EG10893

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Author Information

Karen Dai

Basic Information

  • ID: EG10893
  • Name: rpoA
  • Organism: E. coli
  • 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: 1083 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 361 amino acids.
  • Amino Acid sequence:

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

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.
    • MULTISPECIES: DNA-directed RNA polymerase subunit alpha (Proteobacteria), 663/100%/0/100%, WP_001162094.1
    • DNA-directed RNA polymerase subunit alpha (Salmonella enterica), 662/100%/0/99%, WP_057520379.1
    • MULTISPECIES: DNA-directed RNA polymerase subunit alpha (Enterobacteriaceae), 662/100%/0/99%, WP_008457196.1
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0645.

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: E.coli Proteomic Expression data
  • 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: EG10894
  • 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