EG11897

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Author Information

Max Kucera

Basic Information

  • ID: EG11897
  • Name: rpoE
  • Organism: E. coli
  • Description: Sigma E is a minor sigma factor, specializing in responses to the effects of heat shock and other stresses on membrane and periplasmic proteins. It is regulated by a multistep protease system that sense disruptions in those proteins. Its transcriptional initiation targets include another minor sigma factor, Sigma 32. Furthermore, Sigma E drives transcription of a number of genes whose functions are similar and deal with heat shock.[1] [2]
  • DNA Length: 576
  • DNA sequence:

atgAGCGAGC AGTTAACGGA CCAGGTCCTG GTTGAACGGG TCCAGAAGGG AGATCAGAAA GCCTTTAACT TACTGGTAGT GCGCTATCAG CATAAAGTGG CGAGTCTGGT TTCCCGCTAT GTGCCGTCGG GTGATGTTCC CGATGTGGTA CAAGAAGCTT TTATTAAAGC CTATCGTGCG CTGGATTCGT TCCGGGGAGA TAGCGCTTTT TATACATGGC TGTATCGGAT TGCTGTAAAT ACAGCGAAAA ATTACCTGGT TGCTCAGGGG CGTCGTCCAC CTTCCAGTGA TGTGGATGCC ATTGAAGCTG AAAACTTCGA AAGTGGCGGC GCGTTGAAAG AAATTTCGAA CCCTGAGAAC TTAATGTTGT CAGAAGAACT GAGACAGATA GTTTTCCGAA CTATTGAGTC CCTCCCGGAA GATTTACGCA TGGCAATAAC CTTGCGGGAG CTGGATGGCC TGAGCTATGA AGAGATAGCC GCTATCATGG ATTGTCCGGT AGGTACGGTG CGTTCACGTA TCTTCCGAGC GAGGGAAGCT ATTGATAACA AAGTTCAACC GCTTATCAGG CGTtga

  • Amino Acid length: 192
  • Amino Acid sequence:

MSEQLTDQVL VERVQKGDQK AFNLLVVRYQ HKVASLVSRY VPSGDVPDVV QEAFIKAYRA LDSFRGDSAF YTWLYRIAVN TAKNYLVAQG RRPPSSDVDA IEAENFESGG ALKEISNPEN LMLSEELRQI VFRTIESLPE DLRMAITLRE LDGLSYEEIA AIMDCPVGTV RSRIFRAREA IDNKVQPLIR R

Function and Homologs

  • Product: RNA polymerase, sigma 24 (sigma E) factor
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: ECF RNA polymerase sigma-E factor [Proteobacteria], 389/100%/4e-137/100%, [1]
    • MULTISPECIES: ECF RNA polymerase sigma-E factor [Gammaproteobacteria], 388/100%/1e-136/99%, [2]
    • MULTISPECIES: ECF RNA polymerase sigma-E factor [Enterobacteriaceae], 388/100%/2e-136/99%, [3]
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0128

Expression

  • Expression Level: [medium]
  • Expression Level Hypothesis: This gene is used in heat shock in cell membranes. The JCVI equivalent occurred in high frequency while this e-coli equivalent occurs at a medium frequency. This might be because relatively the e-coli cells do not need to be as protected from overheating than other cells need to be.
  • Expression Level References and Description: I found out that the protein is produced a lot at 565 proteins/cell through the File:EcoliProteomicExpressionData.xlsx [3] I learned about the cells function from the ecocyc database. [4]
  • Expression Time: [early]
  • Expression Level Hypothesis: This gene helps regulate the transcription of heat shock proteins. This happens during the growth of the cell and is a crucial part of the central dogma components so it happens early on in the process.
  • Expression Time References and Description: First I looked into the different components of the cell cycle to determine when the transcription takes places. I also used the ecocyc page of the gene to see how it interacts with the cell process as a whole. [5] [6]

Gene Context

  • Other Components: EG10894
  • Possible Dependencies: This gene initiates the transcription of peptidyl-prolyl cis-trans isomerase FkpA [[4]]. The FkpA also acts as a chaperone to the periplasm, so without this gene, our RNA would not be able to carry out its regulation of the transcription. [7]
  • Process: RNA Polymerase, transcription [8]
    • Inputs: DNA
    • Outputs: mRNA

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • http://www.uniprot.org/uniprot/B7MIQ8
  • http://e80boot.org/index.php?title=File:EcoliProteomicExpressionData.xlsx
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • http://www.atdbio.com/content/14/Transcription-Translation-and-Replication
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • Retrieved from "http://e80boot.org/index.php?title=EG11897&oldid=11824"