RegulonDB

Gene
Name:	tig
Synonym(s):	ECK0430, EG11003, b0436
Genome position(nucleotides):	455133 --> 456431 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.19
External database links:

ASAP:	ABE-0001511
CGSC:	35681
ECHOBASE:	EB0996
OU-MICROARRAY:	b0436
PortEco:	tig
STRING:	511145.b0436
COLOMBOS:	tig

Gene

Name:

tig

Synonym(s):

ECK0430, EG11003, b0436

Genome position(nucleotides):

455133 --> 456431 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

51.19

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

150 -> 246

TWKEKDGAVEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELP

118 -> 118

158 -> 236

VEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAIN

374 -> 387

MASAYEDPKEVIEF

44 -> 46

FRK

Type

Positions

Sequence

150 -> 246

TWKEKDGAVEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELP

118 -> 118

158 -> 236

VEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAIN

374 -> 387

MASAYEDPKEVIEF

44 -> 46

FRK

1 -> 143

MQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYGASVRQDVLGDLMSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVELQGLEAIEVEKPIVEVTDADVDGMLDT

113 -> 149

PEVELQGLEAIEVEKPIVEVTDADVDGMLDTLRKQQA

148 -> 251

QATWKEKDGAVEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELPELTAE

161 -> 246

EDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELP

247 -> 432

ELTAEFIKRFGVEDGSVEGLRAEVRKNMERELKSAIRNRVKSQAIEGLVKANDIDVPAALIDSEIDVLRRQAAQRFGGNEKQALELPRELFEEQAKRRVVVGLLLGEVIRTNELKADEERVKGLIEEMASAYEDPKEVIEFYSKNKELMDNMRNVALEEQAVEAVLAKAKVTEKETTFNELMNQQA

140 -> 140

262 -> 412

SVEGLRAEVRKNMERELKSAIRNRVKSQAIEGLVKANDIDVPAALIDSEIDVLRRQAAQRFGGNEKQALELPRELFEEQAKRRVVVGLLLGEVIRTNELKADEERVKGLIEEMASAYEDPKEVIEFYSKNKELMDNMRNVALEEQAVEAVL

279 -> 287

KSAIRNRVK

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)

5 - cell processes --> 5.1 - cell division

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol

molecular_function

GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0043022 - ribosome binding
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity
GO:0042802 - identical protein binding
GO:0044183 - protein folding chaperone

biological_process

GO:0051301 - cell division
GO:0006457 - protein folding
GO:0007049 - cell cycle
GO:0009408 - response to heat
GO:0015031 - protein transport
GO:0065003 - protein-containing complex assembly
GO:0051083 - 'de novo' cotranslational protein folding
GO:0061077 - chaperone-mediated protein folding
GO:0043335 - protein unfolding
GO:0000413 - protein peptidyl-prolyl isomerization

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_561	454664	forward	nd	[RS-EPT-CBR]	[14]
promoter	tigp	454994	forward	nd	[AIPP], [RS-EPT-CBR]	[14], [15]
promoter	TSS_563	454999	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_564	455004	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_565 (cluster)	455007	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 455007 to 455008, where the highest frequency is at position 454232. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[14]
promoter	TSS_566	455378	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_567	455382	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_568	455792	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_569 (cluster)	456551	forward	For this promoter, there is a cluster of 5 transcription start sites,in the interval 456551 to 456555, where the highest frequency is at position 455778. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[14]
promoter	TSS_570	456560	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_572	456594	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_573	456597	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_575	456643	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_576	457052	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_577 (cluster)	457151	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 457151 to 457152, where the highest frequency is at position 456376. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[14]
promoter	TSS_578	457171	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_580	457296	forward	nd	[RS-EPT-CBR]	[14]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_561

454664

forward

[RS-EPT-CBR]

[14]

promoter

tigp

454994

forward

[AIPP], [RS-EPT-CBR]

[14], [15]

promoter

TSS_563

454999

forward

[RS-EPT-CBR]

[14]

promoter

TSS_564

455004

forward

[RS-EPT-CBR]

[14]

promoter

TSS_565 (cluster)

455007

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[14]

promoter

TSS_566

455378

forward

[RS-EPT-CBR]

[14]

promoter

TSS_567

455382

forward

[RS-EPT-CBR]

[14]

promoter

TSS_568

455792

forward

[RS-EPT-CBR]

[14]

promoter

TSS_569 (cluster)

456551

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[14]

promoter

TSS_570

456560

forward

[RS-EPT-CBR]

[14]

promoter

TSS_572

456594

forward

[RS-EPT-CBR]

[14]

promoter

TSS_573

456597

forward

[RS-EPT-CBR]

[14]

promoter

TSS_575

456643

forward

[RS-EPT-CBR]

[14]

promoter

TSS_576

457052

forward

[RS-EPT-CBR]

[14]

promoter

TSS_577 (cluster)

457151

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[14]

promoter

TSS_578

457171

forward

[RS-EPT-CBR]

[14]

promoter

TSS_580

457296

forward

[RS-EPT-CBR]

[14]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[AIPP] Automated inference of promoter position

