MMSYN1 0540

From BioE80 Boot
Jump to: navigation, search

Author Information

Luísa Galhardo

Basic Information

  • ID: MMSYN1_0540
  • Name: rpsB
  • Organism: JCVI-Syn3.0
  • Description:

This gene codes for the S2 protein, a component of the 30S subunit of the ribosome. It is a necessary structural component of the ribosome (UniProt), which contains a 30S and 50S subunit. S2 is required for S1 (another ribosome structural protein) binding to the ribosome (EcoCyc). Expression of S2 is autoregulated, involving conserved elements located in the 5' UTR of the rpsB-tsf mRNA. Regulation may also involve the S1 protein (EcoCyc). This gene is generally well-conserved as ribosomal proteins tend to be, since they are so necessary for cell survival and reproduction. Ribosomes are central to translation of RNA to protein. S2 is involved in the formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome (InterPro).


  • DNA Length: 879 base pairs.
  • DNA sequence:

ATG TCA CGC GAG ATC ACG CGC GAA GAA CTT AGC GCT GCG GGT GTA CAG TAT GGG CAT CAG ACT AAA CGC TGG AAT CCA AAG ATG AAG TCG TAC ATT TATGGC GTT AAA AAT AAG AAT CAC ATT ATC GAC CTT GAG AAG ACC ATT ACG CAT CTT AAC ACT GCC CAG AAA TTA TTA GAG ACC CTT GGA AGT AAG CAG CAAAAG ATC CTT TTC GTT GGA ACG AAG CGT TCC GGT AAA AAT GCC GTC AAA GAA GCC GCC TTA CGC TCC GGG AAC TTC TAT ATT AAT AAC CGC TGG CTT GGAGGC ACA TTA ACG AAT TTG AAA ACC ATT TTA ATT CGT ATT AAA GCC TTG TGG GAA ATT GAG GAA GAA GAG AAA AAG GGC CGC TTG TCT TTA CGC ACT AAGAAA GAG CAG ATT AAG ATC TTG AAA GAA AAA GCA AAA TTA GAG AAG GCA CTT GGA GGC ATT AAA CAA ATG CAT AAA TTG CCA GCC GCA ATT GTA GTA GTCGAT CCA AAG GGC GAT GAG ATC GCC GTT AAG GAA GCG AAG AAA TTA AAT ATT CCC GTA ATT GCA ATT TGT GAC ACC AAC GCC GAT CCT GAC ATG ATT GACTAC GTT ATC CCC GGT AAT GAC GAT TTG CAA GAG AGT GTG AAT CTG ATT ATC AAT ATT CTG GTT GAG GCA TAC GCT GAA GGC GCC CAG ATT AAG ATG AATCCA TCC GTA TTA AAG ACT GTG GCT CCC AAA CGT GAG CCT CGT CAG AAC CGT GTC ATG ACG CCT GTG GTA GAG AAT CAG TCA ACG GAG CAA CAA GCT TCCGAG AAT GTC TCG AAT ACA CAA GTT AGC AAC GAG CCC GTG ACG CCT GTA GTG GAG GTT GAG AAG AGT TCA GAA CCG AAG GCA GAA TAG

  • Amino Acid length: 292 amino acids.
  • Amino Acid sequence:

MSREITREELSAAGVQYGHQTKRWNPKMKSYIYGVKNKNHIIDLEKTITHLNTAQKLLETLGSKQQKILFVGTKRSGKNAVKEAALRSGNFYINNRWLGGTLTNLKTILIRIKALWEIEEEEKKGRLSLRTKKEQIKILKEKAKLEKALGGIKQMHKLPAAIVVVDPKGDEIAVKEAKKLNIPVIAICDTNADPDMIDYVIPGNDDLQESVNLIINILVEAYAEGAQIKMNPSVLKTVAPKREPRQNRVMTPVVENQSTEQQASENVSNTQVSNEPVTPVVEVEKSSEPKAE

Function and Homologs

  • Product: Ribosome 30s subunit S2 component
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 30S ribosomal protein S2 [Mycoplasma capricolum subsp. capricolum], 528/100%/0.0/91%, Q2SSA8.1
    • 30S ribosomal protein S2 [Mesoplasma florum], 373/82%/4e-130/73%, Q6F0Q4.2
    • 30S ribosomal protein S2 [Spiroplasma citri], 282/84%/5e-93/57%, P19679.2
  • Equivalent E. coli protein: EG10901.

Expression

  • Expression Level: high
    • Expression Level Hypothesis:

The ribosome is necessary for translation to make proteins, so we would need a lot of this subunit to help for the ribosome in the cell.

    • Expression Level References and Description:

File:MgenitaliumSimProteinCounts.xlsx shows that this protein is expressed at a high level. This makes sense with UniProt which describes this subunit as integral to ribosome formation.

  • Expression Time: early
    • Expression Time References and Description:

Ribosomes are not necessary for originally transcribing DNA to RNA, so this would likely not be needed right at the beginning, but the subunit would still be necessary early on since it is integral to forming ribosomes for making proteins (UniProt).

Gene Context

  • Other Components: The 30S part of the ribosome also needs the rpsL subunit.
  • Possible Dependencies: The ribosome depends on tRNA for translation to happen.
  • Process: Lengthening an amino acid chain
    • Inputs: amino acid chain(n), charged tRNA
    • Outputs: amino acid chain(n+1), tRNA

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