RegulonDB

Gene
Name:	secE
Synonym(s):	ECK3972, EG10939, b3981, mbrC, prlG
Genome position(nucleotides):	4177358 --> 4177741
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.95
External database links:

ASAP:	ABE-0013023
CGSC:	34108
ECHOBASE:	EB0932
ECOLIHUB:	secE
OU-MICROARRAY:	b3981
STRING:	511145.b3981
COLOMBOS:	secE

Gene

Name:

secE

Synonym(s):

ECK3972, EG10939, b3981, mbrC, prlG

Genome position(nucleotides):

4177358 --> 4177741

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.95

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

1 -> 18

MSANTEAQGSGRGLEAMK

N-terminal cytoplasmic domain

20 -> 32

VVVVALLLVAIVG

UniProt: Helical.

37 -> 45

RDIMLPLRA

periplasmic domain

49 -> 60

VILIAAAGGVAL

UniProt: Helical.

64 -> 93

KGKATVAFAREARTEVRKVIWPTRQETLHT

cytoplasmic loop

Type

Positions

Sequence

Comment

1 -> 18

MSANTEAQGSGRGLEAMK

N-terminal cytoplasmic domain

20 -> 32

VVVVALLLVAIVG

UniProt: Helical.

37 -> 45

RDIMLPLRA

periplasmic domain

49 -> 60

VILIAAAGGVAL

UniProt: Helical.

64 -> 93

KGKATVAFAREARTEVRKVIWPTRQETLHT

cytoplasmic loop

70 -> 122

AFAREARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFI

78 -> 78

E → A: growth defect in minimal media at 30°C; eliminates coimmunoprecipitation of SecY; E →P: growth defect in minimal media and rich media at 30°C

81 -> 81

K → A: growth defect in minimal media at 30°C plus defect in protein secretion; K →G: growth defect in minimal media at 30°C

85 -> 85

P → V: growth defect in minimal media at 30°C

98 -> 115

AAVTAVMSLILWGLDGIL

UniProt: Helical.

105 -> 105

S → P: PrlG phenotype; suppressor of mutant signal sequence

108 -> 108

L → R: PrlG phenotype; suppressor of mutant signal sequence

112 -> 112

D → P: defect in protein secretion

118 -> 118

L → M: growth defect in minimal media at 30°C plus defect in protein secretion

120 -> 120

UniProt: Massive ion flux when cross-linked to SecY C-67 mutation..

Multifun Terms (GenProtEC)

4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.5 - The Type II (General) Secretory Pathway (IISP) Family

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
GO:0031522 - cell envelope Sec protein transport complex

molecular_function

GO:0005515 - protein binding
GO:0008320 - protein transmembrane transporter activity

biological_process

GO:0015031 - protein transport
GO:0006605 - protein targeting
GO:0006886 - intracellular protein transport
GO:0009306 - protein secretion
GO:0065002 - intracellular protein transmembrane transport
GO:0032978 - protein insertion into membrane from inner side
GO:0043952 - protein transport by the Sec complex
GO:0006616 - SRP-dependent cotranslational protein targeting to membrane, translocation

RNA cis-regulatory element

Attenuation:	Transcriptional

RNA cis-regulatory element

Attenuation:

Transcriptional

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_4709 (cluster)	4175958	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4710	4175968	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4711	4176116	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4712	4176325	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4713	4176332	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4714	4176429	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4715	4176443	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4716	4176445	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4717	4176452	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4718 (cluster)	4176586	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4719	4176591	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4720 (cluster)	4176593	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4721	4176597	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4722 (cluster)	4176659	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4723 (cluster)	4176669	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4724	4176704	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4725	4176727	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4726	4176739	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4727	4176975	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4728	4177213	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4729 (cluster)	4177243	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4730	4177246	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4731 (cluster)	4177278	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4732 (cluster)	4177295	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4733 (cluster)	4177301	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4734 (cluster)	4177329	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4735	4177340	forward	nd	[RS-EPT-CBR]	[13]
promoter	TSS_4736	4177443	reverse	nd	[RS-EPT-CBR]	[13]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_4709 (cluster)

4175958

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4710

4175968

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4711

4176116

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4712

4176325

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4713

4176332

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4714

4176429

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4715

4176443

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4716

4176445

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4717

4176452

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4718 (cluster)

4176586

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4719

4176591

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4720 (cluster)

4176593

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4721

4176597

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4722 (cluster)

4176659

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4723 (cluster)

4176669

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4724

4176704

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4725

4176727

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4726

4176739

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4727

4176975

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4728

4177213

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4729 (cluster)

4177243

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4730

4177246

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4731 (cluster)

4177278

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4732 (cluster)

4177295

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4733 (cluster)

4177301

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4734 (cluster)

4177329

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4735

4177340

forward

[RS-EPT-CBR]

[13]

promoter

TSS_4736

4177443

reverse

[RS-EPT-CBR]

[13]

