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P63284 (CLPB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Chaperone protein ClpB
Alternative name(s):
Heat shock protein F84.1
Gene names
Name:clpB
Synonyms:htpM
Ordered Locus Names:b2592, JW2573
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length857 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK. Ref.13 Ref.14 Ref.16

Subunit structure

Homohexamer. The oligomerization is ATP-dependent. Ref.12 Ref.17

Subcellular location

Cytoplasm Ref.10.

Induction

By heat shock and other environmental stresses.

Domain

The N-terminal domain probably functions as a substrate-discriminating domain, recruiting aggregated proteins to the ClpB hexamer and/or stabilizing bound proteins. The NBD2 domain is responsible for oligomerization, whereas the NBD1 domain stabilizes the hexamer probably in an ATP-dependent manner. The movement of the coiled-coil domain is essential for ClpB ability to rescue proteins from an aggregated state, probably by pulling apart large aggregated proteins, which are bound between the coiled-coils motifs of adjacent ClpB subunits in the functional hexamer. Ref.13 Ref.14 Ref.16 Ref.21

Miscellaneous

One peptide binds per ClpB hexamer; the binding site is formed only upon ATP-driven oligomerization.

Sequence similarities

Belongs to the ClpA/ClpB family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself2EBI-546182,EBI-546182
yeeDP330143EBI-546182,EBI-9130839

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]
Isoform ClpB (identifier: P63284-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform ClpB-3 (identifier: P63284-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-148: Missing.
     149-149: V → M
Note: ClpB-3 ATPase activity is not activated by proteins, as it is in ClpB.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 857857Chaperone protein ClpB
PRO_0000005491

Regions

Nucleotide binding206 – 2138ATP 1
Nucleotide binding605 – 6128ATP 2
Region1 – 143143N-terminal
Region159 – 340182NBD1
Region341 – 545205Linker
Region555 – 765211NBD2
Region766 – 85792C-terminal
Coiled coil391 – 525135 By similarity

Amino acid modifications

Modified residue961N6-acetyllysine Ref.23
Modified residue1761N6-acetyllysine Ref.23
Modified residue6401N6-acetyllysine Ref.23

Natural variations

Alternative sequence1 – 148148Missing in isoform ClpB-3.
VSP_018703
Alternative sequence1491V → M in isoform ClpB-3.
VSP_018987

Experimental info

Mutagenesis71T → A: Loss of chaperone activity. Ref.19
Mutagenesis841S → A: No effect. Ref.19
Mutagenesis931L → Q: Loss of chaperone activity. Retains ATPase activity. Ref.25
Mutagenesis971L → Q: 75% decrease in chaperone activity; retains ATPase activity. Ref.25
Mutagenesis1031D → A: Loss of chaperone activity. Ref.19
Mutagenesis1091E → A: Loss of chaperone activity. Ref.19
Mutagenesis1101L → Q: 30% decrease in chaperone activity; retains ATPase activity. Ref.25
Mutagenesis2121K → T: Loss of ability to form oligomers even in the presence of ATP. Loss of chaperone activity. Ref.12 Ref.14 Ref.20
Mutagenesis2511Y → A: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity. Ref.18
Mutagenesis2541E → A: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity; when associated with A-257. Ref.18
Mutagenesis2571E → A: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity; when associated with A-254. Ref.18
Mutagenesis2791E → A: No effect on oligomerization. Ref.14
Mutagenesis3321R → A: Loss of ability to form oligomers. Ref.14
Mutagenesis5431W → F: No effect on chaperone activity or ability to form oligomers. Ref.14
Mutagenesis6111K → T: No effect on ability to form oligomers. Loss of chaperone activity. Ref.12 Ref.14 Ref.20
Mutagenesis6781E → A: No effect on oligomerization. Ref.14
Mutagenesis7561R → A: No effect on oligomerization. Loss of ATPase activity. Ref.14
Mutagenesis7971D → A: No effect. Ref.20
Mutagenesis813 – 8153GAR → AAA: No effect on oligomerization. Ref.14 Ref.20
Mutagenesis8151R → A: Loss of ability to form oligomers; loss of chaperone activity. Ref.20
Mutagenesis8191R → A: Loss of ability to form oligomers; loss of chaperone activity. Ref.20
Mutagenesis8261E → A: No effect. Ref.20
Sequence conflict96 – 972KL → NV in AAA24422. Ref.1
Sequence conflict1221L → V in AAA24422. Ref.1

