MMSYN1 0803

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Author Information

Cindy Zang Liu

Basic Information

  • ID: MMSYN1_0803
  • Name: rpoC
  • Organism: JCVI-Syn3.0
  • 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: 3768 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 1255 amino acids.
  • Amino Acid sequence:

MENLNRKKAIKIELANPDTIRSWSHGEVLKPETINYKTLKAEKDGLFDERIFGPTKNYECVCGRYKKANPMNKGKKCEKCGVELTESIVRRERMGHIELEEPVTHIWMLKVAPYRIAAILDLKAKELEEVVYFVSHIVLEQGNQKHFIEKEVLDLGSSRITKTREKLQLTILDVIDLINDPNHRDTKKANRLLEELKNTAVPFSIDEATSLISKYTGAKFGIGARAVEYLLEKVDLKKEIEAIKVQLENSKKTPNERTKLLKRLETFDALKRSNQRPEWMVMRVIPVIPPDIRPIIQLDGGRFTTSEINDLYRRIIIRNERLKKVKEMGAPSIIVNNEKRMLQEAVDALFDNERKPKPVQGKNKRPLKSLTSVLKGKQGCFRQNLLGKRVDYSARSVIAIGPDLKMYQAGLPREMAITLFKPFVIQWLQDHEYAENVKIAEKMLLQNDPKVWEALEQVIKDRPVLLNRAPTLHRLGIQAFEPKLVKGKAIRLHPLVTTAFNADFDGDQMAVHVPITKEAVAESRALMLGSSAILGPKDGKAIVTPGQDIILGNYYLTTEEKYAKGQGMIFSSLDEAFMAYKSNQADLNSLIGIALSALPEQKFSDKNQRLNSYLLTTVGKLYFNQIFDDNFPWINSNNIWNAKEAVKEFIYDFSQDIDKVIENVQVQQPIKKKELSLIIERYFETHGARKTAEMLDKMKDLGFSFSTKSGTTISAGDVVAFTHKYDEFKQADQKVEQITDFYNMGMLTNSEKKRRIIEVWSDVKDKIQNELATVLRKDVKNPIFVMVDSGARGNVSNFTQLVGMRGLMNDTKGDIKEIPIKSSFREGLTVSEYFVSTHGARKGMADIALKTADSGYLTRRLVDVSQEIVVVNEDCEPTKGFEVSAIIDTKHDNVIVPLKDRLVGRFTFEDIYDDNKNLIVSANTLIDKNIADKIIMAGISSVIIRSVLTCDNKRGVCQKCYGLNLATASVVNIGEPVGVIAAQSIGEPGTQLTMRNFHTGGVAGNVDITQGLPRIKELLDVTTPKGAVAIISEVDGVVSEIEDYNGVFVINIVTENEEVKKYKTEFNSVLRVEQGSSVVAGQKLTEGAIDLHQLLEFGGIQDVQNYILKEVQKVYRLQGIEISDKYIEIIIKQMLNKVKITDSGDSDLLPGEVITIQNCKEVVQDCIVKSIRPPLSKAQIFGIKKAPLESSSWLSSASFQDTARVLTRAIIKGKEDKLEGLKENIMLGNLIPAGTGLTGTQEVELLAEQYHNNEY

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 subunit beta' [Mycoplasma mycoides], 2572/100%/0.0/100%, WP_020862997.1
    • DNA-directed RNA polymerase subunit beta' [Mycoplasma mycoides], 2553/100%/0.0/99%, WP_017698239.1
    • DNA-directed RNA polymerase subunit beta' [Mycoplasma mycoides], 2551/100%/0.0/99%, WP_013729908.1
  • Equivalent E. coli protein: EG10895

Expression

  • Expression Level: medium
  • 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; so, it would be expected that the expression level is high (as in rpoC for E.coli). However, the expression in JCVI may be medium due to differences in binning for high vs. medium vs. low based on a lower number of proteins analyzed in JCVI, causing potentially more error/noise.
  • Expression Level References and Description: M. genitalium model data, File:MgenitaliumSimProteinCounts.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