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

Evidence

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

Reference(s)
[1] Baars L., Wagner S., Wickstrom D., Klepsch M., Ytterberg AJ., van Wijk KJ., de Gier JW., 2008, Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli., J Bacteriol 190(10):3505-25
[2] Bieker KL., Silhavy TJ., 1990, PrlA (SecY) and PrlG (SecE) interact directly and function sequentially during protein translocation in E. coli., Cell 61(5):833-42
[3] Flower AM., Doebele RC., Silhavy TJ., 1994, PrlA and PrlG suppressors reduce the requirement for signal sequence recognition., J Bacteriol 176(18):5607-14
[4] Flower AM., Osborne RS., Silhavy TJ., 1995, The allele-specific synthetic lethality of prlA-prlG double mutants predicts interactive domains of SecY and SecE., EMBO J 14(5):884-93
[5] Kaufmann A., Manting EH., Veenendaal AK., Driessen AJ., van der Does C., 1999, Cysteine-directed cross-linking demonstrates that helix 3 of SecE is close to helix 2 of SecY and helix 3 of a neighboring SecE., Biochemistry 38(28):9115-25
[6] Kontinen VP., Yamanaka M., Nishiyama K., Tokuda H., 1996, Roles of the conserved cytoplasmic region and non-conserved carboxy-terminal region of SecE in Escherichia coli protein translocase., J Biochem 119(6):1124-30
[7] Matsuyama S., Akimaru J., Mizushima S., 1990, SecE-dependent overproduction of SecY in Escherichia coli. Evidence for interaction between two components of the secretory machinery., FEBS Lett 269(1):96-100
[8] Murphy CK., Beckwith J., 1994, Residues essential for the function of SecE, a membrane component of the Escherichia coli secretion apparatus, are located in a conserved cytoplasmic region., Proc Natl Acad Sci U S A 91(7):2557-61
[9] Nishiyama K., Mizushima S., Tokuda H., 1995, Preferential interaction of Sec-G with Sec-E stabilizes an unstable Sec-E derivative in the Escherichia coli cytoplasmic membrane., Biochem Biophys Res Commun 217(1):217-23
[10] Pohlschroder M., Murphy C., Beckwith J., 1996, In vivo analyses of interactions between SecE and SecY, core components of the Escherichia coli protein translocation machinery., J Biol Chem 271(33):19908-14
[11] Svanberg Frisinger F., Jana B., Donadio S., Guardabassi L., 2021, In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli., Antibiotics (Basel) 10(6)
[12] Veenendaal AK., Van Der Does C., Driessen AJ., 2002, The core of the bacterial translocase harbors a tilted transmembrane segment 3 of SecE., J Biol Chem 277(39):36640-5
[13] 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.

Reference(s)

[1] Baars L., Wagner S., Wickstrom D., Klepsch M., Ytterberg AJ., van Wijk KJ., de Gier JW., 2008, Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli., J Bacteriol 190(10):3505-25

[2] Bieker KL., Silhavy TJ., 1990, PrlA (SecY) and PrlG (SecE) interact directly and function sequentially during protein translocation in E. coli., Cell 61(5):833-42

[3] Flower AM., Doebele RC., Silhavy TJ., 1994, PrlA and PrlG suppressors reduce the requirement for signal sequence recognition., J Bacteriol 176(18):5607-14

[4] Flower AM., Osborne RS., Silhavy TJ., 1995, The allele-specific synthetic lethality of prlA-prlG double mutants predicts interactive domains of SecY and SecE., EMBO J 14(5):884-93

[5] Kaufmann A., Manting EH., Veenendaal AK., Driessen AJ., van der Does C., 1999, Cysteine-directed cross-linking demonstrates that helix 3 of SecE is close to helix 2 of SecY and helix 3 of a neighboring SecE., Biochemistry 38(28):9115-25

[6] Kontinen VP., Yamanaka M., Nishiyama K., Tokuda H., 1996, Roles of the conserved cytoplasmic region and non-conserved carboxy-terminal region of SecE in Escherichia coli protein translocase., J Biochem 119(6):1124-30

[7] Matsuyama S., Akimaru J., Mizushima S., 1990, SecE-dependent overproduction of SecY in Escherichia coli. Evidence for interaction between two components of the secretory machinery., FEBS Lett 269(1):96-100

[8] Murphy CK., Beckwith J., 1994, Residues essential for the function of SecE, a membrane component of the Escherichia coli secretion apparatus, are located in a conserved cytoplasmic region., Proc Natl Acad Sci U S A 91(7):2557-61

[9] Nishiyama K., Mizushima S., Tokuda H., 1995, Preferential interaction of Sec-G with Sec-E stabilizes an unstable Sec-E derivative in the Escherichia coli cytoplasmic membrane., Biochem Biophys Res Commun 217(1):217-23

[10] Pohlschroder M., Murphy C., Beckwith J., 1996, In vivo analyses of interactions between SecE and SecY, core components of the Escherichia coli protein translocation machinery., J Biol Chem 271(33):19908-14

[11] Svanberg Frisinger F., Jana B., Donadio S., Guardabassi L., 2021, In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli., Antibiotics (Basel) 10(6)

[12] Veenendaal AK., Van Der Does C., Driessen AJ., 2002, The core of the bacterial translocase harbors a tilted transmembrane segment 3 of SecE., J Biol Chem 277(39):36640-5

[13] 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.