RegulonDB

Gene
Name:	thiI
Synonym(s):	ECK0417, G6238, b0423, nuvA, yajK
Genome position(nucleotides):	441549 --> 442997
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.17
External database links:

ASAP:	ABE-0001470
ECHOBASE:	EB3058
ECOLIHUB:	thiI
OU-MICROARRAY:	b0423
STRING:	511145.b0423
COLOMBOS:	thiI

Gene

Name:

thiI

Synonym(s):

ECK0417, G6238, b0423, nuvA, yajK

Genome position(nucleotides):

441549 --> 442997

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.17

External database links:

ASAP:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

28 -> 161

GNIRNVLKHYDETLAVVRHWDNIEVRAKDENQRLAIRDALTRIPGIHHILEVEDVPFTDMHDIFEKALVQYRDQLEGKTFCVRVKRRGKHDFSSIDVERYVGGGLNQHIESARVKLTNPDVTVHLEVEDDRLLL

61 -> 165

LAIRDALTRIPGIHHILEVEDVPFTDMHDIFEKALVQYRDQLEGKTFCVRVKRRGKHDFSSIDVERYVGGGLNQHIESARVKLTNPDVTVHLEVEDDRLLLIKGR

UniProt: THUMP.

108 -> 108

UniProt: No effect..

175 -> 369

GTQEDVLSLISGGFDSGVSSYMLMRRGCRVHYCFFNLGGAAHEIGVRQVAHYLWNRFGSSHRVRFVAINFEPVVGEILEKIDDGQMGVILKRMMVRAASKVAERYGVQALVTGEALGQVSSQTLTNLRLIDNVSDTLILRPLISYDKEHIINLARQIGTEDFARTMPEYCGVISKSPTVKAVKSKIEAEEEKFDF

183 -> 184

UniProt: ATP.

Type

Positions

Sequence

Comment

28 -> 161

GNIRNVLKHYDETLAVVRHWDNIEVRAKDENQRLAIRDALTRIPGIHHILEVEDVPFTDMHDIFEKALVQYRDQLEGKTFCVRVKRRGKHDFSSIDVERYVGGGLNQHIESARVKLTNPDVTVHLEVEDDRLLL

61 -> 165

LAIRDALTRIPGIHHILEVEDVPFTDMHDIFEKALVQYRDQLEGKTFCVRVKRRGKHDFSSIDVERYVGGGLNQHIESARVKLTNPDVTVHLEVEDDRLLLIKGR

UniProt: THUMP.

108 -> 108

UniProt: No effect..

175 -> 369

GTQEDVLSLISGGFDSGVSSYMLMRRGCRVHYCFFNLGGAAHEIGVRQVAHYLWNRFGSSHRVRFVAINFEPVVGEILEKIDDGQMGVILKRMMVRAASKVAERYGVQALVTGEALGQVSSQTLTNLRLIDNVSDTLILRPLISYDKEHIINLARQIGTEDFARTMPEYCGVISKSPTVKAVKSKIEAEEEKFDF

183 -> 184

UniProt: ATP.

189 -> 189

UniProt: No activity..

202 -> 202

UniProt: No effect..

207 -> 207

UniProt: Enables partial functional complementation in vivo. Four-fold reduction in activity..

321 -> 321

UniProt: Approximately half of wild-type activity..

344 -> 344

UniProt: Cannot functionally complement for wild-type enzyme in vivo. 2700-fold reduction in activity..

404 -> 482

FGPNDVILDIRSIDEQEDKPLKVEGIDVVSLPFYKLSTKFGDLDQNKTWLLWCERGVMSRLQALYLREQGFNNVKVYRP

UniProt: Rhodanese.

456 -> 456

UniProt: No activity..

Multifun Terms (GenProtEC)

1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.8 - thiamin

2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification

Gene Ontology Terms (GO)

cellular_component

GO:1990228 - sulfurtransferase complex
GO:1990221 - L-cysteine desulfurase complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol

molecular_function

GO:0140741 - tRNA U4 sulfurtransferase
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0003723 - RNA binding
GO:0016783 - sulfurtransferase activity
GO:0000049 - tRNA binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004810 - tRNA adenylyltransferase activity
GO:0097163 - sulfur carrier activity

biological_process

GO:0009589 - detection of UV
GO:0009228 - thiamine biosynthetic process
GO:0034227 - tRNA thio-modification
GO:0009229 - thiamine diphosphate biosynthetic process
GO:0052837 - thiazole biosynthetic process
GO:0002937 - tRNA 4-thiouridine biosynthesis
GO:0019448 - L-cysteine catabolic process

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_539	441469		forward	nd	[RS-EPT-CBR]	[18]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_539

441469

forward

[RS-EPT-CBR]

[18]

