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Escherichia coli K-12 substr. MG1655 Polypeptide: 30S ribosomal subunit protein S13



Gene: rpsM Accession Numbers: EG10912 (EcoCyc), b3298, ECK3285

Regulation Summary Diagram: ?

Component of:
30S ribosomal subunit (summary available)
ribosome (summary available)

Summary:
The S13 protein is a component of the 30S subunit of the ribosome, playing a key role in subunit association and the fidelity of translocation. The crystal structure of the ribosome [Schuwirth05], cryo-EM reconstructions [Gao03], and crosslinking experiments [Lambert81] show that the S13 protein contacts the L5 protein of the large subunit of the ribosome.

S13 is thought to be involved in maintenance of pre-translocation state [Cukras03, Cukras05]. In vitro, a small subunit of the ribosome lacking S13 associates only poorly with the large subunit; the presence of tRNA and mRNA in the assay restores 70S complex formation [Cukras05]. In the absence of S13, initiation complex formation is defective [Cukras05], and the ribosome shows increased rates of factor-independent translocation [Cukras05]. In vivo, lack of S13 causes a deficit in polysome formation and the appearance of abundant free 30S and 50S subunits [Cukras05]. Ribosome modulation factor binds near S13, L2, and L13 [Yoshida02].

S13 forms a complex with S19 in order to bind to 16S rRNA at its specific site [Dijk77, Pohl88]. The C-terminal domain of S13 is primarily responsible for rRNA binding; its N-terminal domain may be responsible for association with S19 [Schwarzbauer85]. S13 can be crosslinked to 16S rRNA [Hajnsdorf86, Osswald87]; the sites of interaction have been identified by hydroxyl radical probing [Powers88, Powers95, Heilek96]. S13 crosslinks to tRNA at the P site of the ribosome and weakly to tRNA at the A site [Osswald95]. Structural modelling suggested that the C-terminal region of S13 interacts with the P-site tRNA. Studies with rpsM mutants lacking this region show that the C-terminal tail is not essential for the function of S13, but such mutants have slower growth rates. In vitro, deletion of the C-terminal tail of S13 causes a lower affinity of the 30S subunit for tRNAs [Hoang04].

S13 was also shown to crosslink to IF2 and IF3 [Boileau83]

rpsM is not essential for viability of E. coli, but an rpsM deletion strain has a severe growth defect [Cukras05]. An S13 mutant decreases in vivo translation efficiency and acts as antisuppressor of some suppressor tRNAs [Faxen94]. Suppressors of rimM point and deletion mutations localize to the C terminus of S13 [Bylund97, Lovgren04].

Gene Citations: [Post80, Meek84, Jaskunas75]

Locations: cytosol, ribosome

Map Position: [3,440,137 <- 3,440,493] (74.15 centisomes)
Length: 357 bp / 118 aa

Molecular Weight of Polypeptide: 13.099 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010809 , CGSC:219 , DIP:DIP-35855N , EchoBASE:EB0905 , EcoGene:EG10912 , EcoliWiki:b3298 , Mint:MINT-1290225 , OU-Microarray:b3298 , PortEco:rpsM , PR:PRO_000023866 , Pride:P0A7S9 , Protein Model Portal:P0A7S9 , RefSeq:NP_417757 , RegulonDB:EG10912 , SMR:P0A7S9 , String:511145.b3298 , UniProt:P0A7S9

Relationship Links: InterPro:IN-FAMILY:IPR001892 , InterPro:IN-FAMILY:IPR010979 , InterPro:IN-FAMILY:IPR018269 , InterPro:IN-FAMILY:IPR019980 , InterPro:IN-FAMILY:IPR027437 , Panther:IN-FAMILY:PTHR10871 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00416 , Prosite:IN-FAMILY:PS00646 , Prosite:IN-FAMILY:PS50159

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0042254 - ribosome biogenesis Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Essentiality data for rpsM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   No [Baba06, Comment 1]
Low [Bubunenko07]

