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Escherichia coli K-12 substr. MG1655 Polypeptide: Mlc DNA-binding transcriptional repressor



Gene: mlc Accession Numbers: G6852 (EcoCyc), b1594, ECK1589

Synonyms: dgsA

Regulation Summary Diagram: ?

Component of: DgsA-EII

Summary:
DgsA, better known as Mlc, "makes large colonies," [Hosono95] is a transcriptional dual regulator that controls the expression of a number of genes encoding enzymes of the Escherichia coli phosphotransferase (PTS) and phosphoenolpyruvate (PEP) systems [Plumbridge02, Pradhanang05]. It also regulates genes involved in the uptake of glucose [Plumbridge01]. It is considered a global regulator of carbohydrate metabolism [Decker98, Kimata98]. In addition, Mlc regulates expression of the MalT transcriptional regulator, the activator of the maltose regulon [Decker98].

Mlc repressor function is disabled by binding of Mlc to an actively-transported and dephosphorylated form of PtsG (EIICBGlc) [Lee00, Nam01]. The membrane-bound part of EIICBGlc is essential for Mlc inactivation [Nam01, Seitz03]. Analysis of the crystal structures of the tetrameric Mlc/EIIB complex shows a molecular mechanism of Mlc inactivation by membrane sequestration, in which Mlc loss its DNA binding ability in vivo due to the conformational obstruction by EIIB molecules [Nam08].

The crystal structure of Mlc has been determined [Gerber05, Schiefner05] to 2.85 and 2.7 Å resolution and Mlc in complex with four molecules of enzyme IIBGlc (EIIB) [Nam08] to 2.85 Å resolution. Mlc forms stable dimers and binds to palindromic operator sites. The N-terminal region has a helix-turn-helix domain, and a C-terminal helix is implicated in EIICBGlc binding [Seitz03]. Mlc forms tetramers in solution [Gerber05, Seitz03, Nam01]. The Mlc monomer is composed of three domains: a DNA-binding motif (D-domain), an EIICBGlc-binding motif (E-domain), and an oligomerization domain (O-domain) [Nam08].

Mlc is autoregulated [Decker98, Shin01a], but it is also repressed and activated by CRP [Shin01a]. Mlc binds to sites with a length of 23 bp. Its consensus sequence has been determined [Plumbridge01].

The intracellular concentration of Mlc is very limited [Nam01]. Zinc mediates the Mlc repressor function [Schiefner05]. Mlc has a high homology with the NagC transcriptional dual regulator (40% identity and 80% similarity) [Hosono95, Cho05]. At the post-transcriptional level, Mlc interacts with MtfA, which is involved in the regulation of the ptsG [Becker06].

Mlc is a member of the ROK (repressor, ORFs, kinases) (NagC/XylR) family of proteins, which contains at least two distinct classes of proteins: xylose repressor (XylR) and a series of glucose/fructose kinases [Titgemeyer94, Hansen02a].

Citations: [Plumbridge98b]

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [1,665,368 <- 1,666,588] (35.89 centisomes)
Length: 1221 bp / 406 aa

Molecular Weight of Polypeptide: 44.316 kD (from nucleotide sequence)

pI: 6.03

Unification Links: ASAP:ABE-0005323 , DIP:DIP-10219N , EchoBASE:EB2950 , EcoGene:EG13156 , EcoliWiki:b1594 , ModBase:P50456 , OU-Microarray:b1594 , PortEco:dgsA , PR:PRO_000023242 , Pride:P50456 , Protein Model Portal:P50456 , RefSeq:NP_416111 , RegulonDB:G6852 , SMR:P50456 , String:511145.b1594 , UniProt:P50456

Relationship Links: InterPro:IN-FAMILY:IPR000600 , InterPro:IN-FAMILY:IPR011991 , PDB:Structure:1Z6R , PDB:Structure:3BP8 , Pfam:IN-FAMILY:PF00480 , Prosite:IN-FAMILY:PS01125

In Paralogous Gene Group: 118 (7 members)

In Reactions of unknown directionality:

Not in pathways:
Mlc + EIICBGlc = DgsA-EII

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Decker98]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Plumbridge01]
GO:0005515 - protein binding Inferred from experiment [Gohler12, Becker06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Author statement [Plumbridge02]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of macromolecules (cellular constituents) cytoplasmic polysaccharides
regulation genetic unit regulated global
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 23 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: aTtaTTTcgctgcgcgAAAttaa

Regulated Transcription Units (7 total): ?

Notes:

Essentiality data for mlc 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]

Credits:
Last-Curated ? 04-Apr-2008 by Santos-Zavaleta A , UNAM


Subunit of: DgsA-EII

Subunit composition of DgsA-EII = [Mlc][EIICBGlc]
         Mlc DNA-binding transcriptional repressor = Mlc (extended summary available)

Sequence Length: 406 AAs

In Reactions of unknown directionality:

Not in pathways:
Mlc + EIICBGlc = DgsA-EII

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of macromolecules (cellular constituents) cytoplasmic polysaccharides
regulation genetic unit regulated global
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
DNA-Binding-Region 33 -> 42
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 179
[Hosono95, UniProt10]
Alternate sequence: G → A; UniProt: (in Ref. 1; BAA06978);
Metal-Binding-Site 247
[UniProt10]
UniProt: Zinc;
Mutagenesis-Variant 257
[Schiefner05, UniProt11]
Alternate sequence: C → S; UniProt: Strongly reduced activity.
Alternate sequence: C → A; UniProt: Strongly reduced activity.
Metal-Binding-Site 257
[UniProt10]
UniProt: Zinc;
Mutagenesis-Variant 259
[Schiefner05, UniProt11]
Alternate sequence: C → S; UniProt: Strongly reduced activity.
Alternate sequence: C → A; UniProt: Strongly reduced activity.
Metal-Binding-Site 259
[UniProt10]
UniProt: Zinc;
Metal-Binding-Site 264
[UniProt10]
UniProt: Zinc;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Becker06: Becker AK, Zeppenfeld T, Staab A, Seitz S, Boos W, Morita T, Aiba H, Mahr K, Titgemeyer F, Jahreis K (2006). "YeeI, a Novel Protein Involved in Modulation of the Activity of the Glucose-Phosphotransferase System in Escherichia coli K-12." J Bacteriol 188(15);5439-49. PMID: 16855233

