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Escherichia coli K-12 substr. MG1655 Protein: NusB-NusE complex

Subunit composition of NusB-NusE complex = [RpsJ][NusB]
         30S ribosomal subunit protein S10 = RpsJ (extended summary available)
         transcription antitermination protein NusB = NusB (extended summary available)

Gene-Reaction Schematic: ?

GO Terms:

Molecular Function: GO:0003723 - RNA binding Inferred from experiment [Luttgen02]

Credits:
Created 02-Jul-2010 by Keseler I , SRI International


Subunit of NusB-NusE complex: 30S ribosomal subunit protein S10

Synonyms: NusE, RpsJ

Gene: rpsJ Accession Numbers: EG10909 (EcoCyc), b3321, ECK3308

Locations: cytosol, ribosome

Sequence Length: 103 AAs

Molecular Weight: 11.736 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11, Arifuzzaman06, Mason92, Butland05]
GO:0000049 - tRNA binding Inferred by computational analysis [GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01a]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, Hardy69]
GO:0005622 - intracellular Inferred by computational analysis [GOA01a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11a, GOA01a]
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
regulation type of regulation transcriptional level

Unification Links: DIP:DIP-35797N , EcoliWiki:b3321 , Mint:MINT-1283940 , ModBase:P0A7R5 , PR:PRO_000023863 , Pride:P0A7R5 , Protein Model Portal:P0A7R5 , RefSeq:NP_417780 , SMR:P0A7R5 , String:511145.b3321 , UniProt:P0A7R5

Relationship Links: InterPro:IN-FAMILY:IPR001848 , InterPro:IN-FAMILY:IPR018268 , InterPro:IN-FAMILY:IPR027486 , Panther:IN-FAMILY:PTHR11700 , 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:2KVQ , 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:3D3B , PDB:Structure:3D3C , 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:3IMQ , 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:PF00338 , Prints:IN-FAMILY:PR00971 , Prosite:IN-FAMILY:PS00361

Summary:
The S10 protein (NusE) is a component of the 30S subunit of the ribosome and, in a complex with NusB, plays a role in transcription antitermination.

S10 can be crosslinked to tRNA in the ribosomal P site [Riehl82] and may contact 16S rRNA in two separate domains [Powers88].

S10 may be directly involved in the regulation of transcription termination [Das84, Warren84, Das85]. The nusE71 mutation in the rpsJ gene was first shown to affect regulation of transcription termination by the bacteriophage λ antiterminator N [Friedman81]. The nusE71 allele is a point mutation, changing a single amino acid, Ala86, to Asp. It is the only rpsJ allele known to have a Nus- phenotype [Court95]. The nusE71 mutation may be specific for λ antitermination; it appears to have no effect on boxA-mediated increase in the rate of transcription of rrn operons [Zellars99].

S10 is also suggested to function in rrn antitermination. S10 can form a heterodimer with NusB [Mason92]; the heterodimer can bind to the rrn boxA sequence [Nodwell93, Luttgen02]. Detailed analysis of the assembly pathway for the boxA-containing core antitermination complex has been performed [Greive05]. S10 was shown to bind RNA non-specifically and increases the affinity of NusB for boxA RNA [Greive05].

NusE: "N utilization substance E"

Reviews: [Squires00, Weisberg08]

Essentiality data for rpsJ knockouts: ?

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

Subunit of NusB-NusE complex: transcription antitermination protein NusB

Synonyms: SsyB, SsaD, NusB

Gene: nusB Accession Numbers: EG10666 (EcoCyc), b0416, ECK0410

Locations: cytosol

Sequence Length: 139 AAs

Molecular Weight: 15.689 kD (from nucleotide sequence)

Molecular Weight: 14 kD (experimental) [Swindle81]

pI: 7.3 [Maekawa85]

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006353 - DNA-templated transcription, termination Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05, Mason92]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm

MultiFun Terms: information transfer RNA related Transcription related

Unification Links: DIP:DIP-48254N , EcoliWiki:b0416 , Mint:MINT-1220894 , ModBase:P0A780 , PR:PRO_000023446 , Pride:P0A780 , Protein Model Portal:P0A780 , RefSeq:NP_414950 , SMR:P0A780 , String:511145.b0416 , UniProt:P0A780

Relationship Links: InterPro:IN-FAMILY:IPR006027 , InterPro:IN-FAMILY:IPR011605 , Panther:IN-FAMILY:PTHR11078 , PDB:Structure:1EY1 , PDB:Structure:3D3B , PDB:Structure:3D3C , PDB:Structure:3IMQ , Pfam:IN-FAMILY:PF01029

Summary:
Transcription antitermination protein NusB is involved in antitermination in the transcription of a number of genes. In particular, NusB is required for proper transcription of the ribosomal RNA (rRNA) genes.