Credits:
Last-Curated ? 20-Mar-2006 by Keseler I , SRI International


Subunit of: 30S ribosomal subunit

Synonyms: ribosome, small subunit

Subunit composition of 30S ribosomal subunit = [RrsA][RpsA][RpsB][RpsC][RpsD][RpsE][RpsF][RpsG][RpsH][RpsI][RpsJ][RpsK][RpsL][RpsM][RpsN][RpsO][RpsP][RpsQ][RpsR][RpsS][RpsT][RpsU][Sra]
         16S ribosomal RNA (rrsA) = RrsA (extended summary available)
         30S ribosomal subunit protein S1 = RpsA (extended summary available)
         30S ribosomal subunit protein S2 = RpsB (summary available)
         30S ribosomal subunit protein S3 = RpsC (summary available)
         30S ribosomal subunit protein S4 = RpsD (extended summary available)
         30S ribosomal subunit protein S5 = RpsE (extended summary available)
         30S ribosomal subunit protein S6 = RpsF (extended summary available)
         30S ribosomal subunit protein S7 = RpsG (extended summary available)
         30S ribosomal subunit protein S8 = RpsH (extended summary available)
         30S ribosomal subunit protein S9 = RpsI (extended summary available)
         30S ribosomal subunit protein S10 = RpsJ (extended summary available)
         30S ribosomal subunit protein S11 = RpsK (summary available)
         30S ribosomal subunit protein S12 = RpsL (extended summary available)
         30S ribosomal subunit protein S13 = RpsM (extended summary available)
         30S ribosomal subunit protein S14 = RpsN (summary available)
         30S ribosomal subunit protein S15 = RpsO (extended summary available)
         30S ribosomal subunit protein S16 = RpsP (summary available)
         30S ribosomal subunit protein S17 = RpsQ (summary available)
         30S ribosomal subunit protein S18 = RpsR (extended summary available)
         30S ribosomal subunit protein S19 = RpsS (summary available)
         30S ribosomal subunit protein S20 = RpsT (extended summary available)
         30S ribosomal subunit protein S21 = RpsU (summary available)
         30S ribosomal subunit protein S22 = Sra (summary available)

Component of: ribosome (summary available)

Summary:
Assembly of the 30S ribosomal subunit has been studied in real time. Initial assembly is linked to the formation of structured 16S rRNA regions, while later steps involve induced fit between ribosomal proteins and the rRNA [Adilakshmi08]. Discovery single-particle profiling was used to visualize assembly of the 30S ribosomal subunit by indentifying and following changes among 14 subunit assembly intermediates over time [Mulder10]. The kinetically favored assembly pathway of the 30S preinitiation complex has been determined [Milon12].

The function of the ribosomal P site has been reviewed [Noller05].

Relationship Links: PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:2AVY

Enzymes activated by 30S ribosomal subunit, sorted by the type of activation, are:

Activator (Mechanism unknown) of: GTPase [Daigle04, Himeno04]

