Escherichia coli K-12 substr. MG1655 Polypeptide: H-NS- and StpA-binding protein

Gene: cnu Accession Numbers: G6869 (EcoCyc), b1625, ECK1621

Synonyms: ydgT

Regulation Summary Diagram: ?

Regulation summary diagram for cnu

YdgT (Cnu) is a paralog of the Hha protein and can partially compensate for the phenotypes of a hha mutant. YdgT interacts with H-NS and StpA and appears to protect StpA from proteolytic degradation [Paytubi04]. A heteromeric YdgT-H-NS complex binds the origin of replication (oriC) at a specific 26-bp sequence that overlaps a DnaA binding site [Kim05c].

Both YdgT and HolE appear to influence expression of tnaA by enhancing transcription termination at the leader DNA sequence [Dietrich14].

A solution structure of YdgT has been determined. The H-NS binding site includes the flexible C-terminal region of YdgT [Bae08]. Residues important for the interaction with H-NS have been identified by random mutagenesis [Yun12]. Expression of the K9E mutant leads to decreased DicA production, possibly by inhibiting DicA binding to its own promoter, and resulting in a temperature-dependent filamentous growth phenotype [Yun12a].

YdgT expression is increased in a hha mutant background [Paytubi04]. Single ydgT or hha mutants show no effect on replication, but a ydgT hha double mutant has a slightly increased generation time [Kim05c]. In competitive growth experiments, a ydgT hha double mutant is outcompeted by wild type cells. The presence of pHly152 further lowers the competitive fitness of the ydgT hha double mutant; overexpression of H-NS suppresses the fitness defect [Aznar13]. A ydgT deletion mutant shows increased biofilm formation, while overexpression of ydgT leads to decreased biofilm formation [Hong10]. Overexpression of YdgT suppresses the transcriptional polarity relief phenotype of rho and nusG point mutants [Saxena11].

The transcriptome of a ydgT hha double mutant was compared to that of an hns stpA double mutant [Ueda13]. Microarray analysis of a ydgT mutant showed altered expression of a set of genes that overlapped significantly with genes whose expression was changed in a holE mutant [Dietrich14].

Cnu: "oriC-binding nucleoid-associated" [Kim05c]

Review: [Madrid07]

Citations: [Pedro11, Srinivasan13]

Locations: cytosol

Map Position: [1,702,973 -> 1,703,188] (36.7 centisomes, 132°)
Length: 216 bp / 71 aa

Molecular Weight of Polypeptide: 8.417 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005443 , DIP:DIP-48011N , EchoBASE:EB4050 , EcoGene:EG14303 , EcoliWiki:b1625 , Mint:MINT-8175315 , ModBase:P64467 , OU-Microarray:b1625 , PortEco:cnu , PR:PRO_000022307 , Protein Model Portal:P64467 , RefSeq:NP_416142 , RegulonDB:G6869 , SMR:P64467 , String:511145.b1625 , Swiss-Model:P64467 , UniProt:P64467

Relationship Links: InterPro:IN-FAMILY:IPR007985 , PDB:Structure:2JQT , Pfam:IN-FAMILY:PF05321

GO Terms:

Biological Process: GO:0060566 - positive regulation of DNA-templated transcription, termination Inferred from experiment [Saxena11]
GO:1900232 - negative regulation of single-species biofilm formation on inanimate substrate Inferred from experiment [Hong10]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [deAlba11, Butland05, Paytubi04]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation

Essentiality data for cnu 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 Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
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]

Last-Curated ? 21-Jan-2014 by Keseler I , SRI International

Sequence Features

Protein sequence of H-NS- and StpA-binding protein with features indicated

Feature Class Location Citations Comment
Amino-Acid-Site 44
UniProt: Interacts with H-NS; Sequence Annotation Type: site.
Mutagenesis-Variant 44
[deAlba11, UniProt14]
UniProt: Abolishes heterocomplex formation with H-NS.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Aznar13: Aznar S, Paytubi S, Juarez A (2013). "The Hha protein facilitates incorporation of horizontally acquired DNA in enteric bacteria." Microbiology 159(Pt 3);545-54. PMID: 23258263

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

Bae08: Bae SH, Liu D, Lim HM, Lee Y, Choi BS (2008). "Structure of the nucleoid-associated protein Cnu reveals common binding sites for H-NS in Cnu and Hha." Biochemistry 47(7);1993-2001. PMID: 18189420

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

deAlba11: de Alba CF, Solorzano C, Paytubi S, Madrid C, Juarez A, Garcia J, Pons M (2011). "Essential residues in the H-NS binding site of Hha, a co-regulator of horizontally acquired genes in Enterobacteria." FEBS Lett 585(12);1765-70. PMID: 21600204

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

Dietrich14: Dietrich M, Pedro L, Garcia J, Pons M, Huttener M, Paytubi S, Madrid C, Juarez A (2014). "Evidence for moonlighting functions of the θ subunit of Escherichia coli DNA polymerase III." J Bacteriol 196(5);1102-12. PMID: 24375106

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

Hong10: Hong SH, Wang X, Wood TK (2010). "Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli." Microb Biotechnol 3(3);344-56. PMID: 21255333

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

Kim05c: Kim MS, Bae SH, Yun SH, Lee HJ, Ji SC, Lee JH, Srivastava P, Lee SH, Chae H, Lee Y, Choi BS, Chattoraj DK, Lim HM (2005). "Cnu, a novel oriC-binding protein of Escherichia coli." J Bacteriol 187(20);6998-7008. PMID: 16199570

Madrid07: Madrid C, Balsalobre C, Garcia J, Juarez A (2007). "The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins." Mol Microbiol 63(1);7-14. PMID: 17116239

Paytubi04: Paytubi S, Madrid C, Forns N, Nieto JM, Balsalobre C, Uhlin BE, Juarez A (2004). "YdgT, the Hha paralogue in Escherichia coli, forms heteromeric complexes with H-NS and StpA." Mol Microbiol 54(1);251-63. PMID: 15458420

Pedro11: Pedro L, Banos RC, Aznar S, Madrid C, Balsalobre C, Juarez A (2011). "Antibiotics shaping bacterial genome: deletion of an IS91 flanked virulence determinant upon exposure to subinhibitory antibiotic concentrations." PLoS One 6(11);e27606. PMID: 22096603

Saxena11: Saxena S, Gowrishankar J (2011). "Modulation of Rho-dependent transcription termination in Escherichia coli by the H-NS family of proteins." J Bacteriol 193(15);3832-41. PMID: 21602341

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Srinivasan13: Srinivasan R, Chandraprakash D, Krishnamurthi R, Singh P, Scolari VF, Krishna S, Seshasayee AS (2013). "Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12." Mol Biosyst 9(8);2021-33. PMID: 23661089

Ueda13: Ueda T, Takahashi H, Uyar E, Ishikawa S, Ogasawara N, Oshima T (2013). "Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in Escherichia coli." DNA Res 20(3);263-71. PMID: 23543115

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Yun12: Yun SH, Ji SC, Jeon HJ, Wang X, Lee Y, Choi BS, Lim HM (2012). "A mutational study of Cnu reveals attractive forces between Cnu and H-NS." Mol Cells 33(2);211-6. PMID: 22358512

Yun12a: Yun SH, Ji SC, Jeon HJ, Wang X, Kim SW, Bak G, Lee Y, Lim HM (2012). "The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in E. coli." PLoS One 7(9);e45236. PMID: 23028867

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Oct 9, 2015, BIOCYC14B.