Escherichia coli K-12 substr. MG1655 Polypeptide: transcription termination/antitermination L factor

Gene: nusA Accession Numbers: EG10665 (EcoCyc), b3169, ECK3158

Regulation Summary Diagram: ?

Regulation summary diagram for nusA

Transcription termination/antitermination L factor (NusA) is a key component in both prevention and enhancement of transcriptional termination. It is important in both Rho-dependent and intrinsic termination, as well as in lambda and other phage antitermination systems.

NusA was originally identified based on its involvement in antitermination in lambda phage, as reviewed in [Das92].

NusA is also involved in transcriptional antitermination in the cell [Ward81, Greenblatt80]. It has been shown to specifically aid in readthrough of the RNA polymerase genes rpoB and rpoC, as well as in successful synthesis of the ribosomal RNA genes [Linn92, Squires93, Vogel97, Quan05].

In addition to its antitermination role, NusA is required for both Rho-dependent and intrinsic transcriptional termination. NusA is required for Rho-dependent termination in lambda phage and in the cell [Greenblatt81, Schmidt87a]. It is also frequently involved in intrinsic termination and the inhibition of RNA elongation [Farnham82, Zengel92, Sha95, Vogel97, Carlomagno03, Schmidt84].

Though NusA interacts with all three subunits of RNA polymerase, its termination activity primarily depends on its interaction with the carboxy-terminus of RpoA [Ito91, Ito96, Liu96a]. The presence of NusA induces a conformational change in RNA polymerase prevents RNA interaction with RpoA [Zhang94, Liu95, Liu95a]. This binding in turn activates NusA, allowing it to bind RNA and promote formation of hairpins at intrinsic termination sites [Mah00, Gusarov01].

NusA interacts with many components of the transcriptional machinery, in addition to those interactions noted above. NusA binds Rho, and competes with sigma70 for binding to the core RNA polymerase complex [Schmidt84a, Gill91]. It does not compete with NusG for binding to either Rho or the polymerase, despite modulating the same process as NusG in both cases [Burns98].

NusA contains two homology regions, S1 and KH, that are important for its activity, as well as two RNA polymerase binding regions [Mah99]. NusA is monomeric [Gill91a]. The carboxy-terminus of NusA has been examined via NMR [Eisenmann04, Eisenmann05].

In nusA mutants, total cellular RNA abundance drops due to increased termination [Miyashita82].

NusA downregulates its own expression, which generally mirrors the expression levels of cellular sigma factors [Nakamura85, Plumbridge85, Ishihama87].

Cohen et al. (2009) suggested that NusA is directed by the translesion DNA synthesis activity of DinB to sites of active transcription. In turn, DinB might affect NusA-dependent transcription termination, which would provide another level of SOS control of gene expression (negative or positive) [Cohen09].

Gene Citations: [Sands88, Nakamura85a, Neidhardt96, Regnier89, Regnier90]

Locations: cytosol

Map Position: [3,314,061 <- 3,315,548] (71.43 centisomes, 257°)
Length: 1488 bp / 495 aa

Molecular Weight of Polypeptide: 54.871 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010413 , CGSC:441 , DIP:DIP-47857N , EchoBASE:EB0659 , EcoGene:EG10665 , EcoliWiki:b3169 , Mint:MINT-1220515 , ModBase:P0AFF6 , OU-Microarray:b3169 , PortEco:nusA , PR:PRO_000023445 , Pride:P0AFF6 , Protein Model Portal:P0AFF6 , RefSeq:NP_417638 , RegulonDB:EG10665 , SMR:P0AFF6 , String:511145.b3169 , Swiss-Model:P0AFF6 , UniProt:P0AFF6

Relationship Links: InterPro:IN-FAMILY:IPR003029 , InterPro:IN-FAMILY:IPR003583 , InterPro:IN-FAMILY:IPR004087 , InterPro:IN-FAMILY:IPR004088 , InterPro:IN-FAMILY:IPR009019 , InterPro:IN-FAMILY:IPR010213 , InterPro:IN-FAMILY:IPR010214 , InterPro:IN-FAMILY:IPR010995 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013735 , InterPro:IN-FAMILY:IPR015946 , InterPro:IN-FAMILY:IPR022967 , InterPro:IN-FAMILY:IPR025249 , InterPro:IN-FAMILY:IPR028620 , PDB:Structure:1U9L , PDB:Structure:1WCL , PDB:Structure:1WCN , PDB:Structure:2JZB , PDB:Structure:2KWP , Pfam:IN-FAMILY:PF00575 , Pfam:IN-FAMILY:PF08529 , Pfam:IN-FAMILY:PF13184 , Prosite:IN-FAMILY:PS50084 , Prosite:IN-FAMILY:PS50126 , Smart:IN-FAMILY:SM00278 , Smart:IN-FAMILY:SM00316 , Smart:IN-FAMILY:SM00322

Genetic Regulation Schematic: ?

