MMSYN1 0365

From BioE80 Boot
Jump to: navigation, search

Author Information

Blake Salvador

Basic Information

  • ID: MMSYN1_0365
  • Name: rplS (Ribosomal protein L19)
  • Organism: JCVI-Syn3.0
  • Description: Ribosomes are the organelles in the cell responsible for translation of mRNA into a protein. Bacterial ribosomes are made of two subunits - the smaller 30S subunit and the larger 50S subunit - as well as ribosomal RNA (rRNA) bound together by the subunits. This gene encodes a protein component of the 50S subunit known as ribosomal protein L19. It belongs to the L19E family of ribosomal proteins, and is located in the cytoplasm. [1] Specifically, L19 will bind rRNA, holding it in place for stabilization of the ribosome and forming a protein-RNA complex [2].
  • DNA Length: 384 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 127 amino acids.
  • Amino Acid sequence:

MSSKATKTVKSKFDIINNQLRNDLIDFRSGDTIRVDVKIKEGDKFRIQSFEGLVIKTQGSGITYSVVVRKMSNGVFVERTFPLHSPIIDSVTLIKRGKVRRSRIYYIRNLSGKAARIKEIMPTKQAK

Function and Homologs

  • Product: Ribosomal Protein L19
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 50S ribosomal protein L19 (Mycoplasma feriruminatoris), 248/100%/2e-83/97%, [WP_008363858.1]
    • 50S ribosomal protein L19 (Mycoplasma capricolum), 248/100%/2e-83/98%, [ WP_046784124.1]
    • 50S ribosomal protein L19 (Mycoplasma putrefaciens), 238/100%/3e-79/92%, [WP_014035142.1]
  • Equivalent E. coli / JCVI functional protein: EG10880.

Expression

  • Expression Level: High.
  • Expression Level Hypothesis: This gene is a subunit of the bacterial ribosome, a structure which translates mRNA into protein. I hypothesize that the expression level is high because the ribosome is an essential cellular structure present throughout the cell, so too low of an expression level will limit cell fitness. This fits with the "high" expression level seen with other ribosomal proteins in Mycoplasma genitalium.
  • Expression Level References and Description: The Mycoplasma genitalium cell model of protein expression from Karr et. al: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: Right at beginning
  • Expression Level Hypothesis: Proteins must be produced through translation throughout a cell's life, and ribosomes are always present in a cell. Since an equilibrium level of protein requires some expression (as proteins are constantly degraded), and since ribosomal subunits are expressed at especially high levels, expression time is "right at beginning".
  • Expression Time References and Description: Wikipedia provides a general treatment of ribosomes: https://en.wikipedia.org/wiki/Ribosome, as does this website: http://bscb.org/learning-resources/softcell-e-learning/ribosome/. Neither address specifically when ribosomes begin to be expressed in the cell's life cycle, but it implies they are present constantly in the cell, which would require expression of the protein throughout the cell's life.

Gene Context

  • Other Components: MMSYN1_0669 --> Ribosomal protein L23 is also a subunit of the ribosome.
  • Possible Dependencies: MMSYN_0529 --> This protein is involved with binding of phenylalanine to tRNA, and thus the ribosome depends on it for proper functioning.
  • Process: 16S rRNA binding to stabilize ribosome
    • Inputs: 16S rRNA, ribosomal protein L19
    • Outputs: 16S rRNA-ribosomal protein L19 complex

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