Notes For:
The 16S rRNA is the RNA component of the small subunit (30S subunit) of the E. coli ribosome.
There are seven ribosomal RNA (rRNA) operons, called rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, and rrsH |CITS: [COLISALII]|. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrsD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes |CITS: [COLISALII]|. Regarding nomenclature, rrs genes encode 16S rRNAs, rrl genes encode 23S rRNAs, and rrf genes encode 5S rRNAs |CITS: [COLISALII]|. rrsB has the highest promoter activity among rRNA operon mutants lacking HNS |CITS:[ 26717514]|.
The sequence and structure of the 16S rRNA has been described |CITS: [5340599], [4868442], [4299552], [4311070], [4903099], [4910391], [4927343], [4916974], [4932242], [4941835], [4935734], [4935735], [4935736], [4569972], [4569973], [4551094], [4562230], [4354606], [4356617], [4597768], [4620018], [4371816], [4374383], [4616170], [1106773], [1091918], [1089909], [167351], [1099457], [1103089], [809718], [780350], [818623], [787927], [786726], [322143], [379604], [347396], [351619], [358146], [368799], [362531], [477513], [387717], [388420], [392471], [93692], [6153384], [6159576], [6160459], [6160460], [6996708], [6784944], [6162161], [6163215], [6170942], [6170632], [7024918], [7029465], [7030394], [6285311], [6750555], [6188539], [6340066], [6194995], [6359058], [6363901], [6401121], [6200766], [6207855], [3882675], [3923479], [3907698], [3935157], [2997731], [2418415], [3720727], [3299045], [3126826], [3323531], [2853815], [2451022], [2482760], [2453025], [2457499], [2837729], [3048381], [3048388], [2457514], [2468977], [2464291], [2464693], [2642480], [2686708], [2654936], [2476177], [2675971], [2477554], [2689654], [2179567], [2408047], [2207172], [2171681], [2236056], [2001727], [1712940], [1712293], [1872848], [1960712], [1896466], [1547215], [1374556], [1280994], [1280995], [7681419], [7691600], [8241431], [7518524], [8643402], [8643405], [7543481], [7567470], [8721993], [7479839], [8658142], [8910275], [9122161], [9174095], [9222495], [9171076], [9271564], [9281424], [9310353], [9354641], [9421514], [9677294], [9784367], [9799506], [9814765], [9835591], [9893990], [10347223], [10411129], [10536142], [10747796], [10793686], [10864503], [11000271], [11090278], [11214183], [11243814], [11327780], [11502181], [11552678], [11812846], [11860288], [11947429], [12126618], [12126619], [12788352], [12836305], [12859155]|.
The relationship of the 16S rRNA to ribosome assembly, structure, and function has been characterized |CITS: [4551094], [4589452], [4594437], [4592471], [4597072], [4610566], [4371816], [1090843], [1092437], [803646], [765770], [1219394], [167351], [1098691], [766751], [1104582], [1107998], [765762], [764867], [768982], [823528], [778638], [782519], [786726], [794830], [323854], [400797], [327330], [329865], [341969], [354688], [360077], [370785], [375223], [107964], [387717], [388420], [114214], [385051], [398003], [6996748], [7019858], [6986611], [6998892], [6996708], [7003539], [6163479], [7029211], [7011367], [6165012], [7013827], [6170320], [7029538], [7030394], [6274438], [6173062], [6750359], [6813860], [6340734], [6349628], [6348775], [6354253], [6385981], [6197085], [6422982], [6422983], [6366737], [6396503], [2578388], [2582234], [3907695], [3907696], [3900929], [3510432], [3003738], [3513310], [3521723], [2425339], [2430725], [3126826], [2451022], [3277159], [2839766], [3283702], [2457498], [2457499], [3139078], [3288986], [2455279], [2459390], [3048388], [2461734], [3186700], [2476074], [3061811], [3078239], [2540813], [2540814], [2686708], [2657653], [2658053], [2473900], [2662189], [2476177], [2514787], [2689654], [2690012], [2405162], [1689824], [2156079], [2179567], [2186363], [2207172], [2207173], [1702020], [2216755], [2171681], [1993193], [1708125], [1662543], [1764523], [1720670], [1720674], [1742366], [1712292], [1907...
