MMSYN1 0645

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Author Information

Karen Dai

Basic Information

  • ID: MMSYN1 0645
  • Name: rpoA: DNA-directed RNA polymerase, alpha subunit
  • Organism: JCVI-Syn3.0
  • Description: rpoA encodes the alpha subunit of the RNA polymerase core enzyme. RNA polymerase’s core enzyme is made up of two alpha subunits, along with one beta, one beta-prime, and one omega subunit [1]. RNA polymerase plays a central role in the central dogma, catalyzing the transcription of DNA into RNA. The amino-terminus of the alpha subunit is necessary and sufficient for the dimerization of the alpha subunit and the assembly of the RNA polymerase core complex [2]. The carboxy-terminal of the alpha subunit is utilized in antitermination and rho-dependent termination, and is involved in interactions with transcription termination/antitermination protein NusA [3]. The carboxy-terminal is also needed for transcriptional initiation [4].
  • DNA Length: 951 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 317 amino acids.
  • Amino Acid sequence:

MKQFVRPEFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIAGATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPVYAGDLDIPAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREISVLEVIGTNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLGRKSLKEIKDKVASLGLAFRQS

Function and Homologs

  • Product: DNA-directed RNA polymerase subunit alpha.
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA-directed RNA polymerase subunit alpha (Mycoplasma mycoides) 629/100%/0/100% WP_013729784.1
    • DNA-directed RNA polymerase subunit alpha (Mycoplasma feriruminatoris), 622/100%/0/98%, WP_008362471.1
    • DNA-directed RNA polymerase subunit alpha (Mycoplasma capricolum), 619/100%/0/97%, WP_011387528.1
  • Equivalent E. coli / JCVI functional protein: EG10893.

Expression Level/Time

  • Expression Level Estimate: High
    • Expression Level Hypothesis: rpoA encodes the alpha subunit of RNA polymerase and is thus crucial for transcription. Since transcription is a critical function of every cell, the expression level of rpoA is estimated to be high.
    • Expression Level References and Description: This expression level is estimated using the M. genitalium model data. Since M. genitalium is closely related to M. mycoides, it can be used as an estimate gene expression levels in M. mycoides.
  • Expression Time Estimate: Early
    • Expression Time Hypothesis: As part of the RNA polymerase, it is needed for transcription to produce mRNA, which is then translated to proteins. Thus, rpoA needs to be expressed early on to have a functioning RNA polymerase in order to synthesize later components.
    • Expression Time References and Description: I made this expression time estimate based on what is known about the importance and ubiquity of the transcriptional process.

Gene Context

  • Other components: MMSYN1_0804
  • Possible Dependencies: Nucleotide Synthesis
  • Process:
    • Inputs: mRNA(n) + Nucleoside triphosphate
    • Outputs: mRNA(n+1) + diphosphate
    • Reference: [5]

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