EC maynardl FNR

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Author Information

Lucy Maynard

Basic Information

  • ID: EG10325
  • Name: FNR
  • Organism: E. coli
  • UniProt ID: [1]
  • Description: This gene encodes for fumarate and nitrogen reductase, a DNA-binding transcriptional activator that influences the expression of almost 300 identified genes [1] . This enzyme mediates the transition between aerobic and anaerobic respiration and growth, and represses aerobic activity in favor of anaerobic processes. [2]. FNR is also involved in many other cellular pathways and processes, including acid resistance, chemotaxis, cell structure, and molecular biosynthesis [3].

I would be interested in collaborating with another student to incorporate FNR binding sites in the DNA sequence upstream of their assigned gene. Ideally this gene should be considered highly important to cell life, and 'worthy' of transcriptional enhancement. In E.coli, FNR is regulated by interconversion between active and inactive forms.

  • DNA Length: 753 base pairs.
  • DNA sequence:

ATGATCCCGGAAAAGCGAATTATACGGCGCATTCAGTCTGGCGGTTGTGCTATCCATTGCCAGGATTGCA GCATCAGCCAGCTTTGCATCCCGTTCACACTCAACGAACATGAGCTTGATCAGCTTGATAATATCATTGA GCGGAAGAAGCCTATTCAGAAAGGCCAGACGCTGTTTAAGGCTGGTGATGAACTTAAATCGCTTTATGCC ATCCGCTCCGGTACGATTAAAAGTTATACCATCACTGAGCAAGGCGACGAGCAAATCACTGGTTTCCATT TAGCAGGCGACCTGGTGGGATTTGACGCCATCGGCAGCGGCCATCACCCGAGCTTCGCGCAGGCGCTGGA AACCTCGATGGTATGTGAAATCCCGTTCGAAACGCTGGACGATTTGTCCGGTAAAATGCCGAATCTGCGT CAGCAGATGATGCGTCTGATGAGCGGTGAAATCAAAGGCGATCAGGACATGATCCTGCTGTTGTCGAAGA AAAATGCCGAGGAACGTCTGGCTGCATTCATCTACAACCTGTCCCGTCGTTTTGCCCAACGCGGCTTCTC CCCTCGTGAATTCCGCCTGACGATGACTCGTGGCGATATCGGTAACTATCTGGGCCTGACGGTAGAAACC ATCAGCCGTCTGCTGGGTCGCTTCCAGAAAAGCGGCATGCTGGCAGTCAAAGGTAAATACATCACCATCG AAAATAACGATGCGCTGGCCCAGCTTGCTGGTCATACGCGTAACGTTGCCTGA

  • Amino Acid length: 250 amino acids.
  • Amino Acid sequence:

MIPEKRIIRRIQSGGCAIHCQDCSISQLCIPFTLNEHELDQLDN IIERKKPIQKGQTLFKAGDELKSLYAIRSGTIKSYTITEQGDEQITGFHLAGDLVGFD AIGSGHHPSFAQALETSMVCEIPFETLDDLSGKMPNLRQQMMRLMSGEIKGDQDMILL LSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRF QKSGMLAVKGKYITIENNDALAQLAGHTRNVA

Function and Homologs

  • Product: fumarate and nitrate reductase
  • Module: Transcription. This protein is only active in a reduced form, FNR-[4Fe-4S]2+. This protein is inactive when oxidized (FNR-[2Fe-2S]2+)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.

BLAST was taking >10min, so Uniprot BLAST tool was used:

    • Fumarate and nitrate reduction regulatory protein, 1280/100%/3.6e-176/100% [2]
    • DNA-binding transcriptional dual regulator, global regulator of anaerobic growth, 1280/100%/3.6e-176/100%, [3]
    • Fumarate and nitrate reduction regulatory protein, 1280/100%/3.6e-176/100%, [4]
  • Equivalent E. coli / JCVI functional protein: This is my extra credit construct.

Expression

  • Expression Level: [medium].
  • Expression Level Hypothesis: Since FNR encodes for enzymes that support respiration, a vital cellular process, these genes should be expressed at a medium level. It also regulates the transition between aerobic and anaerobic respiration.
  • Expression Level References and Description: Information was gathered from the following resources:

FNR EcoCyc: [5]

[4]

  • Expression Time: [unknown]
  • Expression Level Hypothesis: This could be an important factor in cellular development, and would show gain of homeostatic function via response to external environmental conditions and energy status of the cell.
  • Expression Time References and Description:

FNR Uniprot: [6]

[5]

Gene Context

  • Other Components: The FNR transcription activator is a self-contained protein, but it is regulated via oxgyen-level, which control the oxidation status of FNR's iron (III) core. Therefore FNR is oxygen-dependent if desiring to promote aerobic respiration.
  • Possible Dependencies: This interacts with many other gene loci, so could influence the transcription of other genes.
  • Process: Transcriptional activation
    • Inputs: oxidized/reduced iron core depending on which transition is being made from aerobic to anaerobic respiration.
    • Outputs: reduced/oxidized iron core

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
  • Spiro, Stephen, and John R. Guest. "FNR and its role in oxygen-regulated gene expression in Escherichia coli." FEMS microbiology reviews 6.4 (1990): 399-428.
  • Green, Jeffrey, et al. "Characterization of the FNR Protein of Escherichid coli, an Iron-Binding Transcriptional Regulator." Proceedings of the Royal Society of London B: Biological Sciences 244.1310 (1991): 137-144.
  • Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem. 278(32):29837-55
  • Myers, Kevin S., et al. "Genome-scale analysis of Escherichia coli FNR reveals complex features of transcription factor binding." PLoS Genet 9.6 (2013): e1003565.
  • Constantinidou, Chrystala, et al. "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." Journal of Biological Chemistry 281.8 (2006): 4802-4815.
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