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Escherichia coli K-12 substr. MG1655 Polypeptide: flavoprotein involved in biotin synthesis



Gene: mioC Accession Numbers: EG11199 (EcoCyc), b3742, ECK3736

Synonyms: yieB

Regulation Summary Diagram: ?

Summary:
MioC is a flavoprotein (FMN binding) that is necessary for activity of biotin synthase in an in vitro system [Birch00]. MioC is suggested to play a role in electron transport during catalysis of the biotin synthase reaction [Birch00].

MioC, the protein, is not required for wild-type DNA replication at oriC [LobnerOlesen87].

Protein structure is predicted to exhibit an alpha/beta twisted open-sheet fold, based on sequence similarity among flavodoxin family proteins [Grandori94]. Predictions are made regarding the region that interacts with FMN [Grandori94].

Mutations in mioC do not cause defects in cell growth or size, in the amount of DNA or number of origins of DNA replication measured per cell, or in timing of oriC replication initiation [LobnerOlesen92b].

MioC has similarity to flavodoxin family proteins [Grandori94, Birch00].

Purification of MioC is described [Birch00].

Reports differ about whether [LobnerOlesen87, Ogawa91, Zyskind92] or not [Asai90, LobnerOlesen92b, Bates97] transcription originating at the mioC promoter contributes to wild-type DNA replication at oriC. Transcription of mioC has been proposed to inhibit replication initiation [Theisen93, Ogawa94], but other reports indicate that this is not the case [Bogan96]. Differences in replication between chromosomal and plasmid contexts may confuse the integration of interpretations of various experiments [LobnerOlesen92b]. The DnaA binding site (DnaA box) upstream of mioC is involved in DNA replication at oriC [Seufert88, LobnerOlesen87]. Transcription from the mioC promoter crosses oriC [Kolling88].

Regulation has been described [LobnerOlesen87, Chiaramello89, Ogawa91, Theisen93, Ogawa94, Bogan96, Bogan97, Wei01a, Atlung02]. DnaA regulates mioC transcription via an upstream binding site (DnaA box) [LobnerOlesen87]. Transcription from mioC is subject to stringent control [Ogawa91, Zyskind92]. Transcription is decreased at the time of initiation of DNA replication [Theisen93, Ogawa94, Bogan96].

The mioC RNA shows a 1.51 minute half life [Chiaramello89].

Reviews: [Zyskind92].

Gene Citations: [Gielow88]

Locations: cytosol

Map Position: [3,924,035 <- 3,924,478] (84.58 centisomes)
Length: 444 bp / 147 aa

Molecular Weight of Polypeptide: 15.808 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012235 , CGSC:18154 , EchoBASE:EB1185 , EcoGene:EG11199 , EcoliWiki:b3742 , ModBase:P03817 , OU-Microarray:b3742 , PortEco:mioC , PR:PRO_000023240 , Pride:P03817 , Protein Model Portal:P03817 , RefSeq:NP_418198 , RegulonDB:EG11199 , SMR:P03817 , String:511145.b3742 , UniProt:P03817

Relationship Links: InterPro:IN-FAMILY:IPR008254 , PDB:Structure:2HNA , PDB:Structure:2HNB , Pfam:IN-FAMILY:PF00258 , Prosite:IN-FAMILY:PS50902

In Paralogous Gene Group: 187 (14 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009102 - biotin biosynthetic process Inferred from experiment [Birch00]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0010181 - FMN binding Inferred from experiment Inferred by computational analysis [GOA01a, Birch00]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer DNA related DNA replication
metabolism biosynthesis of building blocks cofactors, small molecule carriers biotin

Essentiality data for mioC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Frutiger96, Birch00, UniProt12a]
UniProt: Removed.
Chain 2 -> 147
[UniProt09]
UniProt: Protein mioC;
Conserved-Region 4 -> 143
[UniProt09]
UniProt: Flavodoxin-like;
Sequence-Conflict 56 -> 99
[Hirota81, UniProt10a]
Alternate sequence: THGAGDIPDNLSPFYEALQEQKPDLSAVRFGAIGIGSREYDTFC → PTVPEIFRTTFLLSMKHCRNRSPIFLQSALAQSVLAVVNMTPFV; UniProt: (in Ref. 3; AAA24247);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3742 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11199; confirmed by SwissProt match.