Secondary structure

............................................................ 857
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform ClpB [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: FD38CD96B2F7C32A

FASTA85795,585
        10         20         30         40         50         60 
MRLDRLTNKF QLALADAQSL ALGHDNQFIE PLHLMSALLN QEGGSVSPLL TSAGINAGQL 

        70         80         90        100        110        120 
RTDINQALNR LPQVEGTGGD VQPSQDLVRV LNLCDKLAQK RGDNFISSEL FVLAALESRG 

       130        140        150        160        170        180 
TLADILKAAG ATTANITQAI EQMRGGESVN DQGAEDQRQA LKKYTIDLTE RAEQGKLDPV 

       190        200        210        220        230        240 
IGRDEEIRRT IQVLQRRTKN NPVLIGEPGV GKTAIVEGLA QRIINGEVPE GLKGRRVLAL 

       250        260        270        280        290        300 
DMGALVAGAK YRGEFEERLK GVLNDLAKQE GNVILFIDEL HTMVGAGKAD GAMDAGNMLK 

       310        320        330        340        350        360 
PALARGELHC VGATTLDEYR QYIEKDAALE RRFQKVFVAE PSVEDTIAIL RGLKERYELH 

       370        380        390        400        410        420 
HHVQITDPAI VAAATLSHRY IADRQLPDKA IDLIDEAASS IRMQIDSKPE ELDRLDRRII 

       430        440        450        460        470        480 
QLKLEQQALM KESDEASKKR LDMLNEELSD KERQYSELEE EWKAEKASLS GTQTIKAELE 

       490        500        510        520        530        540 
QAKIAIEQAR RVGDLARMSE LQYGKIPELE KQLEAATQLE GKTMRLLRNK VTDAEIAEVL 

       550        560        570        580        590        600 
ARWTGIPVSR MMESEREKLL RMEQELHHRV IGQNEAVDAV SNAIRRSRAG LADPNRPIGS 

       610        620        630        640        650        660 
FLFLGPTGVG KTELCKALAN FMFDSDEAMV RIDMSEFMEK HSVSRLVGAP PGYVGYEEGG 

       670        680        690        700        710        720 
YLTEAVRRRP YSVILLDEVE KAHPDVFNIL LQVLDDGRLT DGQGRTVDFR NTVVIMTSNL 

       730        740        750        760        770        780 
GSDLIQERFG ELDYAHMKEL VLGVVSHNFR PEFINRIDEV VVFHPLGEQH IASIAQIQLK 

       790        800        810        820        830        840 
RLYKRLEERG YEIHISDEAL KLLSENGYDP VYGARPLKRA IQQQIENPLA QQILSGELVP 

       850 
GKVIRLEVNE DRIVAVQ 

« Hide

Isoform ClpB-3 [UniParc].

Checksum: 60270862D6198B55
Show »

