Escherichia coli K-12 substr. MG1655 Polypeptide: hemolysin E

Gene: hlyE Accession Numbers: G6619 (EcoCyc), b1182, ECK1170

Synonyms: ycgD, clyA, hpr, sheA

Regulation Summary Diagram: ?

Regulation summary diagram for hlyE

Hemolysin E causes lysis of mammalian cells [Lai00]. Secretion of hemolysin E into the medium is independent of its cytolytic activity and paralleled by transient leakage of periplasmic contents [delCastillo01]. Outer-membrane vesicles (OMVs) were shown to contain oligomeric pore assemblies formed by HlyE; these vesicles had higher cytotoxic activity than purified HlyE protein [Wai03]. The C terminus of HlyE has been implicated in secretion and formation of pore assemblies; mutant proteins are able to interact with the wild-type protein and have a dominant negative effect [Wai03a]. A putative transmembrane motif in the N-terminal region of HlyE has been implicated in maintaining lytic activity [Yadav09].

Regulation has been described [Fern98, Ludwig99, Westermark00, Wyborn04]. hlyE is not expressed at detectable levels [Oscarsson96]. Many pathogenic strains of E. coli contain the hlyE gene, and its expression is controlled by SlyA [Ludwig04]. A mutation in the HU protein that generates positive superhelicity and causes the conversion of E. coli K-12 from commensal to an invasive form, activates the promoter that transcribes the hlyE gene [Koli11].

A crystal structure of the soluble monomer has been solved at 2 Å resolution [Wallace00]. A 3.3 Å crystal structure of a 400kDa dodecameric transmembrane pore formed by hemolysin E has been reported. The structure of the protomer shows substantial rearrangement of the monomer and a mechanism for membrane insertion and pore assembly has been proposed [Mueller09].

Citations: [Roderer14]

Locations: periplasmic space, extracellular space, membrane

Map Position: [1,228,706 <- 1,229,617] (26.48 centisomes, 95°)
Length: 912 bp / 303 aa

Molecular Weight of Polypeptide: 33.758 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003962 , DIP:DIP-9915N , EchoBASE:EB3032 , EcoGene:EG13243 , EcoliWiki:b1182 , Mint:MINT-2737936 , ModBase:P77335 , OU-Microarray:b1182 , PortEco:hlyE , PR:PRO_000022906 , Protein Model Portal:P77335 , RefSeq:NP_415700 , RegulonDB:G6619 , SMR:P77335 , String:511145.b1182 , UniProt:P77335

Relationship Links: InterPro:IN-FAMILY:IPR027018 , PDB:Structure:1QOY , PDB:Structure:2WCD , PDB:Structure:4PHO , PDB:Structure:4PHQ , Pfam:IN-FAMILY:PF06109

Genetic Regulation Schematic: ?

Genetic regulation schematic for hlyE

GO Terms:

Biological Process: GO:0009405 - pathogenesis Inferred from experiment Inferred by computational analysis [GOA01, Lai00]
GO:0044179 - hemolysis in other organism Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, delCastillo97]
GO:0044532 - modulation of apoptotic process in other organism Inferred from experiment [Lai00]
GO:0051715 - cytolysis in other organism Inferred from experiment [Lai00]
GO:0019835 - cytolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0042802 - identical protein binding Inferred from experiment [Eifler06]
Cellular Component: GO:0005576 - extracellular region Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Ludwig99]
GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Ludwig99]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]
GO:0020002 - host cell plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0030288 - outer membrane-bounded periplasmic space [Ludwig99]
GO:0033644 - host cell membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes protection cell killing

Essentiality data for hlyE 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]

