EG10894

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Author Information

Cindy Zang Liu

Basic Information

  • ID: EG10894
  • Name: rpoB
  • Organism: E. coli
  • Description: rpoB encodes the beta subunit of DNA-directed RNA polymerase. The RNA polymerase contains a core with multiple subunits: 2 alpha, 1 beta, 1 beta’, and 1 omega (UniProt). The enzyme catalyzes DNA transcription into RNA (UniProt). The beta subunit of the RNA polymerase, along with the beta’ subunit, may be integral in interacting with DNA in the enzyme active site (in E. coli; Chenchik 1982, Simpson 1979, Ross 1993, Kashlev 1990, Landick 1990). The beta subunit also plays a role in RNA polymerase assembly through two conserved sites at the C-terminus (in E. coli; Wang 1997). There is also a “flexible flap” element of the beta subunit containing a hydrophobic patch, which interacts with sigma factors used in initiation of transcription (in E. coli; Geszvain 2004, Kuznedelov 2002, Wigneshweraraj 2003).
  • DNA Length: 4029 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 1342 amino acids.
  • Amino Acid sequence:

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

Function and Homologs

  • Product: RNA polymerase subunit beta
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA-directed RNA polymerase [Trichuris trichiura], 2750/100%/0.0/99%, CDW59665.1
    • MULTISPECIES: DNA-directed RNA polymerase subunit beta [Proteobacteria], 2742/100%/0.0/100%, WP_000263098.1
    • DNA-directed RNA polymerase subunit beta [Escherichia coli], 2742/100%/0.0/99%, WP_024175906.1

Expression

  • Expression Level: high
  • Expression Level Hypothesis: rpoB is part of functioning RNA polymerases, which the cell needs for transcription to produce mRNA (then translated into proteins), rRNA (components of ribosomes), and other RNAs. All of these RNA products are important for proteins and other necessary cellular functions, so a large number of RNA polymerases facilitates faster cell growth.
  • Expression Level References and Description: E.coli Proteomic Expression data, File:EcoliProteomicExpressionData.xlsx
  • Expression Time: Early
  • Expression Level Hypothesis: RNA polymerase is needed to produce mRNA, which will then be used by ribosomes to create new proteins within the cell. So, we need functioning RNA polymerase to synthesize later components.
  • Expression Time References and Description: Research description above

Gene Context

  • Other Components: rpoC, beta’ subunit of DNA-directed RNA polymerase
  • Possible Dependencies: Nucleotide biosynthesis RNA polymerase adds nucleotides to the growing RNA strands, so it requires that new nucleotides are synthesized in the cell in order for transcription to occur.
  • Process: transcription elongation

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file