Genetic regulation schematic for nusA

GO Terms:

Biological Process: GO:0031564 - transcription antitermination Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Kim06e]
GO:0006281 - DNA repair Inferred by computational analysis [GOA01a]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006353 - DNA-templated transcription, termination Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0031554 - regulation of DNA-templated transcription, termination Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Cohen09]
GO:0000166 - nucleotide binding Inferred by computational analysis [GOA01a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Watt07]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level

Essentiality data for nusA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Last-Curated ? 25-Jul-2006 by Shearer A , SRI International

Sequence Features

Protein sequence of transcription termination/antitermination L factor with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 104
[Ito91, UniProt13]
UniProt: In nusA10-1.
Conserved-Region 135 -> 200
UniProt: S1 motif;
Mutagenesis-Variant 181
[Ito91, UniProt13]
UniProt: In nusa11; inability to terminate transcription normally at termination sites.
Mutagenesis-Variant 183
[Ito91, UniProt13]
UniProt: In nusA1; restricts lambda growth by preventing antitermination activity of lambda N protein.
Mutagenesis-Variant 212
[Ito91, UniProt13]
UniProt: In nusA10-2.
Conserved-Region 230 -> 293
UniProt: KH 1.
Conserved-Region 302 -> 368
UniProt: KH 2.
Protein-Segment 364 -> 489
UniProt: 2 X 51 AA approximate repeats; Sequence Annotation Type: region of interest;
Repeat 364 -> 414
UniProt: 1;
Repeat 439 -> 489
UniProt: 2;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3169 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10665; confirmed by SwissProt match.


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

Burns98: Burns CM, Richardson LV, Richardson JP (1998). "Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli." J Mol Biol 278(2);307-16. PMID: 9571053

Carlomagno03: Carlomagno MS, Nappo A (2003). "NusA modulates intragenic termination by different pathways." Gene 308;115-28. PMID: 12711396

Cohen09: Cohen SE, Godoy VG, Walker GC (2009). "Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli." J Bacteriol 191(2);665-72. PMID: 18996995

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

Eisenmann04: Eisenmann A, Schwarz S, Rosch P, Schweimer K (2004). "Sequence-specific 1H, 13C, 15N resonance assignments and secondary structure of the carboxyterminal domain of the E. coli transcription factor NusA." J Biomol NMR 28(2);193-4. PMID: 14755165

Eisenmann05: Eisenmann A, Schwarz S, Prasch S, Schweimer K, Rosch P (2005). "The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and lambdaN interaction." Protein Sci 14(8);2018-29. PMID: 15987884

Farnham82: Farnham PJ, Greenblatt J, Platt T (1982). "Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli." Cell 29(3);945-51. PMID: 6758952

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gill91: Gill SC, Weitzel SE, von Hippel PH (1991). "Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex." J Mol Biol 220(2);307-24. PMID: 1856861

Gill91a: Gill SC, Yager TD, von Hippel PH (1991). "Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states." J Mol Biol 220(2);325-33. PMID: 1856862

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."

Greenblatt80: Greenblatt J, Li J, Adhya S, Friedman DI, Baron LS, Redfield B, Kung HF, Weissbach H (1980). "L factor that is required for beta-galactosidase synthesis is the nusA gene product involved in transcription termination." Proc Natl Acad Sci U S A 77(4);1991-4. PMID: 6154941

Greenblatt81: Greenblatt J, McLimont M, Hanly S (1981). "Termination of transcription by nusA gene protein of Escherichia coli." Nature 292(5820);215-20. PMID: 6265785

Gusarov01: Gusarov I, Nudler E (2001). "Control of intrinsic transcription termination by N and NusA: the basic mechanisms." Cell 107(4);437-49. PMID: 11719185

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

Ishihama87: Ishihama A, Honda A, Nagasawa-Fujimori H, Glass RE, Maekawa T, Imamoto F (1987). "Multivalent regulation of the nusA operon of Escherichia coli." Mol Gen Genet 206(2);185-91. PMID: 3035333

Ito91: Ito K, Egawa K, Nakamura Y (1991). "Genetic interaction between the beta' subunit of RNA polymerase and the arginine-rich domain of Escherichia coli nusA protein." J Bacteriol 173(4);1492-501. PMID: 1847365

Ito96: Ito K, Nakamura Y (1996). "Localization of nusA-suppressing amino acid substitutions in the conserved regions of the beta' subunit of Escherichia coli RNA polymerase." Mol Gen Genet 251(6);699-706. PMID: 8757401

Kim06e: Kim HC, Washburn RS, Gottesman ME (2006). "Role of E.coli NusA in phage HK022 Nun-mediated transcription termination." J Mol Biol 359(1);10-21. PMID: 16631197

Linn92: Linn T, Greenblatt J (1992). "The NusA and NusG proteins of Escherichia coli increase the in vitro readthrough frequency of a transcriptional attenuator preceding the gene for the beta subunit of RNA polymerase." J Biol Chem 267(3);1449-54. PMID: 1370474