FASTA70979,870

References

« Hide 'large scale' references
[1]"Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes."
Gottesman S., Squires C., Pichersky E., Carrington M., Hobbs M., Mattick J.S., Dalrymple B., Kuramitsu H., Shiroza T., Foster T., Clark W.P., Ross B., Squires C.L., Maurizi M.R.
Proc. Natl. Acad. Sci. U.S.A. 87:3513-3517(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. expand/collapse author list , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32)."
Kitagawa M., Wada C., Yoshioka S., Yura T.
J. Bacteriol. 173:4247-4253(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-593.
Strain: K12.
[6]"Nucleotide sequence of the rrnG ribosomal RNA promoter region of Escherichia coli."
Shen W.-F., Squires C., Squires C.L.
Nucleic Acids Res. 10:3303-3313(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 753-857.
[7]Ogura T., Tomoyasu T.
Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-31.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]"ClpB proteins copurify with the anaerobic Escherichia coli reductase."
Pontis E., Sun X.Y., Joernvall H., Krook M., Reichard P.
Biochem. Biophys. Res. Commun. 180:1222-1226(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-14; 150-157; 355-364 AND 452-460.
[9]"ClpB is the Escherichia coli heat shock protein F84.1."
Squires C.L., Pedersen S., Ross B.M., Squires C.
J. Bacteriol. 173:4254-4262(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION AS A HEAT SHOCK PROTEIN.
[10]"Site-directed mutagenesis of the dual translational initiation sites of the clpB gene of Escherichia coli and characterization of its gene products."
Park S.K., Kim K.I., Woo K.M., Seol J.H., Tanaka K., Ichihara A., Ha D.B., Chung C.H.
J. Biol. Chem. 268:20170-20174(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: ALTERNATIVE INITIATION, ATPASE ACTIVITY, SUBCELLULAR LOCATION.
[11]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[12]"Heptameric ring structure of the heat-shock protein ClpB, a protein-activated ATPase in Escherichia coli."
Kim K.I., Cheong G.-W., Park S.-C., Ha J.-S., Woo K.M., Choi S.J., Chung C.H.
J. Mol. Biol. 303:655-666(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, MUTAGENESIS OF LYS-212 AND LYS-611.
[13]"Structure and activity of ClpB from Escherichia coli. Role of the amino- and -carboxyl-terminal domains."
Barnett M.E., Zolkiewska A., Zolkiewski M.
J. Biol. Chem. 275:37565-37571(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF DOMAINS.
[14]"Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity."
Mogk A., Schlieker C., Strub C., Rist W., Weibezahn J., Bukau B.
J. Biol. Chem. 278:17615-17624(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF DOMAINS, MUTAGENESIS OF LYS-212; GLU-279; ARG-332; TRP-543; LYS-611; GLU-678; ARG-756 AND 813-GLY--ARG-815.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[15]"Characterization of a trap mutant of the AAA+ chaperone ClpB."
Weibezahn J., Schlieker C., Bukau B., Mogk A.
J. Biol. Chem. 278:32608-32617(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: BINDING TO PROTEIN AGGREGATES, INTERACTION WITH DNAK.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[16]"Structure and function of the middle domain of ClpB from Escherichia coli."
Kedzierska S., Akoev V., Barnett M.E., Zolkiewski M.
Biochemistry 42:14242-14248(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF MIDDLE DOMAIN.
[17]"Nucleotide-induced switch in oligomerization of the AAA+ ATPase ClpB."
Akoev V., Gogol E.P., Barnett M.E., Zolkiewski M.
Protein Sci. 13:567-574(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: OLIGOMERIZATION, NUCLEOTIDE-BINDING.
Strain: K12 / MC1000 / ATCC 39531.
[18]"Substrate recognition by the AAA+ chaperone ClpB."
Schlieker C., Weibezahn J., Patzelt H., Tessarz P., Strub C., Zeth K., Erbse A., Schneider-Mergener J., Chin J.W., Schultz P.G., Bukau B., Mogk A.
Nat. Struct. Mol. Biol. 11:607-615(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBSTRATE-BINDING, MUTAGENESIS OF TYR-251; GLU-254 AND GLU-257.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[19]"Conserved amino acid residues within the amino-terminal domain of ClpB are essential for the chaperone activity."
Liu Z., Tek V., Akoev V., Zolkiewski M.
J. Mol. Biol. 321:111-120(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF THR-7; SER-84; ASP-103 AND GLU-109.
[20]"Site-directed mutagenesis of conserved charged amino acid residues in ClpB from Escherichia coli."
Barnett M.E., Zolkiewski M.
Biochemistry 41:11277-11283(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYS-212; LYS-611; ASP-797; ARG-815; ARG-819 AND GLU-826.
[21]"Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB N-terminal domain."
Li J., Sha B.
Acta Crystallogr. D 57:1933-1935(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION OF N-TERMINAL DOMAIN.
[22]"Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 nucleotide-binding domain 2 (NBD2)."
Li J., Sha B.
Acta Crystallogr. D 58:1030-1031(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION OF NBD2.
[23]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-96; LYS-176 AND LYS-640, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[24]"Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity."
Li J., Sha B.
J. Mol. Biol. 318:1127-1137(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 159-351.
[25]"Crystal structure of the E. coli Hsp100 ClpB N-terminal domain."
Li J., Sha B.
Structure 11:323-328(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 4-142, MUTAGENESIS OF LEU-93; LEU-97 AND LEU-110.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M29364 Genomic DNA. Translation: AAA24422.1.
U00096 Genomic DNA. Translation: AAC75641.1.
AP009048 Genomic DNA. Translation: BAA16476.1.
X57620 Genomic DNA. Translation: CAA40846.1.
V00350 Genomic DNA. Translation: CAA23639.1.
U50134 Genomic DNA. Translation: AAA92959.1.
PIRD35905. C65037.
RefSeqNP_417083.1. NC_000913.3.
YP_490816.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JBKX-ray1.80A159-351[»]
1KHYX-ray1.95A/B/C/D1-148[»]
4CIUX-ray3.50A143-857[»]
ProteinModelPortalP63284.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid851414. 30 interactions.
DIPDIP-35844N.
IntActP63284. 77 interactions.
MINTMINT-1222117.
STRING511145.b2592.