Reference(s): |
|
[1] Leontis NB, Westhof E, 1998, A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs., J Mol Biol, 283(3):571 10.1006/jmbi.1998.2106 |
[2] Brimacombe R., Atmadja J., Stiege W., Schuler D., 1988, A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit., J Mol Biol 199(1):115-36 |
[3] Woese CR, Winker S, Gutell RR, 1990, Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"., Proc Natl Acad Sci U S A, 87(21):8467 10.1073/pnas.87.21.8467 |
[4] Santer M, Shane S, 1977, Area of 16S ribonucleic acid at or near the interface between 30S and 50S ribosomes of Escherichia coli., J Bacteriol, 130(2):900 10.1128/jb.130.2.900-910.1977 |
[5] Nowotny V., Nierhaus KH., 1988, Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7., Biochemistry 27(18):7051-5 |
[6] Wakao H., Romby P., Laalami S., Ebel JP., Ehresmann C., Ehresmann B., 1990, Binding of initiation factor 2 and initiator tRNA to the Escherichia coli 30S ribosomal subunit induces allosteric transitions in 16S rRNA., Biochemistry 29(35):8144-51 |
[7] Lasater LS, Olson HM, Cann PA, Glitz DG, 1988, Complementary oligodeoxynucleotide probes of RNA conformation within the Escherichia coli small ribosomal subunit., Biochemistry, 27(13):4687 10.1021/bi00413a016 |
[8] Brosius J, Palmer ML, Kennedy PJ, Noller HF, 1978, Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli., Proc Natl Acad Sci U S A, 75(10):4801 10.1073/pnas.75.10.4801 |
[9] Chiam CL, Wagner R, 1983, Composition of the Escherichia coli 70S ribosomal interface: a cross-linking study., Biochemistry, 22(5):1193 10.1021/bi00274a032 |
[10] Mandiyan V, Hainfeld JF, Wall JS, Boublik M, 1988, Conformational analysis of 16 S ribosomal RNA from Escherichia coli by scanning transmission electron microscopy., FEBS Lett, 236(2):340 10.1016/0014-5793(88)80052-8 |
[11] Horie K., Wada A., Fukutome H., 1981, Conformational studies of Escherichia coli ribosomes with the use of acridine orange as a probe., J Biochem (Tokyo) 90(2):449-61 |
[12] 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 |
[13] Magrum L, Zablen L, Stahl D, Woese C, 1975, Corrections in the catalogue of oliogonucleotides produced by digestion of Escherichia coli 16S rRNA with T1 RNase., Nature, 257(5525):423 10.1038/257423a0 |
[14] Noah JW, Wollenzien P, 1998, Dependence of the 16S rRNA decoding region structure on Mg2+, subunit association, and temperature., Biochemistry, 37(44):15442 10.1021/bi981148m |
[15] Woese CR, Gutell R, Gupta R, Noller HF, 1983, Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids., Microbiol Rev, 47(4):621 10.1128/mr.47.4.621-669.1983 |
[16] Cunningham C, Ganoza MC, 1984, Detection of a 16S rRNA . initiator-tRNA complex by a new selective labelling method., Mol Biol Rep, 10(2):115 10.1007/BF00776984 |
[17] Morris DR., Dahlberg JE., Dahlberg AE., 1974, Detection of cation-specific conformational changes in ribosomal RNA by gel electrophoresis., Nucleic Acids Res 1(10):1249-58 |
[18] Newcomb LF, Noller HF, 1999, Directed hydroxyl radical probing of 16S ribosomal RNA in 70S ribosomes from internal positions of the RNA., Biochemistry, 38(3):945 10.1021/bi981644a |
[19] Ramakrishnan V, 1986, Distribution of protein and RNA in the 30S ribosomal subunit., Science, 231(4745):1562 10.1126/science.3513310 |
[20] Trudel M, Dondon J, Grunberg-Manago M, Finelli J, Buckingham RH, 1981, Effect of oligonucleotide AGAGGAGGU on protein synthesis in vitro., Biochimie, 63(3):235 10.1016/s0300-9084(81)80197-6 |
[21] Klein BK, Romero J, Schlessinger D, 1985, Electron microscopy of the secondary structure in partially denatured rRNAs of Escherichia coli and Bacillus stearothermophilus., J Bacteriol, 161(3):981 10.1128/jb.161.3.981-988.1985 |
