MMSYN1 0253

From BioE80 Boot
Jump to: navigation, search

Author Information

Taylor Harris

Basic Information

  • ID: MMSYN1_0253.
  • Name: greA
  • Organism: JCVI-Syn3.0
  • Description:

MMSYN1-0253, also known as greA, encodes the greA protein in mycoplasma mycoides. greA plays a role in transcription. Specifically, greA possesses transcription elongation activity due to its role in allowing RNA polymerase to bypass arresting sites in DNA. Such arresting sites can cause RNA polymerase to stall and form an immovable aggregation of the RNA polymerase, nascent RNA transcript, and DNA template. greA cleaves a few ribonucleotides from the 3’ end of the RNA transcript, thereby allowing RNA polymerase to continue elongating the RNA transcript from the new 3’ end. greB plays a similar role to greA in mycoplasma mycoides. greA’s function in mycoplasma mycoides has been extrapolated from the function of homologous proteins in other species. [1]

  • DNA Length: 474 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 157 amino acids.
  • Amino Acid sequence:

MSKEIILTQEGLEELKAELKYLLEVVRPKVIEELVEARNQGDLSENADYDAARNRQAEVEARIKEVETLINRAKVIDDSKTHSTGEVKIGSTVQFVSSLDNKLKEIKIVGAIEADPFSNLISNESPIAKAIIGKKVNTTVEIKDISKPYKITIKSIK

Function and Homologs

  • Product: Transcription elongation factor GreA
  • Module: RNA elongation.
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • transcription elongation factor GreA [Mycoplasma feriruminatoris], 290/100%/7e-99/95%, [2]
    • transcription elongation factor GreA [Mycoplasma capricolum], 281/100%/2e-95/92%, [3]
    • transcription elongation factor GreA [Mycoplasma yeatsii], 265/100%/6e-89/86%, [4]
  • Equivalent E. coli functional protein: EG10415.

Expression

  • Expression Level: High.
  • Expression Level Hypothesis: GreA likely needs to be expressed at high levels because it is a necessary part of the transcription machinery. Whenever RNA polymerase transcribes DNA, which is a very common cellular process, GreA is needed to prevent the polymerase from getting trapped by the DNA indefinitely.
    • Expression Level References and Description: This expression level was gathered from data on Mycoplasma genitalium protein counts; given how closely related it is to Mycoplasma mycoides, it can be used to estimate expression levels in Mycoplasma mycoides as well.
  • Expression Time: Immediately.
  • Expression Time Hypothesis: To express other genes and corresponding proteins, RNA polymerase is necessary to transcribe such genes. Thus, everything required for transcription needs to be produced first, which includes GreA, before the cell can even begin expressing other genes. Furthermore, RNA polymerase plays a role in controlling the expression timing of other genes, and, again, transcription machinery must be expressed before anything else can be expressed.
    • Expression Time References and Description: I used my own knowledge of GreA to inform my hypothesis. I then verified my hypothesis with research into the literature regarding RNA polymerase. [5]

Gene Context

  • Other Components: MMSYN1 0645, RNA polymerase subunit rpoA
  • Possible Dependencies: Nucleotide Synthesis, greA functionality requires available ribonucleotides to be added to mRNA by RNA polymerase before it can cleave a few from the nascent mRNA chain.
  • Process: transcription elongation
    • Inputs: mRNA (n)
    • Outputs: mRNA (n-2 or n-3), 2-3 ribonucleotides
    • References: [6]

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