EG10895

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Author Information

Cindy Zang Liu

Basic Information

  • ID: EG10895
  • Name: rpoC
  • Organism: E. coli
  • Description: rpoC 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 at the promoter melting stage and in interacting with DNA in the enzyme active site (in E. coli; Chenchik 1982, Simpson 1979, Ross 1993, Nedea 99). This subunit also binds RNA polymerase sigma 70 factor during promoter melting / initiation, with interactions between the rpoC N-terminus and a site on the sigma factor (in E. coli; Naryshkina 2001, Luo 1996, Arthur 1998, Brodolin 2000, Young 2004). The subunit contains a “jaw” domain that stabilizes the open promoter complex (in E. coli; Wigneshweraraj 2005). rpoC is also involved in chelating a magnesium ion in RNA polymerase catalysis and coordinating a zinc ion (in E. coli; Zaychikov 1996, Markov 1999). The C-terminus of the beta’ subunit interacts with DNA topoisomerase 1, preventing supercoiling (in E. coli; Cheng 2003).
  • DNA Length: 4224 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 1407 amino acids.
  • Amino Acid sequence:

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

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], 2887/100%/0.0/99%, CDW59665.1
    • MULTISPECIES: DNA-directed RNA polymerase subunit beta' [Proteobacteria], 2886/100%/0.0/100%, WP_000653944.1
    • DNA-directed RNA polymerase subunit beta' [Escherichia coli], 2885/100%/0.0/99%, WP_073514629.1

Expression

  • Expression Level: high
  • Expression Level Hypothesis: rpoC 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: rpoB, 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