MMSYN1 0524

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Author Information

Eva Frankel

Basic Information

  • ID: MMSYN1_0524
  • Name: rsmH
  • Organism: JCVI-Syn3.0
  • Description: These gene codes for the enzyme ribosomal RNA small subunit methyltransferase H, which catalyzes the reaction S-adenosyl-L-methionine + cytosine(1402) in 16S rRNA = S-adenosyl-L-homocysteine + N(4)-methylcytosine(1402) in 16S rRNA. This enzyme is found in the cytoplasm. [1] Methyltransferases are responsible for transferring methyl between molecules. [2]
  • DNA Length: 927
  • DNA sequence:

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

  • Amino Acid length: 308
  • Amino Acid sequence:

MDKHIPVLLKESIEYLNIKPDGIYVDCTLGRAGHSSEILKKLNQKGFLYAIDQDQIAIDQAKEKLEQINNNFLLIQGNFSNLSALLAINHVFNVDGILYDLGVSSPQIDIASRGFSYKMDGPLDMRMDLNSTLTAHQVINTYSESQISEILFKYGEESFSKSISKKIVESRPINSTLELVEIIKSVLPQKVLKQKKHPAKKTFQALRIYINNELIALENSLKQALDLLNSKARICVITFHSLEEKIVKNIFNNSTNYYQEQLLSNLPIKANLNSKFKLVIKKPIKPSLLELEQNHRSHSAKLWVIEKN

Function and Homologs

  • Product: Ribosomal RNA small subunit methyltransferase H
  • Module: RNA base methylation
  • Closest homologous proteins:
    • 16S rRNA (cytosine(1402)-N(4))-methyltransferase [Mycoplasma feriruminatoris], 578/100%/0.0/92%, [3]
    • 16S rRNA (cytosine(1402)-N(4))-methyltransferase [Mycoplasma capricolum], 546/100%/0.0/86%, [4]
    • 16S rRNA (cytosine(1402)-N(4))-methyltransferase [Mycoplasma leachii], 541/100%/0.0/85%, [5]
  • Equivalent E. coli / JCVI functional protein: EG11085

Expression

  • Expression Level: High
  • Expression Level Hypothesis:  rsmH is thought to increase translational accuracy (specifically, methylation of cytosine 1402 is involved in increasing the decoding fidelity by fine-tuning the shape and functions of the peptidyl site). Because translation is extremely important and needs to be successful for every strand of mRNA to form a protein, rsmH would be expressed at a high level.
  • Expression Level References and Description: I used the M. genitalium database, where rsmH is called mraW and is expressed at 263 proteins/cell (high). I also used the function, which I found information about here.
  • Expression Time: Early
  • Expression Level Hypothesis: The small subunit of rRNA, which contains 16S rRNA (both the input and the output of the process this enzyme catalyzes), is crucial for proper translation of mRNA. For anything else in the cell to work, mRNA needs to be properly translated into a protein chain. Since ribosome activity and translation is one of the first processes the cell undergoes, this gene should be expressed early.
  • Expression Time References and Description: Guesses from function, which was found here.

Gene Context

  • Other Components: MMSYN1 0202, any other piece of the ribosome
  • Possible Dependencies: This gene is involved in methylating 16S rRNA. Therefore, it would be dependent upon the proper expression of a gene like MMSYN1 0403, which is responsible for processing 16S rRNA.
  • Process: S-adenosyl-L-methionine + cytosine(1402) in 16S rRNA = S-adenosyl-L-homocysteine + N(4)-methylcytosine(1402) in 16S rRNA [6]
    • Inputs: S-adenosyl-L-methionine, cytosine(1402) in 16S rRNA
    • Outputs: S-adenosyl-L-homocysteine, N(4)-methylcytosine(1402) in 16S rRNA

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