MMSYN1 0012 sflamen

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Author Information

Steph Flamen

Basic Information

  • ID: MMSYN1_0012
  • Name: metG
  • Organism: JCVI-Syn3.0
  • Description: The metG gene encodes methionyl-tRNA synthase which is essential for the initiation of mRNA translation and for the elongation of protein synthesis. This enzyme attaches the amino acid to the appropriate tRNA (coupling methionine to methionyl-tRNA), which then allows for protein synthesis initiation or elongation. [1]
  • DNA Length: 1530 base pairs.
  • DNA sequence:

ATG AGC AAG AAG TTT TAC ATC ACC ACT CCG ATC TAT TAC CCG AGC GGC AAT CTT CAC CTT GGA CAT GCA TAT ACT ACA ACACTT GCT GAC ATT TTA AAC CGT TAC AAG AAA GAA CAA GGG TAT GAG ACT TTT TTC TTG ACG GGA TCG GAT GAG CAT GGA CAAAAA ATT GAA AAT AAA GCC AAG GAA GCG AAT TTG ACG CCG CTG GAA TAT CTG AAC CCG AAG GTC CAA GCA TTT AAA GAC TTGTGG ACT AAG CTG AAC ATC AAT TAC GAT AAA TTT ATT CGT ACC ACC GAC GAC TAC CAT GAA AAA GCG GTA CAG AAA ATT TTCACA ATC CTT CTG GAG AAA GGG TAC ATT TAC AAG GGT CAA TAC GAA GGC ATT TAC TGT GTC TCA TGT GAA GAG TTC TTG ACTAAC GAA CAA ATT GAC GAA AAT GGA CTG TGC AAA ATC TCG AAT ACT AAG CCG CAG TTA GTA AAT GAG GAT ACT TAC TTC TTGAAG GTT TCA CAG TTT CAG GAG TTC GTT CAA AAC GTA CTG AAG TCC GAT TTC CTG ATC CCA GAG TAC CGT CGT AAC GAA ATGCTT AAG AAC TTT GTT GAA CCA GGT TTA AAG GAT CTT AGT GTA ACC CGC GTT TCC TTT AAA TGG GGG ATT CCT ATC ACA GAAGAC CAA CGT CAC ATC ATC TAT GTA TGG TTA GAT GCT TTG TCA AAC TAC ATC ACG GCG TTA GGG TAC TTG CAG GAA GAC GATTCA CTT TTT AAG AAA TTT TGG CAA AAT GAC GAC TGT GAG ATT CTT CAG CTT GCT GGG AAG GAG ATC ATT CGT TTT CAT AGTATT TAC TGG CCG GTC ATG CTT GAA GCT CTT AAT CTT AAA CAG CCT ACT CAC CTT TTA GGT CAT GGG TGG ATC TTA AAC AAAAAC ACG AAG ATG TCT AAA TCC CTT GGG AAC GTC ATT GAT CCG GTG AAA ATT ATT GAG TTA TAT TCA GCG GAC GCT TTG CGCTTT TAT ATT GCA AAT GAT TTA CCA ACT GAA AAA GAC GGG AAT TTC AGT TTA GAA TTA TTC ATT GAA AGT TTT AAC GCA CACTTG GCA AAC AAC GTA GGG AAT TTA ATT AGT CGT ACA CAC AAT ATG ATC TCC AAA TAT TTT AAT GGG TAC ATC AAC TTA TCTAAT GTT AAT TAT GAT CAG GAG TTG ATC AAC CTG GGA ATC AAG ACG ATT GAC AAT TAT GTT TTT AAT ATG GAC CAG TAC AAAATT TCC GAG AGT ATC AAA GCG GTG CTT GAG TTG TCG AAT GCC TGC AAT AAA TAC ATT GAG ACC AAG GCT CCG TGG AAC CTTGAG AAA GAG AAC AAG ATC GAG GAG CTT AAA ACA GTT CTG GCA ACA TTA CAG CGC AAT ATT GCG ATC ATT TCA TAC CTT CTGAAA CCA GTG TTG GTC GAT AGT TAC AAG GAT ATG ATC GAG CAA TCT GGT TTA GAA AAC GTT CAA ATT GAT TTT GAG AAC CTTAAG TCC TTT AGT AAC ATC AAA TTC AAC AAG TTG AAC AAC AAG AAA GTG ATT TTC AAC CGT ATT AAA GAA TAA Note: sequence includes complexities in codon optimization: region of low GC content on or near the 3' end

