RegulonDB

Gene
Name:	lepA
Synonym(s):	ECK2567, EG10529, b2569
Genome position(nucleotides):	2705325 <-- 2707124 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.72
External database links:

ASAP:	ABE-0008452
CGSC:	18199
ECHOBASE:	EB0524
OU-MICROARRAY:	b2569
PortEco:	lepA
STRING:	511145.b2569
COLOMBOS:	lepA

Gene

Name:

lepA

Synonym(s):

ECK2567, EG10529, b2569

Genome position(nucleotides):

2705325 <-- 2707124 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.72

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

156 -> 185

TDAVRCSAKTGVGVQDVLERLVRDIPPPEG

487 -> 592

INGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQLRKNVLAKCYGGDISRKKKLLQKQKEGKKRMKQIGNVELPQEAFLAIL

2 -> 181

KNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIP

399 -> 482

LREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVR

266 -> 266

Type

Positions

Sequence

156 -> 185

TDAVRCSAKTGVGVQDVLERLVRDIPPPEG

487 -> 592

INGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQLRKNVLAKCYGGDISRKKKLLQKQKEGKKRMKQIGNVELPQEAFLAIL

2 -> 181

KNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIP

399 -> 482

LREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVR

266 -> 266

14 -> 19

DHGKST

81 -> 81

131 -> 134

NKID

205 -> 275

GVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELKCGEVGWLVCAIKDIHGAPVGDTLT

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation

5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes

5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane

molecular_function

GO:0003746 - translation elongation factor activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0043022 - ribosome binding
GO:0000166 - nucleotide binding
GO:0003924 - GTPase activity
GO:0005525 - GTP binding
GO:0042802 - identical protein binding
GO:0043023 - ribosomal large subunit binding
GO:0043024 - ribosomal small subunit binding
GO:0097216 - guanosine tetraphosphate binding

biological_process

GO:0006412 - translation
GO:0006414 - translational elongation
GO:0009409 - response to cold
GO:0009268 - response to pH
GO:0009651 - response to salt stress
GO:0042274 - ribosomal small subunit biogenesis
GO:0045727 - positive regulation of translation

RNA cis-regulatory element

Attenuation:	Transcriptional

RNA cis-regulatory element

Attenuation:

Transcriptional

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	lepBp1	2705464	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -2.87. P-value: 6.443e-5 Read more >	[ICWHO]	[10]
promoter	TSS_2866	2706051	reverse	nd	[RS-EPT-CBR]	[11]
promoter	TSS_2867	2707204	reverse	nd	[RS-EPT-CBR]	[11]
promoter	TSS_2868 (cluster)	2707211	reverse	For this promoter, there is a cluster of 4 transcription start sites,in the interval 2707208 to 2707211, where the highest frequency is at position 2705232. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[11]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

lepBp1

2705464

reverse

Similarity to the consensus
Read more >

[ICWHO]

[10]

promoter

TSS_2866

2706051

reverse

[RS-EPT-CBR]

[11]

promoter

TSS_2867

2707204

reverse

[RS-EPT-CBR]

[11]

promoter

TSS_2868 (cluster)

2707211

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[11]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[ICWHO] Inferred computationally without human oversight

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

Reference(s)
[1] Gibbs MR., Moon KM., Chen M., Balakrishnan R., Foster LJ., Fredrick K., 2017, Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome., Proc Natl Acad Sci U S A 114(5):980-985
[2] Liu H., Chen C., Zhang H., Kaur J., Goldman YE., Cooperman BS., 2011, The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis., Proc Natl Acad Sci U S A 108(39):16223-8
[3] Liu H., Pan D., Pech M., Cooperman BS., 2010, Interrupted catalysis: the EF4 (LepA) effect on back-translocation., J Mol Biol 396(4):1043-52
[4] Pech M., Karim Z., Yamamoto H., Kitakawa M., Qin Y., Nierhaus KH., 2011, Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations., Proc Natl Acad Sci U S A 108(8):3199-203
[5] Qin Y., Polacek N., Vesper O., Staub E., Einfeldt E., Wilson DN., Nierhaus KH., 2006, The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome., Cell 127(4):721-33
[6] Sergiev PV., Golovina AY., Sergeeva OV., Osterman IA., Nesterchuk MV., Bogdanov AA., Dontsova OA., 2012, How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?, Nucleic Acids Res 40(12):5694-705
[7] Woolstenhulme CJ., Parajuli S., Healey DW., Valverde DP., Petersen EN., Starosta AL., Guydosh NR., Johnson WE., Wilson DN., Buskirk AR., 2013, Nascent peptides that block protein synthesis in bacteria., Proc Natl Acad Sci U S A 110(10):E878-87
[8] Xie P., 2013, Dynamics of forward and backward translocation of mRNA in the ribosome., PLoS One 8(8):e70789
[9] Zhang D., Liu G., Xue J., Lou J., Nierhaus KH., Gong W., Qin Y., 2012, Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome., Nucleic Acids Res 40(21):10851-65
[10] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[11] 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] Gibbs MR., Moon KM., Chen M., Balakrishnan R., Foster LJ., Fredrick K., 2017, Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome., Proc Natl Acad Sci U S A 114(5):980-985

[2] Liu H., Chen C., Zhang H., Kaur J., Goldman YE., Cooperman BS., 2011, The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis., Proc Natl Acad Sci U S A 108(39):16223-8

[3] Liu H., Pan D., Pech M., Cooperman BS., 2010, Interrupted catalysis: the EF4 (LepA) effect on back-translocation., J Mol Biol 396(4):1043-52

[4] Pech M., Karim Z., Yamamoto H., Kitakawa M., Qin Y., Nierhaus KH., 2011, Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations., Proc Natl Acad Sci U S A 108(8):3199-203

[5] Qin Y., Polacek N., Vesper O., Staub E., Einfeldt E., Wilson DN., Nierhaus KH., 2006, The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome., Cell 127(4):721-33

[6] Sergiev PV., Golovina AY., Sergeeva OV., Osterman IA., Nesterchuk MV., Bogdanov AA., Dontsova OA., 2012, How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?, Nucleic Acids Res 40(12):5694-705

[7] Woolstenhulme CJ., Parajuli S., Healey DW., Valverde DP., Petersen EN., Starosta AL., Guydosh NR., Johnson WE., Wilson DN., Buskirk AR., 2013, Nascent peptides that block protein synthesis in bacteria., Proc Natl Acad Sci U S A 110(10):E878-87

[8] Xie P., 2013, Dynamics of forward and backward translocation of mRNA in the ribosome., PLoS One 8(8):e70789

[9] Zhang D., Liu G., Xue J., Lou J., Nierhaus KH., Gong W., Qin Y., 2012, Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome., Nucleic Acids Res 40(21):10851-65

[10] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[11] 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.