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

[AIPP] Automated inference of promoter position

Reference(s)
[1] Crooke E., Brundage L., Rice M., Wickner W., 1988, ProOmpA spontaneously folds in a membrane assembly competent state which trigger factor stabilizes., EMBO J 7(6):1831-5
[2] Eisner G., Moser M., Schafer U., Beck K., Muller M., 2006, Alternate recruitment of signal recognition particle and trigger factor to the signal sequence of a growing nascent polypeptide., J Biol Chem 281(11):7172-9
[3] Kramer G., Rutkowska A., Wegrzyn RD., Patzelt H., Kurz TA., Merz F., Rauch T., Vorderwulbecke S., Deuerling E., Bukau B., 2004, Functional dissection of Escherichia coli trigger factor: unraveling the function of individual domains., J Bacteriol 186(12):3777-84
[4] Lill R., Crooke E., Guthrie B., Wickner W., 1988, The "trigger factor cycle" includes ribosomes, presecretory proteins, and the plasma membrane., Cell 54(7):1013-8
[5] Liu CP., Zhou QM., Fan DJ., Zhou JM., 2010, PPIase domain of trigger factor acts as auxiliary chaperone site to assist the folding of protein substrates bound to the crevice of trigger factor., Int J Biochem Cell Biol 42(6):890-901
[6] Raine A., Ivanova N., Wikberg JE., Ehrenberg M., 2004, Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome., Biochimie 86(7):495-500
[7] Schaffitzel E., Rudiger S., Bukau B., Deuerling E., 2001, Functional dissection of trigger factor and DnaK: interactions with nascent polypeptides and thermally denatured proteins., Biol Chem 382(8):1235-43
[8] Stoller G., Tradler T., Rucknagel KP., Rahfeld J-U., Fischer G., 1996, An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl-prolyl cis/trans isomerase activity., FEBS Lett 384(2):117-22
[9] Teter SA., Houry WA., Ang D., Tradler T., Rockabrand D., Fischer G., Blum P., Georgopoulos C., Hartl FU., 1999, Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains., Cell 97(6):755-65
[10] Ullers RS., Houben EN., Brunner J., Oudega B., Harms N., Luirink J., 2006, Sequence-specific interactions of nascent Escherichia coli polypeptides with trigger factor and signal recognition particle., J Biol Chem 281(20):13999-4005
[11] Ullers RS., Houben EN., Raine A., ten Hagen-Jongman CM., Ehrenberg M., Brunner J., Oudega B., Harms N., Luirink J., 2003, Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome., J Cell Biol 161(4):679-84
[12] Valent QA., de Gier JW., von Heijne G., Kendall DA., ten Hagen-Jongman CM., Oudega B., Luirink J., 1997, Nascent membrane and presecretory proteins synthesized in Escherichia coli associate with signal recognition particle and trigger factor., Mol Microbiol 25(1):53-64
[13] Wasinger VC., Humphery-Smith I., 1998, Small genes/gene-products in Escherichia coli K-12., FEMS Microbiol Lett 169(2):375-82
[14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[15] Aldea M., Garrido T., Hernandez-Chico C., Vicente M., Kushner SR., 1989, Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene., EMBO J 8(12):3923-31

Reference(s)

[1] Crooke E., Brundage L., Rice M., Wickner W., 1988, ProOmpA spontaneously folds in a membrane assembly competent state which trigger factor stabilizes., EMBO J 7(6):1831-5

[2] Eisner G., Moser M., Schafer U., Beck K., Muller M., 2006, Alternate recruitment of signal recognition particle and trigger factor to the signal sequence of a growing nascent polypeptide., J Biol Chem 281(11):7172-9

[3] Kramer G., Rutkowska A., Wegrzyn RD., Patzelt H., Kurz TA., Merz F., Rauch T., Vorderwulbecke S., Deuerling E., Bukau B., 2004, Functional dissection of Escherichia coli trigger factor: unraveling the function of individual domains., J Bacteriol 186(12):3777-84

[4] Lill R., Crooke E., Guthrie B., Wickner W., 1988, The "trigger factor cycle" includes ribosomes, presecretory proteins, and the plasma membrane., Cell 54(7):1013-8

[5] Liu CP., Zhou QM., Fan DJ., Zhou JM., 2010, PPIase domain of trigger factor acts as auxiliary chaperone site to assist the folding of protein substrates bound to the crevice of trigger factor., Int J Biochem Cell Biol 42(6):890-901

[6] Raine A., Ivanova N., Wikberg JE., Ehrenberg M., 2004, Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome., Biochimie 86(7):495-500

[7] Schaffitzel E., Rudiger S., Bukau B., Deuerling E., 2001, Functional dissection of trigger factor and DnaK: interactions with nascent polypeptides and thermally denatured proteins., Biol Chem 382(8):1235-43

[8] Stoller G., Tradler T., Rucknagel KP., Rahfeld J-U., Fischer G., 1996, An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl-prolyl cis/trans isomerase activity., FEBS Lett 384(2):117-22

[9] Teter SA., Houry WA., Ang D., Tradler T., Rockabrand D., Fischer G., Blum P., Georgopoulos C., Hartl FU., 1999, Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains., Cell 97(6):755-65

[10] Ullers RS., Houben EN., Brunner J., Oudega B., Harms N., Luirink J., 2006, Sequence-specific interactions of nascent Escherichia coli polypeptides with trigger factor and signal recognition particle., J Biol Chem 281(20):13999-4005

[11] Ullers RS., Houben EN., Raine A., ten Hagen-Jongman CM., Ehrenberg M., Brunner J., Oudega B., Harms N., Luirink J., 2003, Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome., J Cell Biol 161(4):679-84

[12] Valent QA., de Gier JW., von Heijne G., Kendall DA., ten Hagen-Jongman CM., Oudega B., Luirink J., 1997, Nascent membrane and presecretory proteins synthesized in Escherichia coli associate with signal recognition particle and trigger factor., Mol Microbiol 25(1):53-64

[13] Wasinger VC., Humphery-Smith I., 1998, Small genes/gene-products in Escherichia coli K-12., FEMS Microbiol Lett 169(2):375-82

[14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

[15] Aldea M., Garrido T., Hernandez-Chico C., Vicente M., Kushner SR., 1989, Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene., EMBO J 8(12):3923-31