Credits:
Created 28-Mar-2006 by Keseler I , SRI International


Subunit of: ribosome

Subunit composition of ribosome = [(RrsA)(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)][(RrlA)(RrfA)(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)]
         30S ribosomal subunit = (RrsA)(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra) (summary available)
                 16S ribosomal RNA (rrsA) = RrsA (extended summary available)
                 30S ribosomal subunit protein S1 = RpsA (extended summary available)
                 30S ribosomal subunit protein S2 = RpsB (summary available)
                 30S ribosomal subunit protein S3 = RpsC (summary available)
                 30S ribosomal subunit protein S4 = RpsD (extended summary available)
                 30S ribosomal subunit protein S5 = RpsE (extended summary available)
                 30S ribosomal subunit protein S6 = RpsF (extended summary available)
                 30S ribosomal subunit protein S7 = RpsG (extended summary available)
                 30S ribosomal subunit protein S8 = RpsH (extended summary available)
                 30S ribosomal subunit protein S9 = RpsI (extended summary available)
                 30S ribosomal subunit protein S10 = RpsJ (extended summary available)
                 30S ribosomal subunit protein S11 = RpsK (summary available)
                 30S ribosomal subunit protein S12 = RpsL (extended summary available)
                 30S ribosomal subunit protein S13 = RpsM (extended summary available)
                 30S ribosomal subunit protein S14 = RpsN (summary available)
                 30S ribosomal subunit protein S15 = RpsO (extended summary available)
                 30S ribosomal subunit protein S16 = RpsP (summary available)
                 30S ribosomal subunit protein S17 = RpsQ (summary available)
                 30S ribosomal subunit protein S18 = RpsR (extended summary available)
                 30S ribosomal subunit protein S19 = RpsS (summary available)
                 30S ribosomal subunit protein S20 = RpsT (extended summary available)
                 30S ribosomal subunit protein S21 = RpsU (summary available)
                 30S ribosomal subunit protein S22 = Sra (summary available)
         50S ribosomal subunit = (RrlA)(RrfA)(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)
                 23S ribosomal RNA (rrlA) = RrlA (extended summary available)
                 5S ribosomal RNA (rrfA) = RrfA (extended summary available)
                 50S ribosomal subunit protein L1 = RplA (extended summary available)
                 50S ribosomal subunit protein L2 = RplB (summary available)
                 50S ribosomal subunit protein L3 = RplC (summary available)
                 50S ribosomal subunit protein L4 = RplD (extended summary available)
                 50S ribosomal subunit protein L5 = RplE (summary available)
                 50S ribosomal subunit protein L6 = RplF (summary available)
                 50S ribosomal protein complex L8 = (RplJ)([RplL]2)2 (summary available)
                         50S ribosomal subunit protein L10 = RplJ (extended summary available)
                         50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                                 50S ribosomal subunit protein L12 = RplL
                 50S ribosomal subunit protein L9 = RplI (summary available)
                 50S ribosomal subunit protein L11 = RplK (extended summary available)
                 50S ribosomal subunit protein L13 = RplM (extended summary available)
                 50S ribosomal subunit protein L14 = RplN (extended summary available)
                 50S ribosomal subunit protein L15 = RplO (summary available)
                 50S ribosomal subunit protein L16 = RplP (extended summary available)
                 50S ribosomal subunit protein L17 = RplQ (summary available)
                 50S ribosomal subunit protein L18 = RplR (extended summary available)
                 50S ribosomal subunit protein L19 = RplS (extended summary available)
                 50S ribosomal subunit protein L20 = RplT (extended summary available)
                 50S ribosomal subunit protein L21 = RplU (summary available)
                 50S ribosomal subunit protein L22 = RplV (extended summary available)
                 50S ribosomal subunit protein L23 = RplW (extended summary available)
                 50S ribosomal subunit protein L24 = RplX (summary available)
                 50S ribosomal subunit protein L25 = RplY (summary available)
                 50S ribosomal subunit protein L27 = RpmA (extended summary available)
                 50S ribosomal subunit protein L28 = RpmB (summary available)
                 50S ribosomal subunit protein L29 = RpmC (summary available)
                 50S ribosomal subunit protein L30 = RpmD (summary available)
                 50S ribosomal subunit protein L31 = RpmE (summary available)
                 50S ribosomal subunit protein L32 = RpmF (summary available)
                 50S ribosomal subunit protein L33 = RpmG (summary available)
                 50S ribosomal subunit protein L34 = RpmH (summary available)
                 50S ribosomal subunit protein L35 = RpmI (summary available)
                 50S ribosomal subunit protein L36 = RpmJ (summary available)

Summary:
The ribosome is a complex machinery that translates the genetic code.

A crystal structure of the E. coli ribosome has been determined at 3.5 Å resolution [Schuwirth05]. Additional crystal structures of the ribosome with tRNA bound in two functionally distinct states reveal how a ratchet-like motion of the small and large subunits contributes to translocation, termination of translation, and ribosome recycling [Zhang09b, Dunkle11].

Approximately eight molecules of Zn2+ are bound to the ribosome; therefore, it appears that a large fraction of intracellular Zn2+ is ribosome-associated [Hensley11].

Selected reviews: [Ramakrishnan02, Yonath05, Ogle05, Kaczanowska07]

Citations: [Kuhlenkoetter11]

Relationship Links: PDB:Structure:3R8N , PDB:Structure:3R8O , PDB:Structure:3R8S , PDB:Structure:3R8T

Credits:
Created 15-Jun-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Lindemann77, UniProt11]
UniProt: Removed.
Chain 2 -> 118
[UniProt09]
UniProt: 30S ribosomal protein S13;
Mutagenesis-Variant 83 -> 118
[UniProt10]
Alternate sequence: LGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK → missing; UniProt: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro;
Extrinsic-Sequence-Variant 89 -> 99
[UniProt10]
Alternate sequence: LRHRRGLPVRG → missing; UniProt: (in PW118; partially suppresses a rimM deletion);
Extrinsic-Sequence-Variant 100 -> 118
[UniProt10]
Alternate sequence: QRTKTNARTRKGPRKPIKK → missing; UniProt: (in rpsM413; pseudorevertant of streptomycin resistance. A strong antisuppressor of two tRNA suppressors, decreases translation step time and growth rate);
Extrinsic-Sequence-Variant 105
[UniProt10]
Alternate sequence: N → K; UniProt: (in PW097; partially suppresses a rimM deletion);
Alternate sequence: N → H; UniProt: (in PW095; partially suppresses a rimM deletion);
Mutagenesis-Variant 114 -> 118
[UniProt10]
Alternate sequence: KPIKK → missing; UniProt: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3298 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10912.


