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Pathway Description
Operon: Ribosomal Protein
Escherichia coli
Category:
Protein Pathway
Sub-Categories:
Gene Regulatory
Cellular Response
Created: 2015-11-03
Last Updated: 2019-11-01
The rpsU-dnaG-rpoD operon in E. coli contains three genes that are involved in protein production and DNA replication. There are no currently known activators of the operon. However, the LexA repressor protein can bind to the promoter region, inhibiting transcription. LexA typically inhibits the transcription of DNA-repair proteins, and in the event of DNA damage indicated by single stranded DNA in the cell, LexA is cleaved, preventing its binding to the promoter and allowing the genes to be transcribed.
The first gene in the operon, rpsU, encodes the 30S ribosomal protein S21, one of the components of the 30S ribosomal subunit.
The second gene in the operon, dnaG, encodes DNA primase, which binds to replicative DNA helicase in the cell. Together, helicase unwinds the double stranded DNA, and DNA primase catalyzes the synthesis RNA primers that are used during DNA replication of the lagging strand, allowing it to be synthesized.
The final gene, rpoD, encodes RNA polymerase sigma 70 (sigma D) factor, which is a subunit of the RNA polymerase sigma 70 protein. This is also known as the housekeeping or primarhy sigma factor, and is used in the transcription of most genes necessary for cellular function. The sigma factor allows specific binding of RNA polymerase to the promoter region of the genes it is responsible for, allowing transcription.
References
Operon: Ribosomal Protein References
Burton Z, Burgess RR, Lin J, Moore D, Holder S, Gross CA: The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889-903.
Pubmed: 6269063
Huerta AM, Collado-Vides J: Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol. 2003 Oct 17;333(2):261-78.
Pubmed: 14529615
Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL: Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA. Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5712-7. doi: 10.1073/pnas.1019383108. Epub 2011 Mar 14.
Pubmed: 21402902
Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P: In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identification of sigmaS-specific promoter sequence elements. Nucleic Acids Res. 2011 Jul;39(13):5338-55. doi: 10.1093/nar/gkr129. Epub 2011 Mar 11.
Pubmed: 21398637
Lupski JR, Smiley BL, Godson GN: Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12. Mol Gen Genet. 1983;189(1):48-57.
Pubmed: 6222240
Nakayama N, Arai N, Bond MW, Kaziro Y, Arai K: Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli. J Biol Chem. 1984 Jan 10;259(1):97-101.
Pubmed: 6323420
Blattner FR, Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL: Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov 25;21(23):5408-17. doi: 10.1093/nar/21.23.5408.
Pubmed: 8265357
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. doi: 10.1126/science.277.5331.1453.
Pubmed: 9278503
Ovchinnikov YA, Monastyrskaya GS, Gubanov VV, Guryev SO, Chertov OYu, Modyanov NN, Grinkevich VA, Makarova IA, Marchenko TV, Polovnikova IN, Lipkin VM, Sverdlov ED: The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit. Eur J Biochem. 1981 Jun 1;116(3):621-9. doi: 10.1111/j.1432-1033.1981.tb05381.x.
Pubmed: 6266829
Meek DW, Hayward RS: Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4? Nucleic Acids Res. 1984 Jul 25;12(14):5813-21. doi: 10.1093/nar/12.14.5813.
Pubmed: 6379605
Igarashi K, Fujita N, Ishihama A: Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase. Nucleic Acids Res. 1990 Oct 25;18(20):5945-8. doi: 10.1093/nar/18.20.5945.
Pubmed: 2235479
Ovchinnikov YA, Lipkin VM, Modyanov NN, Chertov OY, Smirnov YV: Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli. FEBS Lett. 1977 Apr 1;76(1):108-11. doi: 10.1016/0014-5793(77)80131-2.
Pubmed: 323055
Ovchinnikov YuA, Monastyrskaya GS, Gubanov VV, Guryev SO, Salomatina IS, Shuvaeva TM, Lipkin VM, Sverdlov ED: The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit. Nucleic Acids Res. 1982 Jul 10;10(13):4035-44. doi: 10.1093/nar/10.13.4035.
Pubmed: 6287430
Squires C, Krainer A, Barry G, Shen WF, Squires CL: Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC). Nucleic Acids Res. 1981 Dec 21;9(24):6827-40. doi: 10.1093/nar/9.24.6827.
Pubmed: 6278450
Burton Z, Burgess RR, Lin J, Moore D, Holder S, Gross CA: The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889-903. doi: 10.1093/nar/9.12.2889.
Pubmed: 6269063
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. doi: 10.1038/msb4100049. Epub 2006 Feb 21.
Pubmed: 16738553
Horii T, Ogawa T, Ogawa H: Nucleotide sequence of the lexA gene of E. coli. Cell. 1981 Mar;23(3):689-97. doi: 10.1016/0092-8674(81)90432-3.
Pubmed: 7013987
Oertel-Buchheit P, Lamerichs RM, Schnarr M, Granger-Schnarr M: Genetic analysis of the LexA repressor: isolation and characterization of LexA(Def) mutant proteins. Mol Gen Genet. 1990 Aug;223(1):40-8. doi: 10.1007/bf00315795.
Pubmed: 2259342
Miki T, Ebina Y, Kishi F, Nakazawa A: Organization of the lexA gene of Escherichia coli and nucleotide sequence of the regulatory region. Nucleic Acids Res. 1981 Feb 11;9(3):529-43. doi: 10.1093/nar/9.3.529.
Pubmed: 6261224
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