133(4):485-91
[62] Zhang W., Dunkle JA., Cate JH., 2009, Structures of the ribosome in intermediate states of ratcheting., Science 325(5943):1014-7
[63] Zhao Q., Ofverstedt LG., Skoglund U., Isaksson LA., 2004, Morphological variation of individual Escherichia coli 30S ribosomal subunits in vitro and in situ, as revealed by cryo-electron tomography., Exp Cell Res 297(2):495-507
[64] Zimmermann RA., Singh-Bergmann K., 1979, Binding sites for ribosomal proteins S8 and S15 in the 16 S RNA of Escherichia coli., Biochim Biophys Acta 563(2):422-31
[65] Zwieb C., 1992, Conformity of RNAs that interact with tetranucleotide loop binding proteins., Nucleic Acids Res 20(17):4397-400
[66] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.