Cho05: Cho S, Shin D, Ji GE, Heu S, Ryu S (2005). "High-level recombinant protein production by overexpression of Mlc in Escherichia coli." J Biotechnol 119(2);197-203. PMID: 15916829

Decker98: Decker K, Plumbridge J, Boos W (1998). "Negative transcriptional regulation of a positive regulator: the expression of malT, encoding the transcriptional activator of the maltose regulon of Escherichia coli, is negatively controlled by Mlc." Mol Microbiol 1998;27(2);381-90. PMID: 9484893

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

Gerber05: Gerber K, Boos W, Welte W, Schiefner A (2005). "Crystallization and preliminary X-ray analysis of Mlc from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 61(Pt 2);183-5. PMID: 16510988

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

Gohler12: Gohler AK, Staab A, Gabor E, Homann K, Klang E, Kosfeld A, Muus JE, Wulftange JS, Jahreis K (2012). "Characterization of MtfA, a novel regulatory output signal protein of the glucose-phosphotransferase system in Escherichia coli K-12." J Bacteriol 194(5);1024-35. PMID: 22178967

Hansen02a: Hansen T, Reichstein B, Schmid R, Schonheit P (2002). "The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity." J Bacteriol 184(21);5955-65. PMID: 12374829

Hosono95: Hosono K, Kakuda H, Ichihara S (1995). "Decreasing accumulation of acetate in a rich medium by Escherichia coli on introduction of genes on a multicopy plasmid." Biosci Biotechnol Biochem 59(2);256-61. PMID: 7766024

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

Kim99a: Kim SY, Nam TW, Shin D, Koo BM, Seok YJ, Ryu S (1999). "Purification of Mlc and analysis of its effects on the pts expression in Escherichia coli." J Biol Chem 1999;274(36);25398-402. PMID: 10464268

Kimata98: Kimata K, Inada T, Tagami H, Aiba H (1998). "A global repressor (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli." Mol Microbiol 29(6);1509-19. PMID: 9781886

Lee00: Lee SJ, Boos W, Bouche JP, Plumbridge J (2000). "Signal transduction between a membrane-bound transporter, PtsG, and a soluble transcription factor, Mlc, of Escherichia coli." EMBO J 19(20);5353-61. PMID: 11032803

Nam01: Nam TW, Cho SH, Shin D, Kim JH, Jeong JY, Lee JH, Roe JH, Peterkofsky A, Kang SO, Ryu S, Seok YJ (2001). "The Escherichia coli glucose transporter enzyme IICB(Glc) recruits the global repressor Mlc." EMBO J 20(3);491-8. PMID: 11157755

Nam08: Nam TW, Jung HI, An YJ, Park YH, Lee SH, Seok YJ, Cha SS (2008). "Analyses of Mlc-IIBGlc interaction and a plausible molecular mechanism of Mlc inactivation by membrane sequestration." Proc Natl Acad Sci U S A 105(10);3751-6. PMID: 18319344

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Plumbridge01: Plumbridge J (2001). "DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli." Nucleic Acids Res 29(2);506-14. PMID: 11139621

Plumbridge02: Plumbridge J (2002). "Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc." Curr Opin Microbiol 5(2);187-93. PMID: 11934616

Plumbridge98: Plumbridge J (1998). "Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose." Mol Microbiol 1998;29(4);1053-63. PMID: 9767573

Plumbridge98b: Plumbridge J (1998). "Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS." Mol Microbiol 1998;27(2);369-80. PMID: 9484892

Pradhanang05: Pradhanang V, Ghimire S (2005). "Hirsutism: a rare presentation of an adult granulosa cell tumor of ovary." Nepal Med Coll J 7(2);152-4. PMID: 16519088

Schiefner05: Schiefner A, Gerber K, Seitz S, Welte W, Diederichs K, Boos W (2005). "The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli." J Biol Chem 280(32);29073-9. PMID: 15929984

Seitz03: Seitz S, Lee SJ, Pennetier C, Boos W, Plumbridge J (2003). "Analysis of the interaction between the global regulator Mlc and EIIBGlc of the glucose-specific phosphotransferase system in Escherichia coli." J Biol Chem 278(12);10744-51. PMID: 12529317

Shin01a: Shin D, Lim S, Seok YJ, Ryu S (2001). "Heat shock RNA polymerase (E sigma(32)) is involved in the transcription of mlc and crucial for induction of the Mlc regulon by glucose in Escherichia coli." J Biol Chem 276(28);25871-5. PMID: 11340070

Tanaka99: Tanaka Y, Kimata K, Inada T, Tagami H, Aiba H (1999). "Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli." Genes Cells 4(7);391-9. PMID: 10469172

Titgemeyer94: Titgemeyer F, Reizer J, Reizer A, Saier MH (1994). "Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria." Microbiology 140 ( Pt 9);2349-54. PMID: 7952186

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

Other References Related to Gene Regulation

Jiang01a: Jiang GR, Nikolova S, Clark DP (2001). "Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli." Microbiology 147(Pt 9);2437-46. PMID: 11535784

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Dec 17, 2014, biocyc13.