[22] Hochkeppel HK., Craven GR., 1976, Evidence that 16S RNA from E. coli can assume two different biologically active conformations., Nucleic Acids Res 3(8):1883-902 |
[23] Wilms C, Noah JW, Zhong D, Wollenzien P, 1997, Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30S ribosomal subunits., RNA, 3(6):602 None |
[24] Wagner R, Gassen HG, 1976, Identification of a 16S rna sequence located in the decoding site of 30S ribosomes., FEBS Lett, 67(3):312 10.1016/0014-5793(76)80554-6 |
[25] Tewari DS., Burma DP., 1983, Incorporation of 5S RNA into 16S-23S RNA complex., Biochem Biophys Res Commun 114(1):348-54 |
[26] Taniguchi T, Weissmann C, 1978, Inhibition of Qbeta RNA 70S ribosome initiation complex formation by an oligonucleotide complementary to the 3' terminal region of E. coli 16S ribosomal RNA., Nature, 275(5682):770 10.1038/275770a0 |
[27] Stöffler-Meilicke M, Stöffler G, Odom OW, Zinn A, Kramer G, Hardesty B, 1981, Localization of 3' ends of 5S and 23S rRNAs in reconstituted subunits of Escherichia coli ribosomes., Proc Natl Acad Sci U S A, 78(9):5538 10.1073/pnas.78.9.5538 |
[28] Kalurachchi K, Nikonowicz EP, 1998, NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA., J Mol Biol, 280(4):639 10.1006/jmbi.1998.1915 |
[29] Podkowinski J, Gornicki P, 1991, Neighbourhood of the central fold of the tRNA molecule bound to the E. coli ribosome--affinity labeling studies with modified tRNAs carrying photoreactive probes attached to the dihydrouridine loop., Nucleic Acids Res, 19(4):801 10.1093/nar/19.4.801 |
[30] Muto A, 1970, Nucleotide distribution of Escherichia coli 16S ribosomal ribonucleic acid., Biochemistry, 9(19):3683 10.1021/bi00821a006 |
[31] Schwartz I., Gordon E., Ofengand J., 1975, Photoaffinity labeling of the ribosomal A site with S-(p-azidophenacyl)valyl-tRNA., Biochemistry 14(13):2907-14 |
[32] 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 |
[33] 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 |
[34] 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 |
[35] Skold SE., 1981, RNA-protein complexes identified by crosslinking of polysomes., Biochimie 63(1):53-60 |
[36] Giocanti N., Ekert B., 1980, Radiochemical cross-linking of proteins to RNA within ribosomal subunits from E. colil MRE 600., Int J Radiat Biol Relat Stud Phys Chem Med 38(1):63-82 |
[37] Thomas GJ., Prescott B., Hamilton MG., 1980, Raman spectra and conformational properties of ribosomes during various stages of disassembly., Biochemistry 19(15):3604-13 |
[38] 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 |
[39] Ehresmann C, Stiegler P, Ebel JP, 1974, Sequence analysis of the 3'-T1 oligonucleotide of 16S ribosomal RNA from Escherichia coli., FEBS Lett, 49(1):47 10.1016/0014-5793(74)80628-9 |
[40] Wollenzien P, Expert-Bezançon A, Favre A, 1991, Sites of contact of mRNA with 16S rRNA and 23S rRNA in the Escherichia coli ribosome., Biochemistry, 30(7):1788 10.1021/bi00221a009 |
[41] Van Ryk DI, Dahlberg AE, 1995, Structural changes in the 530 loop of Escherichia coli 16S rRNA in mutants with impaired translational fidelity., Nucleic Acids Res, 23(17):3563 10.1093/nar/23.17.3563 |
[42] Morosyuk SV., Cunningham PR., SantaLucia J., 2001, Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure., J Mol Biol 307(1):197-211 |
[43] 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 |
[44] Bogdanov AA, Chichkova NV, Kopylov AM, Mankin AS, Skripkin EA, 1988, Surface topography of ribosomal RNA., Methods Enzymol, 164(None):440 10.1016/s0076-6879(88)64060-2 |