Sequence Features

Protein sequence of hemolysin E with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Oscarsson99, Ludwig99, UniProt11]
UniProt: Removed.
Chain 2 -> 303
UniProt: Hemolysin E, chromosomal;
Disulfide-Bond-Site 87, 285
[Atkins00, Wai03, UniProt11]
UniProt: In monomeric form.
Mutagenesis-Variant 88 -> 90
[Oscarsson99, UniProt11]
UniProt: Abolishes cytotoxic activity.
Mutagenesis-Variant 97
[Atkins00, UniProt11]
UniProt: Strongly reduces cytotoxic activity.
Mutagenesis-Variant 143 -> 144
[Oscarsson99, UniProt15]
UniProt: Abolishes cytotoxic activity.
Mutagenesis-Variant 157
[Atkins00, UniProt11]
UniProt: Strongly reduces cytotoxic activity.
Mutagenesis-Variant 165
[Atkins00, UniProt11]
UniProt: Strongly reduces cytotoxic activity.
Extrinsic-Sequence-Variant 175
UniProt: In strain: CH9802..
Mutagenesis-Variant 183 -> 184
[Oscarsson99, UniProt15]
AG → DD: Abolishes cytotoxic activity.
AGVV → missing: In PMWK16; retained in cytosol. Loss of function.
Transmembrane-Region 183 -> 203
UniProt: Helical;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 187 -> 188
[Oscarsson99, UniProt15]
UniProt: Abolishes cytotoxic activity.
Extrinsic-Sequence-Variant 201
UniProt: In strain: CH9802..
Mutagenesis-Variant 261
[Atkins00, UniProt11]
UniProt: Strongly reduces cytotoxic activity.
Mutagenesis-Variant 268
[Oscarsson99, UniProt11]
UniProt: Strongly reduces cytotoxic activity.
Mutagenesis-Variant 293 -> 294
[Oscarsson99, UniProt15]
UniProt: Strongly reduces cytotoxic activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Atkins00: Atkins A, Wyborn NR, Wallace AJ, Stillman TJ, Black LK, Fielding AB, Hisakado M, Artymiuk PJ, Green J (2000). "Structure-function relationships of a novel bacterial toxin, hemolysin E. The role of alpha G." J Biol Chem 275(52);41150-5. PMID: 11006277

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

delCastillo01: del Castillo FJ, Moreno F, del Castillo I (2001). "Secretion of the Escherichia coli K-12 SheA hemolysin is independent of its cytolytic activity." FEMS Microbiol Lett 204(2);281-5. PMID: 11731136

delCastillo97: del Castillo FJ, Leal SC, Moreno F, del Castillo I (1997). "The Escherichia coli K-12 sheA gene encodes a 34-kDa secreted haemolysin." Mol Microbiol 25(1);107-15. PMID: 11902713

Eifler06: Eifler N, Vetsch M, Gregorini M, Ringler P, Chami M, Philippsen A, Fritz A, Muller SA, Glockshuber R, Engel A, Grauschopf U (2006). "Cytotoxin ClyA from Escherichia coli assembles to a 13-meric pore independent of its redox-state." EMBO J 25(11);2652-61. PMID: 16688219

Fern98: Fern?ndez SV, Xing J, Kapur V, Libby SJ, Barletta RG, Moxley RA (1998). "Regulation of the Escherichia coli sheA gene and characterization of its encoded hemolytic activity." FEMS Microbiol Lett 168(1);85-90. PMID: 9812367

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

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

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

Koli11: Koli P, Sudan S, Fitzgerald D, Adhya S, Kar S (2011). "Conversion of commensal Escherichia coli K-12 to an invasive form via expression of a mutant histone-like protein." MBio 2(5). PMID: 21896677

Lai00: Lai XH, Arencibia I, Johansson A, Wai SN, Oscarsson J, Kalfas S, Sundqvist KG, Mizunoe Y, Sj?stedt A, Uhlin BE (2000). "Cytocidal and apoptotic effects of the ClyA protein from Escherichia coli on primary and cultured monocytes and macrophages." Infect Immun 68(7);4363-7. PMID: 10858262

Ludwig04: Ludwig A, von Rhein C, Bauer S, H?ttinger C, Goebel W (2004). "Molecular analysis of cytolysin A (ClyA) in pathogenic Escherichia coli strains." J Bacteriol 186(16);5311-20. PMID: 15292132