References

Adilakshmi08: Adilakshmi T, Bellur DL, Woodson SA (2008). "Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly." Nature 455(7217);1268-72. PMID: 18784650

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Boileau83: Boileau G, Butler P, Hershey JW, Traut RR (1983). "Direct cross-links between initiation factors 1, 2, and 3 and ribosomal proteins promoted by 2-iminothiolane." Biochemistry 22(13);3162-70. PMID: 6349681

Bubunenko07: Bubunenko M, Baker T, Court DL (2007). "Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli." J Bacteriol 189(7);2844-53. PMID: 17277072

Bylund97: Bylund GO, Persson BC, Lundberg LA, Wikstrom PM (1997). "A novel ribosome-associated protein is important for efficient translation in Escherichia coli." J Bacteriol 179(14);4567-74. PMID: 9226267

Cukras03: Cukras AR, Southworth DR, Brunelle JL, Culver GM, Green R (2003). "Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex." Mol Cell 12(2);321-8. PMID: 14536072

Cukras05: Cukras AR, Green R (2005). "Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation." J Mol Biol 349(1);47-59. PMID: 15876367

Daigle04: Daigle DM, Brown ED (2004). "Studies of the interaction of Escherichia coli YjeQ with the ribosome in vitro." J Bacteriol 186(5);1381-7. PMID: 14973029

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dijk77: Dijk J, Littlechild J, Garrett RA (1977). "The RNA binding properties of "native" protein-protein complexes isolated from the Escherichia coli ribosome." FEBS Lett 77(2);295-300. PMID: 324809

Dunkle11: Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH (2011). "Structures of the bacterial ribosome in classical and hybrid states of tRNA binding." Science 332(6032);981-4. PMID: 21596992

Faxen94: Faxen M, Walles-Granberg A, Isaksson LA (1994). "Antisuppression by a mutation in rpsM(S13) giving a shortened ribosomal protein S13." Biochim Biophys Acta 1218(1);27-34. PMID: 8193163

Gao03: Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J (2003). "Study of the structural dynamics of the E coli 70S ribosome using real-space refinement." Cell 113(6);789-801. PMID: 12809609

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hajnsdorf86: Hajnsdorf E, Favre A, Expert-Bezancon A (1986). "Multiple crosslinks of proteins S7, S9, S13 to domains 3 and 4 of 16S RNA in the 30S particle." Nucleic Acids Res 14(10);4009-23. PMID: 2423965

Heilek96: Heilek GM, Noller HF (1996). "Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S13 using tethered Fe(II)." RNA 2(6);597-602. PMID: 8718688

Hensley11: Hensley MP, Tierney DL, Crowder MW (2011). "Zn(II) binding to Escherichia coli 70S ribosomes." Biochemistry 50(46);9937-9. PMID: 22026583

Himeno04: Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A (2004). "A novel GTPase activated by the small subunit of ribosome." Nucleic Acids Res 32(17);5303-9. PMID: 15466596

Hindennach71: Hindennach I, Stoffler G, Wittmann HG (1971). "Ribosomal proteins. Isolation of the proteins from 30S ribosomal subunits of Escherichia coli." Eur J Biochem 23(1);7-11. PMID: 4942549

Hoang04: Hoang L, Fredrick K, Noller HF (2004). "Creating ribosomes with an all-RNA 30S subunit P site." Proc Natl Acad Sci U S A 101(34);12439-43. PMID: 15308780

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jaskunas75: Jaskunas SR, Burgess RR, Nomura M (1975). "Identification of a gene for the alpha-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome." Proc Natl Acad Sci U S A 72(12);5036-40. PMID: 1108010

Kaczanowska07: Kaczanowska M, Ryden-Aulin M (2007). "Ribosome biogenesis and the translation process in Escherichia coli." Microbiol Mol Biol Rev 71(3);477-94. PMID: 17804668