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] Blondel MO., Favre A., 1988, tRNAPhe and tRNAPro are the near-ultraviolet molecular targets triggering the growth delay effect., Biochem Biophys Res Commun 150(3):979-86
[2] Caldeira de Araujo A., Favre A., 1986, Near ultraviolet DNA damage induces the SOS responses in Escherichia coli., EMBO J 5(1):175-9
[3] Emilsson V., Naslund AK., Kurland CG., 1992, Thiolation of transfer RNA in Escherichia coli varies with growth rate., Nucleic Acids Res 20(17):4499-505
[4] Harris CL., 1990, High-molecular-weight forms of aminoacyl-tRNA synthetases and tRNA modification enzymes in Escherichia coli., J Bacteriol 172(4):1798-803
[5] Harris CL., Kolanko CJ., 1989, A rapid diethylaminoethyl paper disk assay for transfer RNA sulfurtransferase., Anal Biochem 176(1):57-62
[6] Hoerter J., Eisenstark A., 1990, Patterns of protein synthesis in a growth delay mutant (nuv) of Escherichia coli after treatment by near-UV radiation or hydrogen peroxide., J Photochem Photobiol B 6(3):283-9
[7] Kayne MS., LaBone T., 1979, A rapid assay for Escherichia coli 4-thiouridine-tRNA sulfurtransferase., Anal Biochem 98(1):146-53
[8] Kotera M., Bayashi T., Hattori M., Tokimatsu T., Goto S., Mihara H., Kanehisa M., 2010, Comprehensive genomic analysis of sulfur-relay pathway genes., Genome Inform 24:104-15
[9] Lauhon CT., Kambampati R., 2000, The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD., J Biol Chem 275(26):20096-103
[10] Lipsett MN., 1972, Biosynthesis of 4-thiouridylate. Participation of a sulfurtransferase containing pyridoxal 5'-phosphate., J Biol Chem 247(5):1458-61
[11] Oppezzo OJ., Pizarro RA., 2003, Inhibition of sulfur incorporation to transfer RNA by ultraviolet-A radiation in Escherichia coli., J Photochem Photobiol B 71(1-3):69-75
[12] Ryals J., Hsu RY., Lipsett MN., Bremer H., 1982, Isolation of single-site Escherichia coli mutants deficient in thiamine and 4-thiouridine syntheses: identification of a nuvC mutant., J Bacteriol 151(2):899-904
[13] Shi R., Proteau A., Villarroya M., Moukadiri I., Zhang L., Trempe JF., Matte A., Armengod ME., Cygler M., 2010, Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions., PLoS Biol 8(4):e1000354
[14] Shigi N., 2010, [Functions and biosynthesis pathway of sulfur-modifications in tRNA]., Seikagaku 82(7):623-8
[15] Thomas G., Favre A., 1977, [Mutants of Escherichia coli deficient in 4-thiouridine in which growth is insensitive to illumination at 365 nm]., C R Acad Hebd Seances Acad Sci D 284(14):1345-7
[16] Thomas G., Favre A., 1977, [4-Thiouridine and photoprotection in Escherichia coli K 12]., C R Acad Hebd Seances Acad Sci D 284(24):2569-72
[17] Wright CM., Christman GD., Snellinger AM., Johnston MV., Mueller EG., 2006, Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis., Chem Commun (Camb) (29):3104-6
[18] 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] Blondel MO., Favre A., 1988, tRNAPhe and tRNAPro are the near-ultraviolet molecular targets triggering the growth delay effect., Biochem Biophys Res Commun 150(3):979-86

[2] Caldeira de Araujo A., Favre A., 1986, Near ultraviolet DNA damage induces the SOS responses in Escherichia coli., EMBO J 5(1):175-9

[3] Emilsson V., Naslund AK., Kurland CG., 1992, Thiolation of transfer RNA in Escherichia coli varies with growth rate., Nucleic Acids Res 20(17):4499-505

[4] Harris CL., 1990, High-molecular-weight forms of aminoacyl-tRNA synthetases and tRNA modification enzymes in Escherichia coli., J Bacteriol 172(4):1798-803

[5] Harris CL., Kolanko CJ., 1989, A rapid diethylaminoethyl paper disk assay for transfer RNA sulfurtransferase., Anal Biochem 176(1):57-62

[6] Hoerter J., Eisenstark A., 1990, Patterns of protein synthesis in a growth delay mutant (nuv) of Escherichia coli after treatment by near-UV radiation or hydrogen peroxide., J Photochem Photobiol B 6(3):283-9

[7] Kayne MS., LaBone T., 1979, A rapid assay for Escherichia coli 4-thiouridine-tRNA sulfurtransferase., Anal Biochem 98(1):146-53

[8] Kotera M., Bayashi T., Hattori M., Tokimatsu T., Goto S., Mihara H., Kanehisa M., 2010, Comprehensive genomic analysis of sulfur-relay pathway genes., Genome Inform 24:104-15

[9] Lauhon CT., Kambampati R., 2000, The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD., J Biol Chem 275(26):20096-103

[10] Lipsett MN., 1972, Biosynthesis of 4-thiouridylate. Participation of a sulfurtransferase containing pyridoxal 5'-phosphate., J Biol Chem 247(5):1458-61

[11] Oppezzo OJ., Pizarro RA., 2003, Inhibition of sulfur incorporation to transfer RNA by ultraviolet-A radiation in Escherichia coli., J Photochem Photobiol B 71(1-3):69-75

[12] Ryals J., Hsu RY., Lipsett MN., Bremer H., 1982, Isolation of single-site Escherichia coli mutants deficient in thiamine and 4-thiouridine syntheses: identification of a nuvC mutant., J Bacteriol 151(2):899-904

[13] Shi R., Proteau A., Villarroya M., Moukadiri I., Zhang L., Trempe JF., Matte A., Armengod ME., Cygler M., 2010, Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions., PLoS Biol 8(4):e1000354

[14] Shigi N., 2010, [Functions and biosynthesis pathway of sulfur-modifications in tRNA]., Seikagaku 82(7):623-8

[15] Thomas G., Favre A., 1977, [Mutants of Escherichia coli deficient in 4-thiouridine in which growth is insensitive to illumination at 365 nm]., C R Acad Hebd Seances Acad Sci D 284(14):1345-7

[16] Thomas G., Favre A., 1977, [4-Thiouridine and photoprotection in Escherichia coli K 12]., C R Acad Hebd Seances Acad Sci D 284(24):2569-72

[17] Wright CM., Christman GD., Snellinger AM., Johnston MV., Mueller EG., 2006, Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis., Chem Commun (Camb) (29):3104-6

[18] 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.