MMSYN1 0730

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Author Information

Xingkai Eric Chew

Basic Information

  • ID: MMSYN1_0730
  • Name: DeoR
  • Organism: JCVI-Syn3.0
  • Description: Based on the homolog in Mycoplasma feriruminatoris, it is likely that this protein is a DeoR family transcriptional regulator. On further inspection, this homolog is most similar to the DeoR-like helix-turn-helix domain protein on Uniprot.[1] Helix-turn-helix DeoR-type transcriptional regulators act as repressors of the deo operon. [2] Thus, the product is likely a DeoR family helix turn helix transcriptional repressor. DeoR negatively regulates the expression of nucleotide and deoxyribonucleic catabolic enzymes, nupG (a nucleotide specific transport protein), and tsx (a channel-forming protein).[3] It is one of a family of DeoR transcriptional regulators, which includes another transcriptional repressor CytR.[4] DeoR has two domains: an amino terminal domain that can potentially contain a helix-turn-helix motif and a carboxy-terminal domain that is used in the oligomerization and recognition of a possible co-inducer. In solution, DeoR is an octamer, but forms multple oligomers in its target promoters. Cooperative binding to inverted repeat sequences creates a repression DNA loop that regulates the transcription.[5]Deoxyribose-5-phosphate acts as an inducer for DeoR. In its presence, DeoR has a higher disassociation constant, preventing it from binding to DNA operator site and thus allowing the nucleotide and deoxyribonucleic catabolic enzymes, nupG, and tsx to be expressed.[6][7]
  • DNA Length: 600
  • DNA sequence:

ATG TCA TAT CTT TCG CAA ATT CAA AAC CGT ATT GAT CAC TTT GAG CCA ACC AAA ATT TTC ATT TCT AAC GAT TTC CTG GAT ATT GCT TCT AAT GAA ACC GTT CGT CGT ACG CTT AAT AAA CTG GTG GAG GAG GAG AAG ATT AAA CGT ATC ATT AAC GGA TTC TAT TAC AAC CCG ACC TAT ATT GAG TTG ATT CAC GAG TAT GAA CCT TTT GAA GTG GAA GAG TTA GCT TAT TCA ATT GCT CGC AAA TAC AAC TGG GAG ATC GCG CCC TTC GGT ATT GCT TGT CTG AAC ATT CTG GGT CTT TCC ACT CAA GTC CCA GCC AAG ATC ATT TTT GTC TCT AGT GGC AAG AAC AAA ATC TAT AAT ATT GAC GGT TGG ATC ATC GAA TTT AAG AAA GTC AGC AAC AAG GAG ATT TGC AAT ATG TCC TGG AAG ACT AAG ATT GTC ATC CAA GCT ATT AAA GAG ATT GGA AAG AAC AAA TTG ACA AAG AAA GAT ATT CGC ATC ATC CGT AAT TCG TTG TCC GCG CTG GAA AAG CAG AAC TTG CTG AAA GAA ACT AAG TAC ACT ACA ACA TGG ATC TTC GAT TAT ATC AAG CAA ATC TGC AAA GAG TAG

  • Amino Acid length: 199
  • Amino Acid sequence:

MSYLSQIQNRIDHFEPTKIFISNDFLDIASNETVRRTLNKLVEEEKIKRIINGFYYNPTYIELIHEYEPFEVEELAYSIARKYNWEIAPFGIACLNILGLSTQVPAKIIFVSSGKNKIYNIDGWIIEFKKVSNKEICNMSWKTKIVIQAIKEIGKNKLTKKDIRIIRNSLSALEKQNLLKETKYTTTWIFDYIKQICKE

Function and Homologs

  • Functional Category: Based on the homolog in Mycoplasma feriruminatoris, it is likely that this protein falls under Regulation
  • Product: Based on the homolog in Mycoplasma feriruminatoris, it is likely that this protein is a DeoR family helix turn helix transcriptional repressor.
  • Module: Based on the homolog in Mycoplasma feriruminatoris, and the equivalent E. coli protein DeoR, the functional module for this protein is likely the deo operon repressor.[8]
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • hypothetical protein BVA24_03960 [Mycoplasma capricolum subsp. capripneumoniae], 384/100%/6e-135/95%, AQU77718.1
    • hypothetical protein [Mycoplasma leachii], 382/100%/5e-134/94%, WP_013448019.1
    • DeoR family transcriptional regulator [Mycoplasma feriruminatoris], 313/99%/6e-107/77%, WP_008363464.1
  • Equivalent E. coli / JCVI functional protein: EG10223

Expression

  • Expression Level: high
  • Expression Level Hypothesis: Perhaps this uncharacterized variant of HTH transcriptional regulator in M. genitalium has low affinity for the DNA binding site. Thus a large number of them are needed to ensure proper regulation.
  • Expression Level References and Description: This expression level is based off the uncharacterized HTH transcriptional regulator in the M. genitalium model data. The model data says that the uncharacterized regulator is perhaps gntR. We can see in Uniprot that there exists a DeoR-like HTH transcriptional regulator in Mycoides that has an HTH gntR-type DNA binding domain. Thus, because of the similarities with DeoR, I am considering this uncharacterized HTH transcriptional regulator as the closest homolog to the gene, and thus basing the expression level off of it. Also received information about affinity from TA in office hours.
  • Expression Time: early
  • Expression Time Hypothesis: Transcriptional regulators are key to ensuring that proteins are synthesized in the correct proportions. Thus, these regulators must be expressed early in the cell life cycle to ensure proper creation and functioning of proteins later on.
  • Expression Time References and Description: Research description above.

Gene Context

  • Other Components: This protein does not require other components to repress the deo operon.
  • Possible Dependencies: DNA Operator Site The repressor requires a DNA operator site to bind to in order for repression to happen.[9]
  • Process: Induce expression of nupG
    • Inputs: deoxyribose-5-phosphate
    • Outputs: DeoR/deoxyribose-5-phosphate complex, nupG
    • Reference: DeoR. Inducers.
  • http://www.uniprot.org/uniprot/L5L904
  • https://www.ebi.ac.uk/interpro/entry/IPR018356
  • https://www.ebi.ac.uk/interpro/entry/IPR018356
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10200
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10223
  • http://jb.asm.org/content/182/7/1916.full
  • https://en.wikipedia.org/wiki/Inducer
  • https://www.ebi.ac.uk/interpro/entry/IPR018356
  • https://www.wikigenes.org/e/gene/e/3993149.html
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