Kuhlenkoetter11: Kuhlenkoetter S, Wintermeyer W, Rodnina MV (2011). "Different substrate-dependent transition states in the active site of the ribosome." Nature 476(7360);351-4. PMID: 21804565

Lambert81: Lambert JM, Traut RR (1981). "The subunit interface of the Escherichia coli ribosome. Identification of proteins at the interface between the 30 S and 50 S subunits by crosslinking with 2-iminothiolane." J Mol Biol 149(3);451-76. PMID: 7031269

Lindemann77: Lindemann H, Wittmann-Liebold B (1977). "Primary structure of protein S13 from the small subunit of escherichia coli ribosomes." Hoppe Seylers Z Physiol Chem 358(7);843-63. PMID: 330375

Lovgren04: Lovgren JM, Bylund GO, Srivastava MK, Lundberg LA, Persson OP, Wingsle G, Wikstrom PM (2004). "The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits." RNA 10(11);1798-812. PMID: 15496525

Meek84: Meek DW, Hayward RS (1984). "Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?." Nucleic Acids Res 1984;12(14);5813-21. PMID: 6379605

Milon12: Milon P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV (2012). "Real-time assembly landscape of bacterial 30S translation initiation complex." Nat Struct Mol Biol 19(6);609-15. PMID: 22562136

Mulder10: 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. PMID: 21030658

Noller05: Noller HF, Hoang L, Fredrick K (2005). "The 30S ribosomal P site: a function of 16S rRNA." FEBS Lett 579(4);855-8. PMID: 15680962

Ogle05: Ogle JM, Ramakrishnan V (2005). "Structural insights into translational fidelity." Annu Rev Biochem 74;129-77. PMID: 15952884

Osswald87: Osswald M, Greuer B, Brimacombe R, Stoffler G, Baumert H, Fasold H (1987). "RNA-protein cross-linking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S5, S7, S8, S9, S11, S13, S19 and S21 by treatment with methyl p-azidophenyl acetimidate." Nucleic Acids Res 15(8);3221-40. PMID: 2437527

Osswald95: Osswald M, Doring T, Brimacombe R (1995). "The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site." Nucleic Acids Res 23(22);4635-41. PMID: 8524654

Pohl88: Pohl T, Wittmann-Liebold B (1988). "Identification of a cross-link in the Escherichia coli ribosomal protein pair S13-S19 at the amino acid level." J Biol Chem 263(9);4293-301. PMID: 3279034

Post80: Post LE, Arfsten AE, Davis GR, Nomura M (1980). "DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli." J Biol Chem 1980;255(10);4653-59. PMID: 6154696

Powers88: Powers T, Stern S, Changchien LM, Noller HF (1988). "Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14." J Mol Biol 201(4);697-716. PMID: 2459390

Powers95: Powers T, Noller HF (1995). "Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA." RNA 1(2);194-209. PMID: 7585249

Ramakrishnan02: Ramakrishnan V (2002). "Ribosome structure and the mechanism of translation." Cell 108(4);557-72. PMID: 11909526

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Schwarzbauer85: Schwarzbauer J, Craven GR (1985). "Evidence that E. coli ribosomal protein S13 has two separable functional domains involved in 16S RNA recognition and protein S19 binding." Nucleic Acids Res 13(18);6767-86. PMID: 3903659

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

WittmannLiebold73: 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. PMID: 4587209

Yonath05: Yonath A (2005). "Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation." Annu Rev Biochem 74;649-79. PMID: 16180279

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Other References Related to Gene Regulation

Bedwell85: Bedwell D, Davis G, Gosink M, Post L, Nomura M, Kestler H, Zengel JM, Lindahl L (1985). "Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli." Nucleic Acids Res 1985;13(11);3891-903. PMID: 2989779

Deckman87: Deckman IC, Draper DE, Thomas MS (1987). "S4-alpha mRNA translation repression complex. I. Thermodynamics of formation." J Mol Biol 196(2);313-22. PMID: 2443719

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Thomas87a: Thomas MS, Bedwell DM, Nomura M (1987). "Regulation of alpha operon gene expression in Escherichia coli. A novel form of translational coupling." J Mol Biol 196(2);333-45. PMID: 3309351

Yates80: Yates JL, Arfsten AE, Nomura M (1980). "In vitro expression of Escherichia coli ribosomal protein genes: autogenous inhibition of translation." Proc Natl Acad Sci U S A 77(4);1837-41. PMID: 6445562


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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