MMSYN1 0804

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Author Information

Cindy Zang Liu

Basic Information

  • ID: MMSYN1_0804
  • Name: rpoB
  • Organism: JCVI-Syn3.0
  • 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: 3876 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 1291 amino acids.
  • Amino Acid sequence:

MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWFKTKGIQEVLDEFFPILSFDGSSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKEFDGVALDDTLKILTNWLEEKTVSKNITFKQQSQNSYFFELTIKKSDKPDLIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAYFNKELNRKTGEMIYFADIIPSRGTWLEYETDSKKTGADAINPLYVKIDKSRKTTATSLLLAFGISKDDILDIFDNDEVLVETLQQDSIVGDFKIDWSNQVQEIYKKIRQGETATSEGASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNRILNRVIAEDIVDANNNVLVAKDTEVNKHNIKQISEILDQDVMSVDLNYLSDILGTRKVQKIKVYKDSELKTDTTCLIGLTSSSNEEFITVADILSTVSYLLNLKYNIGEIDDIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKPLTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTIITDGESGIRTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIKRFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPIEDMPHLEDGTPVDIILNPQGVPSRMNIGQILEIHLGMAAKKLNQKVITPVFEGLNEKELEEIMAEAGMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGIPESFNVLSKEIMGLGFNMYMIDETGEKSVINAYDKKDFDADNYEDDEILVKTDTLYIDDEDVDAEFEDLTYVDENDILRSFESENDIDEEE

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], 2618/100%/0.0/100%, WP_020862998.1
    • DNA-directed RNA polymerase subunit beta [Mycoplasma mycoides], 2609/100%/0.0/99%, WP_017698238.1
    • DNA-directed RNA polymerase subunit beta [Mycoplasma mycoides], 2606/100%/0.0/99%, WP_013729909.1
  • Equivalent E. coli / JCVI functional protein: EG10894

Expression

  • Expression Level: low
  • 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; so, it would be expected that the expression level is high (as in rpoB for E.coli). However, the expression in JCVI may be low 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: 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