Ludwig99: Ludwig A, Bauer S, Benz R, Bergmann B, Goebel W (1999). "Analysis of the SlyA-controlled expression, subcellular localization and pore-forming activity of a 34 kDa haemolysin (ClyA) from Escherichia coli K-12." Mol Microbiol 31(2);557-67. PMID: 10027972

Mueller09: Mueller M, Grauschopf U, Maier T, Glockshuber R, Ban N (2009). "The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism." Nature 459(7247);726-30. PMID: 19421192

Oscarsson96: Oscarsson J, Mizunoe Y, Uhlin BE, Haydon DJ (1996). "Induction of haemolytic activity in Escherichia coli by the slyA gene product." Mol Microbiol 1996;20(1);191-9. PMID: 8861216

Oscarsson99: Oscarsson J, Mizunoe Y, Li L, Lai XH, Wieslander A, Uhlin BE (1999). "Molecular analysis of the cytolytic protein ClyA (SheA) from Escherichia coli." Mol Microbiol 32(6);1226-38. PMID: 10383763

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Roderer14: Roderer D, Benke S, Muller M, Fah-Rechsteiner H, Ban N, Schuler B, Glockshuber R (2014). "Characterization of Variants of the Pore-Forming Toxin ClyA from Escherichia coli Controlled by a Redox Switch." Biochemistry 53(40);6357-69. PMID: 25222267

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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

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

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

Wai03: Wai SN, Lindmark B, S?derblom T, Takade A, Westermark M, Oscarsson J, Jass J, Richter-Dahlfors A, Mizunoe Y, Uhlin BE (2003). "Vesicle-mediated export and assembly of pore-forming oligomers of the enterobacterial ClyA cytotoxin." Cell 115(1);25-35. PMID: 14532000

Wai03a: Wai SN, Westermark M, Oscarsson J, Jass J, Maier E, Benz R, Uhlin BE (2003). "Characterization of dominantly negative mutant ClyA cytotoxin proteins in Escherichia coli." J Bacteriol 185(18);5491-9. PMID: 12949101

Wallace00: Wallace AJ, Stillman TJ, Atkins A, Jamieson SJ, Bullough PA, Green J, Artymiuk PJ (2000). "E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy." Cell 100(2);265-76. PMID: 10660049

Westermark00: Westermark M, Oscarsson J, Mizunoe Y, Urbonaviciene J, Uhlin BE (2000). "Silencing and activation of ClyA cytotoxin expression in Escherichia coli." J Bacteriol 2000;182(22);6347-57. PMID: 11053378

Wyborn04: Wyborn NR, Stapleton MR, Norte VA, Roberts RE, Grafton J, Green J (2004). "Regulation of Escherichia coli hemolysin E expression by H-NS and Salmonella SlyA." J Bacteriol 186(6);1620-8. PMID: 14996792

Yadav09: Yadav SP, Ahmad A, Pandey BK, Singh D, Asthana N, Verma R, Tripathi RK, Ghosh JK (2009). "A peptide derived from the putative transmembrane domain in the tail region of E. coli toxin hemolysin E assembles in phospholipid membrane and exhibits lytic activity to human red blood cells: Plausible implications in the toxic activity of the protein." Biochim Biophys Acta 1788(2);538-50. PMID: 19111524

Other References Related to Gene Regulation

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Lithgow07: Lithgow JK, Haider F, Roberts IS, Green J (2007). "Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12." Mol Microbiol 66(3);685-98. PMID: 17892462

Navarre05: Navarre WW, Halsey TA, Walthers D, Frye J, McClelland M, Potter JL, Kenney LJ, Gunn JS, Fang FC, Libby SJ (2005). "Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ." Mol Microbiol 56(2);492-508. PMID: 15813739

Shi04b: Shi Y, Latifi T, Cromie MJ, Groisman EA (2004). "Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins." J Biol Chem 279(37);38618-25. PMID: 15208313

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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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