References

Asai90: Asai T, Takanami M, Imai M (1990). "The AT richness and gid transcription determine the left border of the replication origin of the E. coli chromosome." EMBO J 1990;9(12);4065-72. PMID: 2249664

Atlung02: Atlung T, Hansen FG (2002). "Effect of different concentrations of H-NS protein on chromosome replication and the cell cycle in Escherichia coli." J Bacteriol 2002;184(7);1843-50. PMID: 11889089

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bates97: Bates DB, Boye E, Asai T, Kogoma T (1997). "The absence of effect of gid or mioC transcription on the initiation of chromosomal replication in Escherichia coli." Proc Natl Acad Sci U S A 1997;94(23);12497-502. PMID: 9356478

Birch00: Birch OM, Hewitson KS, Fuhrmann M, Burgdorf K, Baldwin JE, Roach PL, Shaw NM (2000). "MioC is an FMN-binding protein that is essential for Escherichia coli biotin synthase activity in vitro." J Biol Chem 2000;275(41);32277-80. PMID: 10913144

Bogan96: Bogan JA, Helmstetter CE (1996). "mioC transcription, initiation of replication, and the eclipse in Escherichia coli." J Bacteriol 1996;178(11);3201-6. PMID: 8655499

Bogan97: Bogan JA, Helmstetter CE (1997). "DNA sequestration and transcription in the oriC region of Escherichia coli." Mol Microbiol 1997;26(5);889-96. PMID: 9426127

Chiaramello89: Chiaramello AE, Zyskind JW (1989). "Expression of Escherichia coli dnaA and mioC genes as a function of growth rate." J Bacteriol 1989;171(8);4272-80. PMID: 2546917

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Frutiger96: Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. (1996). Data submission to UniProtKB on 1996-02.

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gielow88: Gielow A, Kucherer C, Kolling R, Messer W (1988). "Transcription in the region of the replication origin, oriC, of Escherichia coli: termination of asnC transcripts." Mol Gen Genet 214(3);474-81. PMID: 2464126

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Grandori94: Grandori R, Carey J (1994). "Six new candidate members of the alpha/beta twisted open-sheet family detected by sequence similarity to flavodoxin." Protein Sci 3(12);2185-93. PMID: 7756978

Hirota81: Hirota Y, Yamada M, Nishimura A, Oka A, Sugimoto K, Asada K, Takanami M (1981). "The DNA replication origin (ori) of Escherichia coli: structure and function of the ori-containing DNA fragment." Prog Nucleic Acid Res Mol Biol 26;33-48. PMID: 6169112

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kolling88: Kolling R, Gielow A, Seufert W, Kucherer C, Messer W (1988). "AsnC, a multifunctional regulator of genes located around the replication origin of Escherichia coli, oriC." Mol Gen Genet 1988;212(1);99-104. PMID: 2836709

LobnerOlesen87: Lobner-Olesen A, Atlung T, Rasmussen KV (1987). "Stability and replication control of Escherichia coli minichromosomes." J Bacteriol 1987;169(6);2835-42. PMID: 3294807

LobnerOlesen92b: Lobner-Olesen A, Boye E (1992). "Different effects of mioC transcription on initiation of chromosomal and minichromosomal replication in Escherichia coli." Nucleic Acids Res 1992;20(12);3029-36. PMID: 1620598

Ogawa91: Ogawa T, Okazaki T (1991). "Concurrent transcription from the gid and mioC promoters activates replication of an Escherichia coli minichromosome." Mol Gen Genet 1991;230(1-2);193-200. PMID: 1745229

Ogawa94: Ogawa T, Okazaki T (1994). "Cell cycle-dependent transcription from the gid and mioC promoters of Escherichia coli." J Bacteriol 1994;176(6);1609-15. PMID: 8132454

Seufert88: Seufert W, Dobrinski B, Lurz R, Messer W (1988). "Functionality of the dnaA protein binding site in DNA replication is orientation-dependent." J Biol Chem 1988;263(6);2719-23. PMID: 2830261

Theisen93: Theisen PW, Grimwade JE, Leonard AC, Bogan JA, Helmstetter CE (1993). "Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli." Mol Microbiol 1993;10(3);575-84. PMID: 7968535

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wei01a: Wei Y, Lee JM, Smulski DR, LaRossa RA (2001). "Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli." J Bacteriol 2001;183(7);2265-72. PMID: 11244066

Zyskind92: Zyskind JW, Smith DW (1992). "DNA replication, the bacterial cell cycle, and cell growth." Cell 1992;69(1);5-8. PMID: 1555241

Other References Related to Gene Regulation

BenitezPaez12a: Benitez-Paez A, Villarroya M, Armengod ME (2012). "Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase." RNA 18(4);795-806. PMID: 22337945

Eraso14: Eraso JM, Markillie LM, Mitchell HD, Taylor RC, Orr G, Margolin W (2014). "The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli." J Bacteriol 196(11);2053-66. PMID: 24659771

Kolling85: Kolling R, Lother H (1985). "AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli." J Bacteriol 1985;164(1);310-5. PMID: 2864330

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Poggio02: Poggio S, Domeinzain C, Osorio A, Camarena L (2002). "The nitrogen assimilation control (Nac) protein represses asnC and asnA transcription in Escherichia coli." FEMS Microbiol Lett 206(2);151-6. PMID: 11814655

Suzuki03: Suzuki M (2003). "The DNA-binding specificity of eubacterial and archaeal FFRPs. ." Proceedings of the Japan Academy, Series B79B(7); 213-222.

Tobia85: Tobia AJ, Couri D, Sagone A (1985). "The effects of the quinone type drugs on hydroxyl radical (OH.) production by rat liver microsomes." J Toxicol Environ Health 15(2);265-77. PMID: 3925152


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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