MMSYN1 0064

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Author Information

Cayla Hatton

Basic Information

  • ID: MMSYN1_0064
  • Name: LysS
  • Organism: JCVI-Syn3.0
  • Description: MMSYN1_0064 encodes the protein LysS [1] [2]. LysS is an aminoacyl-tRNA synthetase: it is an enzyme that bonds a particular amino acid to its corresponding tRNA [3] [4] [5]. This process, commonly referred to as tRNA charging or tRNA loading, is a critical pathway in translation [6]. More specifically, LysS is a lysine-tRNA ligase: it bonds the amino acid L-lysine to tRNA(Lys) [7]. Due to its role in tRNA charging, LysS is transcribed continuously throughout a cell's lifetime [8] [9].
  • DNA Length: 1500 base pairs (1503 with stop codon).
  • DNA sequence:

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

  • Amino Acid length: 500 amino acids.
  • Amino Acid sequence:

MLDDRKFSEQELVRRNKYKTLVEQNKDPYKITNWKRNTTLLKLNEKYKDYSKEDLLNLNQELVVVAGRIKLYREAGKKAAFVNIDDQDSSIQLYVRLDEIGDQSFEDFRNFDLGDIIGVKGIMMRTDHGELSIRCKEVVLLSKALRPLPDKHAGIQDIEEKYRRRYVDLIMNHDVRKTFQARTKIIRTLQNFLDNKGYMEVETPILHSLKGGASAKPFITHYNVLNTDVYLRIATELHLKRLIVGGFEGVYEIGRIFRNEGMSTRHNPEFTSIELYVAYEDMFFLMDLTEEIFRVCNAAVNSSSIIEYNNVKIDLSKPFKRLHMVDGIKQVTGVDFWQEMTVQQALELAKKHKVHVEKHQESVGHIINLFYEEFVESTIVEPTFVYGHPKEISPLAKSNPSDPRFTDRFELFILGREYANAFSELNDPIDQYERFKAQIEEESKGNDEANDMDIDFIEALEHAMPPTAGIGIGIDRLVMLLTNSESIKDVLLFPQMKPRE

Function and Homologs

  • Product: Lysine-tRNA Ligase
  • Closest homologous proteins:
    • Lysine-tRNA ligase (Mycoplasma feriruminatoris), 996/100%/0.0/96%, WP_008363186.1
    • Lysine-tRNA ligase (Mycoplasma leachii), 987/100%/0.0/94%, WP_013448109.1
    • Lysine-tRNA ligase (Mycoplasma capricolum), 985/100%/0.0/94%, WP_046783763.1
  • Equivalent E. coli functional protein: EG10552

Expression

  • Expression Level: Medium
  • Expression Level Hypothesis, References, & Description: The M. genitalium model data [File:MgenitaliumSimProteinCounts.xlsx] categorizes LysS expression as low, but I recommend a higher level of expression based on the critical role of LysS in translation (see above). Indeed, in E. Coli, LysS has a high level of expression [File:EcoliProteomicExpressionData.xlsx]. The incongruency in the M. genitalium and E.Coli data may differ based on environmental and growth conditions of the samples. Based on the nature of its role in tRNA charging, one would expect LysS expression to depend on the transient concentration of, and demand for, the cognate amino acid (lysine). The expression level of tRNA ligases should positively correlate with translation rate and cell growth [10]. Thus, the M.genitalium model data may be from a cell in which the concentration of lysine and/or the rate of growth is low. Lysine use may also differ by the different proteins needed by various species or environmental demands; perhaps E.Coli utilizes lysine more frequently, or the sample cell was under conditions demanding lysine-dependent peptides. Because this variability in available data indicates some uncertainty, it may be best to target expression level based on our ribosomal expression level. It has been documented that any given aminoacyl-tRNA synthetase is approximately 10-20x less abundant than ribosomes in a given cell. [11]
  • Expression Time: Early
  • Expression Level Hypothesis: The ability to charge tRNA molecules with amino acids is critical to building all of the polypeptides that enstantiate function in our organism; thus, tRNA-ligase will be essential as soon as fundamental translation machineries (i.e., ribosomes) are assembled.

Gene Context

  • Other Components: Lysine-tRNA ligase is a single-component enzyme; it is the smallest functional unit in which the LysS gene takes part. That said, other tRNA ligases, such as GlyRS (MMSYN1 0405), are components of a broader tRNA modification module.
  • Possible Dependency: Lysine Biosynthesis: Lysine-tRNA ligase is useless unless there is Lysine available!
  • Process [12]
    • Inputs: L-Lysine, tRNAlys, ATP
    • Outputs: L-lysyl-[tRNAlys], AMP, diphosphate