EG10915 sflamen

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Author Information

Steph Flamen

Basic Information

  • ID: EG10915
  • Name: rpsP
  • Organism: E. coli
  • Description: The rpsP gene encodes the 30S ribosomal subunit protein S16. According to Ecocyc, this protein “is a component of the 30S subunit of the ribosome” [1] and also acts as a DNA-binding protein. The small 30S ribosomal subunit is essential during the process of mRNA translation, as it facilitates binding between the codon on mRNA and the anticodon on tRNA; it is composed of 16S rRNA and 22 ribosomal proteins [2]. S16 protein component, specifically, binds to the 16S rRNA to stabilize the decoding center of the 30S subunit—protein S16 is necessary for viability. In addition to the 30S subunit, this protein works directly with 16S rRNA. [3]
  • DNA Length: 249 base pairs.
  • DNA sequence:

ATG GTC ACG ATC CGT TTA GCC CGC CAC GGA GCT AAG AAG CGT CCT TTT TAT CAA GTA GTC GTT GCC GAC AGT CGT AAC GCGCGT AAT GGC CGT TTC ATC GAA CGT GTT GGG TTC TTT AAT CCA ATC GCC TCT GAA AAG GAA GAG GGG ACA CGC TTG GAT TTGGAC CGC ATC GCA CAT TGG GTT GGA CAA GGG GCT ACC ATC TCA GAT CGT GTG GCA GCC CTG ATT AAG GAG GTG AAC AAG GCAGCG TAA

  • Amino Acid length: 82 amino acids.
  • Amino Acid sequence:

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA

Function and Homologs

  • Product: 30S Ribosomal Subunit Protein S16
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: 30S ribosomal protein S16 [Proteobacteria], 167/100%/1e-52/100%, [4]
    • 30S ribosomal protein S16 [Salmonella enterica], 165/100%/9e-52/99%, [5]
    • 30S ribosomal protein S16 [Citrobacter amalonaticus], 164/100%/1e-51/98%, [6]

Expression

  • Expression Level: High-136,596 protein copies/cell (source: E. Coli Proteome Dataset)
  • Expression Level Hypothesis: This gene should be expressed at a high level because it encodes a component of the 30S ribosomal subunit (specifically, the 30S ribosomal subunit protein S16) which is especially important because it facilitates binding between the codon on mRNA and the anticodon on tRNA during mRNA translation [7].
  • Expression Level References and Description: I found expression level information for this exact gene in the E. coli dataset and the description of the gene's function here: [8]. Given that this dataset encapsulates measured levels of all expressed proteins under different growth conditions, I believe this expression level is accurate.
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Because this gene encodes a protein that is component of a ribosome subunit, this gene is directly involved in the translation process and thus should expressed right at the beginning (part of the central dogma) [9].
  • 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: [10].

Gene Context

  • Other Components: EG10919: rpsT, 30S ribosomal subunit protein S20 [11]
  • Possible Dependencies: As a structural constituent of the ribosome, one possible dependency of the ribosome, and thus this functional module, is histidine biosynthesis because the ribosome requires amino acids for its functioning.
  • Process: Formation of 30s ribosomal subunit [12]
    • Inputs: 16s ribosomal RNA & the following 30s ribosomal subunit proteins: S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22
    • Outputs: 30s ribosomal subunit

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