Liu95: Liu K, Hanna MM (1995). "NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes." Proc Natl Acad Sci U S A 92(11);5012-6. PMID: 7539140

Liu95a: Liu K, Hanna MM (1995). "NusA contacts nascent RNA in Escherichia coli transcription complexes." J Mol Biol 247(4);547-58. PMID: 7536848

Liu96a: Liu K, Zhang Y, Severinov K, Das A, Hanna MM (1996). "Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor NusA." EMBO J 15(1);150-61. PMID: 8598198

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

Mah00: Mah TF, Kuznedelov K, Mushegian A, Severinov K, Greenblatt J (2000). "The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA." Genes Dev 14(20);2664-75. PMID: 11040219

Mah99: Mah TF, Li J, Davidson AR, Greenblatt J (1999). "Functional importance of regions in Escherichia coli elongation factor NusA that interact with RNA polymerase, the bacteriophage lambda N protein and RNA." Mol Microbiol 34(3);523-37. PMID: 10564494

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

Nakamura85: Nakamura Y, Plumbridge J, Dondon J, Grunberg-Manago M (1985). "Evidence for autoregulation of the nusA-infB operon of Escherichia coli." Gene 36(1-2);189-93. PMID: 2998933

Nakamura85a: Nakamura Y, Mizusawa S (1985). "In vivo evidence that the nusA and infB genes of E. coli are part of the same multi-gene operon which encodes at least four proteins." EMBO J 1985;4(2);527-32. PMID: 2990900

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Plumbridge85: Plumbridge JA, Dondon J, Nakamura Y, Grunberg-Manago M (1985). "Effect of NusA protein on expression of the nusA,infB operon in E. coli." Nucleic Acids Res 13(9);3371-88. PMID: 2987884

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

Regnier89: Regnier P, Grunberg-Manago M (1989). "Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA." J Mol Biol 210(2);293-302. PMID: 2481042

Regnier90: Regnier P, Grunberg-Manago M (1990). "RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression." Biochimie 72(11);825-34. PMID: 2085545

Sands88: 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 1988;16(22);10803-16. PMID: 2849753

Schmidt84: Schmidt MC, Chamberlin MJ (1984). "Amplification and isolation of Escherichia coli nusA protein and studies of its effects on in vitro RNA chain elongation." Biochemistry 23(2);197-203. PMID: 6199039

Schmidt84a: Schmidt MC, Chamberlin MJ (1984). "Binding of rho factor to Escherichia coli RNA polymerase mediated by nusA protein." J Biol Chem 259(24);15000-2. PMID: 6096352

Schmidt87a: Schmidt MC, Chamberlin MJ (1987). "nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites." J Mol Biol 195(4);809-18. PMID: 2821282

Sha95: Sha Y, Lindahl L, Zengel JM (1995). "Role of NusA in L4-mediated attenuation control of the S10 r-protein operon of Escherichia coli." J Mol Biol 245(5);474-85. PMID: 7844821

Squires93: Squires CL, Greenblatt J, Li J, Condon C, Squires CL (1993). "Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components." Proc Natl Acad Sci U S A 90(3);970-4. PMID: 8430111

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Vogel97: Vogel U, Jensen KF (1997). "NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA." J Biol Chem 272(19);12265-71. PMID: 9139668

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

Watt07: Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD (2007). "Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes." Nucleic Acids Res 35(6);e37. PMID: 17272300

Zengel92: Zengel JM, Lindahl L (1992). "Ribosomal protein L4 and transcription factor NusA have separable roles in mediating terminating of transcription within the leader of the S10 operon of Escherichia coli." Genes Dev 6(12B);2655-62. PMID: 1285127

Zhang94: Zhang Y, Hanna MM (1994). "NusA changes the conformation of Escherichia coli RNA polymerase at the binding site for the 3' end of the nascent RNA." J Bacteriol 176(6);1787-9. PMID: 7510675

Other References Related to Gene Regulation

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

Charlier92: Charlier D, Roovers M, Van Vliet F, Boyen A, Cunin R, Nakamura Y, Glansdorff N, Pierard A (1992). "Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression." J Mol Biol 1992;226(2);367-86. PMID: 1640456

Granston90: Granston AE, Thompson DL, Friedman DI (1990). "Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli." J Bacteriol 172(5);2336-42. PMID: 1692017

Ishii84: Ishii S, Kuroki K, Imamoto F (1984). "tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli." Proc Natl Acad Sci U S A 1984;81(2);409-13. PMID: 6364142

Krin03: Krin E, Laurent-Winter C, Bertin PN, Danchin A, Kolb A (2003). "Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12." J Bacteriol 185(10);3139-46. PMID: 12730174

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

Regnier87: Regnier P, Grunberg-Manago M, Portier C (1987). "Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1." J Biol Chem 1987;262(1);63-8. PMID: 2432069

Shimada13: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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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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