[45] Mougel M, Philippe C, Ebel JP, Ehresmann B, Ehresmann C, 1988, The E. coli 16S rRNA binding site of ribosomal protein S15: higher-order structure in the absence and in the presence of the protein., Nucleic Acids Res, 16(7):2825 10.1093/nar/16.7.2825 |
[46] Tate WP, Ward CD, Trotman CN, Lührmann R, Stöffler G, 1983, The Shine and Dalgarno hypothesis for termination: the 3' terminus of the 16S rRNA of the Escherichia coli ribosome can be modified or base-paired with a complementary oligonucleotide without affecting termination in vitro., Biochem Int, 7(4):529 None |
[47] Osterberg R, Sjöberg B, Garrett GA, Müller R, 1980, The conformation of a large RNA fragment from the E.coli ribosomal 16S-RNA. An X-ray and neutron small-angle scattering study., Nucleic Acids Res, 8(24):6221 10.1093/nar/8.24.6221 |
[48] Romby P., Wakao H., Westhof E., Grunberg-Manago M., Ehresmann B., Ehresmann C., Ebel JP., 1990, The conformation of the initiator tRNA and of the 16S rRNA from Escherichia coli during the formation of the 30S initiation complex., Biochim Biophys Acta 1050(1-3):84-92 |
[49] Fellner P, Ehresmann C, Ebel JP, 1972, The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. 1. Nucleotide sequence analysis of T 1 and pancreatic ribonuclease digestion products., Biochimie, 54(7):853 10.1016/s0300-9084(72)80006-3 |
[50] Ehresmann C, Stiegler P, Fellner P, Ebel JP, 1975, The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. III. Further studies., Biochimie, 57(6-7):711 10.1016/s0300-9084(75)80047-2 |
[51] Rinke-Appel J, Jünke N, Stade K, Brimacombe R, 1991, The path of mRNA through the Escherichia coli ribosome; site-directed cross-linking of mRNA analogues carrying a photo-reactive label at various points 3' to the decoding site., EMBO J, 10(8):2195 10.1002/j.1460-2075.1991.tb07755.x |
[52] Fellner P, 1971, The primary structure of the 16S and 23S ribosomal RNAs., Biochimie, 53(5):573 10.1016/s0300-9084(71)80013-5 |
[53] Pon CL, Gualerzi C, 1976, The role of 16S rRNA in ribosomal binding of IF-3., Biochemistry, 15(4):804 10.1021/bi00649a012 |
[54] Uchida T, Bonen L, Schaup HW, Lewis BJ, Zablen L, Woese C, 1974, The use of ribonuclease U2 in RNA sequence determination. Some corrections in the catalog of oligomers produced by ribonuclease T1 digestion of Escherichia coli 16S ribosomal RNA., J Mol Evol, 3(1):63 10.1007/BF01795977 |
[55] Hui Bon Hoa G., Graffe M., Grunberg-Manago M., 1977, Thermodynamic studies of the reversible association of Escherichia coli ribosomal subunits., Biochemistry 16(12):2800-5 |
[56] Wakao H., Romby P., Ebel JP., Grunberg-Manago M., Ehresmann C., Ehresmann B., 1991, Topography of the Escherichia coli ribosomal 30S subunit-initiation factor 2 complex., Biochimie 73(7-8):991-1000 |
[57] Moazed D, Noller HF, 1986, Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes., Cell, 47(6):985 10.1016/0092-8674(86)90813-5 |
[58] Gimautdinova OI., Karpova GG., Kozyreva NA., 1982, [Affinity labeling of ribosomes from Escherichia coli with 4-(N-2-chloroethyl-N-methylamino) benzyl-5'-phosphamides of oligouridylates of different length]., Mol Biol (Mosk) 16(4):752-62 |
[59] Borisova OF, Grechko VV, Kuznetsova NV, Sakharova NK, Timokhina GI, 1987, [Comparison of the conformation of RNA from phage MS2 and 16S rRNA. Interaction with dyes specific for the secondary structure of native RNA and RNA subjected to hydrolysis by nuclease S1]., Mol Biol (Mosk), 21(2):515 None |
[60] 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 |
[61] 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 |
[62] 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 |
RegulonDB