2D gel databases

SWISS-2DPAGEP63284.

Proteomic databases

PaxDbP63284.
PRIDEP63284.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75641; AAC75641; b2592.
BAA16476; BAA16476; BAA16476.
GeneID12931624.
947077.
KEGGecj:Y75_p2541.
eco:b2592.
PATRIC32120587. VBIEscCol129921_2692.

Organism-specific databases

EchoBASEEB0155.
EcoGeneEG10157. clpB.

Phylogenomic databases

eggNOGCOG0542.
HOGENOMHOG000218211.
KOK03695.
OMAGENVNDQ.
OrthoDBEOG65F8SM.
PhylomeDBP63284.

Enzyme and pathway databases

BioCycEcoCyc:EG10157-MONOMER.
ECOL316407:JW2573-MONOMER.
SABIO-RKP63284.

Gene expression databases

GenevestigatorP63284.

Family and domain databases

Gene3D1.10.1780.10. 1 hit.
3.40.50.300. 2 hits.
InterProIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR017730. Chaperonin_ClpB.
IPR019489. Clp_ATPase_C.
IPR004176. Clp_N.
IPR001270. ClpA/B.
IPR018368. ClpA/B_CS1.
IPR028299. ClpA/B_CS2.
IPR023150. Dbl_Clp-N.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF00004. AAA. 1 hit.
PF07724. AAA_2. 1 hit.
PF02861. Clp_N. 2 hits.
PF10431. ClpB_D2-small. 1 hit.
[Graphical view]
PRINTSPR00300. CLPPROTEASEA.
SMARTSM00382. AAA. 2 hits.
SM01086. ClpB_D2-small. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 2 hits.
TIGRFAMsTIGR03346. chaperone_ClpB. 1 hit.
PROSITEPS00870. CLPAB_1. 1 hit.
PS00871. CLPAB_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP63284.
PROP63284.

Entry information

Entry nameCLPB_ECOLI
AccessionPrimary (citable) accession number: P63284
Secondary accession number(s): P03815
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: October 11, 2004
Last modified: July 9, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene