MMSYN1 0448

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Author Information

Joey McKenna 05930701 (mckenj)

Basic Information

  • ID: MMSYN1_0448
  • Name: trmH (spoU) (as per JCVI database and UniProtKB)
  • Organism: JCVI-Syn3.0
  • Description: TrmH is the methyltransferase responsible for 2'-O-methylation of ribose at position G18 in certain tRNAs [Persson97]. Unlike Type I enzymes (e.g. from Thermus thermophilus) that can modify all tRNA species, the E. coli enzyme is a Type II enzyme that only modifies a subset of tRNAs. The catalytic domain of TrmH is responsible for substrate selectivity [Ochi13].

TrmH belongs to the SPOUT superfamily of methyltransferases [Anantharaman02] and was identified early as a member of a protein family predicted to include rRNA methylases [Koonin93].

[Persson97] reported no growth defect of a trmH in LB or MOPS-glucose medium, while [Urbonavicius02] found a lower growth rate in rich-MOPS medium compared to wild type. The ΔspoU3 insertion-deletion allele of trmH causes phenotypes due to polar effects on recG gene expression [Kalman92]. A trmH trmA truB triple mutant shows a defect in the tRNA modifications Gm18, m5U54, and Ψ55 as well as translation defects, heat sensitivity, and a growth defect [Urbonavicius02]. Reference

  • DNA Length: 768 bp
  • DNA sequence:

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

  • Amino Acid length: 255 amino acids.
  • Amino Acid sequence:

MEVISSVSNPKIKEILKLKDRKHRNKQKLFIVEGFHMIMEAYNDQIIKTLLGTSKALEILKDEIPNIEQVIEISENVAKKISDTVTSQQIFAICSMPENTKIDFENNILLLDQIQDPGNLGTLIRSAASFNFKTVIASPNSVNFHNQKVLRSTQGNLFQVNLVNEYLVTVINQLHDNNYIIIGTSLHDDSKPLSKVKFDSDDKYALIIGNEGKGISPELLDLIDLNINIEMAEDVDSINAAVAGSIIMYQINNAK

Function and Homologs

  • Product: rRNA methylase
  • Closest homologous proteins:
    • Name: rRNA methyltransferase [Mycoplasma mycoides], Max Score: 509/Query Cover: 100%/E-Value: 0.0/Ident: 99%, WP_013729611.1
    • Name: rRNA methyltransferase [Mycoplasma leachii], Max Score: 504/Query Cover: 100%/E-Value: 1e-180/Ident: 99%, WP_013447766.1
    • Name: rRNA methyltransferase [Mycoplasma capricolum], Max Score: 501/Query Cover: 100%/E-Value: 2e-179/Ident: 98% WP_011387335.1
  • Equivalent E. coli / JCVI functional protein: EG10967.

Expression

  • Expression Level: [low].
  • Expression Level Hypothesis: After looking at the excel document for genes within Mycoplasma Genitilium, most of the methylase/methyltransferase genes provide a low to medium expression level. Therefore, with that information and the function of RNA methylase, this protein does not require a high expression level. In fact, it is on the lower side.
  • Expression Level References and Description: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: [early].
  • Expression Level Hypothesis: The think the gene is expressed at this time because RNA binding occurs at the latter half of the RNA transcription process before the RNA is translated into a protein. Because of its role in post-transcriptional processes, it should occur early in the lifecycle before mitosis and other processes.
  • Expression Time References and Description: Intuition and Information by Oliviera et al. [1]

Gene Context

  • Other Components in the functional module. MMSYN1_0524
  • Possible Dependencies: rRNA -methyltransferase activity
  • Process: rRNA base methylation
    • Inputs: S-adenosyl-L-methionine, cytosine(1402)
    • Outputs: S-adenosyl-L-homocysteine, N4-methylcytosine(1402) [[2]]

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file