  • Amino Acid length: 509 amino acids.
  • Amino Acid sequence:

MSKKFYITTPIYYPSGNLHLGHAYTTTLADILNRYKKEQGYETFFLTGSDEHGQKIENKAKEANLTPLEYLNPKVQAFKDLWTKLNINYDKFIRTTDDYHEKAVQKIFTILLEKGYIYKGQYEGIYCVSCEEFLTNEQIDENGLCKISNTKPQLVNEDTYFLKVSQFQEFVQNVLKSDFLIPEYRRNEMLKNFVEPGLKDLSVTRVSFKWGIPITEDQRHIIYVWLDALSNYITALGYLQEDDSLFKKFWQNDDCEILQLAGKEIIRFHSIYWPVMLEALNLKQPTHLLGHGWILNKNTKMSKSLGNVIDPVKIIELYSADALRFYIANDLPTEKDGNFSLELFIESFNAHLANNVGNLISRTHNMISKYFNGYINLSNVNYDQELINLGIKTIDNYVFNMDQYKISESIKAVLELSNACNKYIETKAPWNLEKENKIEELKTVLATLQRNIAIISYLLKPVLVDSYKDMIEQSGLENVQIDFENLKSFSNIKFNKLNNKKVIFNRIKE

Function and Homologs

  • Product: Methionyl-tRNA synthase (short name: metRS) (alternative name: Methionine-tRNA ligase)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • methionine--tRNA ligase [Mycoplasma capricolum], 999/100%/0.0/95%, [2]
    • methionine--tRNA ligase [Mycoplasma leachii], 989/100%/0.0/94%, [3]
    • methionine--tRNA ligase [Mycoplasma feriruminatoris], 972/100%/0.0/92%, [4]

Expression

  • Expression Level: Low-5 proteins/cell (source: M. genitalium dataset)
  • Expression Level Hypothesis: Despite the important role metG plays in coupling methionine to methionyl-tRNA, because the methionine amino acid is not used as frequently in mycoplasma genitalium as in some other organisms [5], metG is expressed at a low level. This stands in contrast to the high expression level of the gene in E. coli, where the methionine codon is used relatively frequently compared to other codons. [6]
  • Expression Level References and Description: I found expression level information for this exact gene in the M. genitalium dataset and the description of the gene's function here: [7]. Given that mycoplasma genitalium are closely related to mycoplasma mycoides, I believe this expression level is accurate.
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Because this gene encodes methionyl-tRNA synthase which is essential for the initiation of mRNA translation and elongation of protein synthesis, this gene is directly involved in the central dogma of biology and thus must be expressed right at the beginning. Specifically, this enzyme catalyzes the reaction that couples methionine to methionyl-tRNA; because methionine is a start codon, it is especially important that metG is expressed at the beginning. [8]
  • Expression Time References and Description: As stated in the hypothesis, this gene should be expressed at the beginning because it is needed for translation—part of the central dogma, which must happen right away. I used information about the gene's function that I found here: [9].

Gene Context

  • Other Components: This enzyme acts independently to link an amino acid to its corresponding tRNA molecule (single subunit); no other components are required for this catalyst to work. Mg2+ and Zn2+ are cofactors of this enzyme, though (inferred from E. coli analog: [10]). Although this is not a component, here is a link to another tRNA synthase, MMSYN1_0535.
  • Possible Dependencies: Methionine biosynthesis because methionine—tRNA ligase has no purpose without methionine.
  • Process: Coupling methionine to methionyl-tRNA [11]
    • Inputs: ATP, L-methionine, tRNA(Met)
    • Outputs: AMP, diphosphate, L-methionyl-tRNA(Met)

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