MMSYN1 0004 asli

From BioE80 Boot
Jump to: navigation, search

Author Information

Angela Li (asli)

Basic Information

  • ID: MMSYN1_0004
  • Name: ksgA
  • Organism: JCVI-Syn3.0
  • Description: Ribosomal RNA small subunit methyltransferase A (also known as ksgA) is a dimethyladenosine transferase. It is an enzyme, located in the cytoplasm of the cell, that methylates two adjacent adenines in 16S rRNA (which is part of the small subunit of the ribosome), a process which typically occurs rather late in ribosome maturation. [1] The two A's are part of a hairpin loop that's near the 3' end of the 16S rRNA. This enzyme and the modified adenosine bases are highly conserved in both prokaryotes and eukaryotes. [2] Thus, the role that it performs in pre rRNA processing is considered vital. In fact, it is thought to be crucial for the biogenesis of the 30S subunit. [3]
  • DNA Length: 801 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 266 amino acids.
  • Amino Acid sequence:

MKAKKYYGQNFISDLNLINKIVDVLDQNKDQLIIEIGPGKGALTKELVKRFDKVVVIEIDKDMVEILKTKFNHSNLEIIQADVLEIDLKQLISKYDYKNISIISNTPYYITSEILFKTLQISDLLTKAVFMLQKEVALRICSNKNENNYNNLSACQFYSQRNFEFVVNKKMFYPIPKVDSAIISLTFNDIYKKQVNNDKKFIDFVRLLFNNKRKTILNNLNNIIQNKNKALEYLNTLNISSNLRPEQLDIDQYIKLFNLIYNSNF

Function and Homologs

  • Product: Ribosomal RNA small subunit methyltransferase A
  • Module: rRNA base methylation (GO term)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase [Mycoplasma capricolum], 502/100%/2e-179/97%, WP_036431583.1
    • ribosomal RNA small subunit methyltransferase A [Mycoplasma capricolum], 451/100%/3e-159/96%, WP_011386909.1
    • 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase [Mycoplasma feriruminatoris], 440/100%/1e-154/88%, WP_008363412.1
  • Equivalent E. coli / JCVI functional protein: EG10523.

Expression

  • Expression Level: High
  • Expression Level Hypothesis: This gene is likely highly expressed. Not only is this fact indicated in the Mycoplasma genitalium results, but it also makes biological sense because ksgA is involved in rRNA processing, which is required for ribosome maturation. Ribosomes - protein production machinery - are enormously abundant in the cell.
  • Expression Level References and Description: M. genitalium model data, and the UniProt profile description about ksgA. I am sure about this choice because it is rooted in basic biology.
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Because the rRNA processing that this enzyme does is crucial for ribosome biogenesis, the gene is likely expressed early on so that ribosomes can be functional as soon as possible in order to synthesize all other proteins needed in the cell.
  • Expression Time References and Description: I am sure about this conclusion because it is rooted in basic biology. I did not use external references.

Gene Context

  • Other Components: This module only has one component in the sense that the ksgA protein product is an functional enzyme itself (i.e. it doesn't need any other subunits) and because it directly methylates rRNA it isn't part of a metabolic pathway either. Enzymes that perform related functions of rRNA methylation are rsmH and gidB
  • Possible Dependencies: Era modifies rRNA precursors into 16S rRNA. Therefore, it helps produce the rRNA which ksgA methylates.
  • Process: rRNA methylation
    • Inputs: 4 S-adenosyl-L-methionine, adenine at position 1518, adenine at position 1519
    • Outputs: 4 S-adenosyl-L-homocysteine, N6-dimethyladenine at position 1518, N6-dimethyladenine at position 1519
    • Resource: [UniProt]

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