MMSYN1 0362 sflamen

From BioE80 Boot
Jump to: navigation, search

Author Information

Steph Flamen

Basic Information

  • ID: MMSYN1_0362
  • Name: rpsP
  • Organism: JCVI-Syn3.0
  • Description: The rpsP gene encodes the 30S ribosomal subunit protein S16, which belongs to the bacterial ribosomal protein bS16 family (gene family name: rps16, which is also found in rice, potatoes, coffee, sugarcane and more) and is a component of the 30S ribosomal subunit. 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 [1]. This protein contributes to the structural integrity of the ribosome to aid in the translation process. [2]
  • DNA Length: 279 base pairs.
  • DNA sequence:

ATG GTT AAG TTA CGC CTG AAA CGT ATT GGC AAA AAG CAA GCA CCA TTC TAT CGT ATC GTG GCT GCG GAC TCG CGT ATT AACCGC AAT GGT CAA TAC ATC GAA CTG GTC GGA ACG TTT AAT CCG TTG AAA GAT GAG GTC AAG ATT GAC AAG GAG CTT ACC TTAAAA TGG TTG AAT AAT GGG GCG CAA CCA ACA GAT ACG GTG CGT ACT CTT CTG TCC AAA CAA GGG ATT TTG AAA GCA CTG CACGAG GCC AAA TTC AGT AAG AAC ACC GAG AAA AAA TAA

  • Amino Acid length: 92 amino acids.
  • Amino Acid sequence:

MVKLRLKRIGKKQAPFYRIVAADSRINRNGQYIELVGTFNPLKDEVKIDKELTLKWLNNGAQPTDTVRTLLSKQGILKALHEAKFSKNTEKK

Function and Homologs

  • Product: Ribosomal protein S16
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 30S ribosomal protein S16 [Mycoplasma feriruminatoris], 185/100%/1e-59,98%, [3]
    • 30S ribosomal protein S16 [Mycoplasma capricolum], 181/97%/2e-57/96%, [4]
    • 30S ribosomal protein S16 [Mycoplasma leachii], 179/97%/9e-57/94%, [5]

Expression

  • Expression Level: High-321 proteins/cell (source: M. genitalium 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. [6]
  • Expression Level References and Description: I found expression level information for this exact gene in the M. genitalium dataset and the description of the gene's function here: [7]. Given that mycoplasma genitalium are closely related to mycoplasma mycoides, I believe this expression level is accurate.
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Because this gene encodes a protein that is a component of a ribosome subunit, this gene is directly involved in the translation process (part of the central dogma) and thus should be expressed right at the beginning [8].
  • Expression Time References and Description: As stated in the hypothesis above, 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: [9].

Gene Context

  • Other Components: MMSYN1_0082: rpsT, 30S ribosomal subunit protein S20 [10]
  • 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
    • 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 (inferred from E.coli analog [11])
    • 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