NusB is required for antitermination in lambda phage, as reviewed in [Das92].

NusB is involved in antitermination in the cell [Kuroki82]. NusB is strictly required for antitermination and transcription of rRNA genes [Sharrock85, Zellars99, Torres04, Quan05]. This antitermination role requires weak initial binding of a boxA sequence on the nascent RNA by NusB, followed by stabilizing binding by 30S ribosomal subunit protein S10 [Greive05, Luttgen02, Nodwell93, Mason92].

NusB has also been implicated in termination, including the enhancement of Rho-dependent termination in at least one case [Ward81, Carlomagno01].

A number of structural analyses have been carried out on NusB. It is active as a monomer [Swindle88]. NMR studies of NusB indicate that it is entirely alpha-helical, with six or seven helices [Berglechner97, Altieri97, Altieri00].

NusB is present at about 50-80% of the abundance of the core RNA polymerase [Swindle88]. In the absence of NusB, RNA transcript levels are lower [Miyashita82].

The structural basis of discernment between boxA RNA and its cognate DNA by NusB has been examined [Muhlberger03].

Citations: [Strauch81]

Essentiality data for nusB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   Yes [Baba06, Comment 2]
Low [Bubunenko07]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

References

Altieri00: Altieri AS, Mazzulla MJ, Horita DA, Coats RH, Wingfield PT, Das A, Court DL, Byrd RA (2000). "The structure of the transcriptional antiterminator NusB from Escherichia coli." Nat Struct Biol 7(6);470-4. PMID: 10881193

Altieri97: Altieri AS, Mazzulla MJ, Zhou H, Costantino N, Court DL, Byrd RA (1997). "Sequential assignments and secondary structure of the RNA-binding transcriptional regulator NusB." FEBS Lett 415(2);221-6. PMID: 9351000

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Berglechner97: Berglechner F, Richter G, Fischer M, Bacher A, Gschwind RM, Huenges M, Gemmecker G, Kessler H (1997). "Studies on the NusB protein of Escherichia coli--expression and determination of secondary-structure elements by multinuclear NMR spectroscopy." Eur J Biochem 248(2);338-46. PMID: 9346286

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Carlomagno01: Carlomagno MS, Nappo A (2001). "The antiterminator NusB enhances termination at a sub-optimal Rho site." J Mol Biol 309(1);19-28. PMID: 11491288

Court95: Court DL, Patterson TA, Baker T, Costantino N, Mao X, Friedman DI (1995). "Structural and functional analyses of the transcription-translation proteins NusB and NusE." J Bacteriol 177(9);2589-91. PMID: 7730297

Das84: Das A, Wolska K (1984). "Transcription antitermination in vitro by lambda N gene product: requirement for a phage nut site and the products of host nusA, nusB, and nusE genes." Cell 38(1);165-73. PMID: 6088061

Das85: Das A, Ghosh B, Barik S, Wolska K (1985). "Evidence that ribosomal protein S10 itself is a cellular component necessary for transcription antitermination by phage lambda N protein." Proc Natl Acad Sci U S A 82(12);4070-4. PMID: 2987961

Das92: Das A (1992). "How the phage lambda N gene product suppresses transcription termination: communication of RNA polymerase with regulatory proteins mediated by signals in nascent RNA." J Bacteriol 174(21);6711-6. PMID: 1400223

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

Friedman81: Friedman DI, Schauer AT, Baumann MR, Baron LS, Adhya SL (1981). "Evidence that ribosomal protein S10 participates in control of transcription termination." Proc Natl Acad Sci U S A 78(2);1115-8. PMID: 6453343

GOA01a: 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."

Greive05: Greive SJ, Lins AF, von Hippel PH (2005). "Assembly of an RNA-protein complex. Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in Escherichia coli." J Biol Chem 280(43);36397-408. PMID: 16109710

Hardy69: Hardy SJ, Kurland CG, Voynow P, Mora G (1969). "The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins." Biochemistry 8(7);2897-905. PMID: 4897206

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

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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kuroki82: Kuroki K, Ishii S, Kano Y, Miyashita T, Nishi K, Imamoto F (1982). "Involvement of the nusB gene products in transcription of Escherichia coli tryptophan operon in vitro." Mol Gen Genet 185(2);369-71. PMID: 7045592

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Luttgen02: Luttgen H, Robelek R, Muhlberger R, Diercks T, Schuster SC, Kohler P, Kessler H, Bacher A, Richter G (2002). "Transcriptional regulation by antitermination. Interaction of RNA with NusB protein and NusB/NusE protein complex of Escherichia coli." J Mol Biol 316(4);875-85. PMID: 11884128

Maekawa85: Maekawa T, Nagase T, Imamoto F, Ishii S (1985). "Purification of the NusB gene product of Escherichia coli K12." Mol Gen Genet 200(1);14-20. PMID: 2993809

Mason92: Mason SW, Li J, Greenblatt J (1992). "Direct interaction between two Escherichia coli transcription antitermination factors, NusB and ribosomal protein S10." J Mol Biol 223(1);55-66. PMID: 1731086

Miyashita82: Miyashita T, Kano Y, Kuroki K, Ishii S, Imamoto F (1982). "In vivo evidence for nusA and nusB gene function in general transcription of the Escherichia coli genome." Biken J 25(3);121-30. PMID: 6187334

Muhlberger03: Muhlberger R, Robelek R, Eisenreich W, Ettenhuber C, Sinner EK, Kessler H, Bacher A, Richter G (2003). "RNA DNA discrimination by the antitermination protein NusB." J Mol Biol 327(5);973-83. PMID: 12662923

Nodwell93: Nodwell JR, Greenblatt J (1993). "Recognition of boxA antiterminator RNA by the E. coli antitermination factors NusB and ribosomal protein S10." Cell 72(2);261-8. PMID: 7678781

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

Quan05: Quan S, Zhang N, French S, Squires CL (2005). "Transcriptional polarity in rRNA operons of Escherichia coli nusA and nusB mutant strains." J Bacteriol 187(5);1632-8. PMID: 15716433

Riehl82: Riehl N, Remy P, Ebel JP, Ehresmann B (1982). "Crosslinking of N-acetyl-phenylalanyl [s4U]tRNAPhe to protein S10 in the ribosomal P site." Eur J Biochem 128(2-3);427-33. PMID: 6759118

Sharrock85: Sharrock RA, Gourse RL, Nomura M (1985). "Defective antitermination of rRNA transcription and derepression of rRNA and tRNA synthesis in the nusB5 mutant of Escherichia coli." Proc Natl Acad Sci U S A 82(16);5275-9. PMID: 3161080

Squires00: Squires CL, Zaporojets D (2000). "Proteins shared by the transcription and translation machines." Annu Rev Microbiol 54;775-98. PMID: 11018144

Strauch81: Strauch M, Friedman DI (1981). "Identification of the nusB gene product of Escherichia coli." Mol Gen Genet 182(3);498-501. PMID: 6272065

Swindle81: Swindle J, Ajioka J, Georgopoulos C (1981). "Identification of the E. coli groNB(nusB) gene product." Mol Gen Genet 182(3);409-13. PMID: 6272060

Swindle88: Swindle J, Zylicz M, Georgopoulos C, Li J, Greenblatt J (1988). "Purification and properties of the NusB protein of Escherichia coli." J Biol Chem 263(21);10229-35. PMID: 2839479

Torres04: Torres M, Balada JM, Zellars M, Squires C, Squires CL (2004). "In vivo effect of NusB and NusG on rRNA transcription antitermination." J Bacteriol 186(5);1304-10. PMID: 14973028

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

Ward81: Ward DF, Gottesman ME (1981). "The nus mutations affect transcription termination in Escherichia coli." Nature 292(5820);212-5. PMID: 6265784

Warren84: Warren F, Das A (1984). "Formation of termination-resistant transcription complex at phage lambda nut locus: effects of altered translation and a ribosomal mutation." Proc Natl Acad Sci U S A 81(12);3612-6. PMID: 6233610

Weisberg08: Weisberg RA (2008). "Transcription by moonlight: structural basis of an extraribosomal activity of ribosomal protein S10." Mol Cell 32(6);747-8. PMID: 19111651

Zellars99: Zellars M, Squires CL (1999). "Antiterminator-dependent modulation of transcription elongation rates by NusB and NusG." Mol Microbiol 32(6);1296-304. PMID: 10383769

Zheng11: Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011). "Cross-linking measurements of in vivo protein complex topologies." Mol Cell Proteomics 10(10);M110.006841. PMID: 21697552


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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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