MMSYN1 0809

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Author Information

Jonah Eisenberg

Basic Information

  • ID: MMSYN1_0809
  • Name: rplA
  • Organism: JCVI-Syn3.0
  • UniProt ID: [1]
  • Description: The L1 protein is a component of the 50S subunit of the ribosome and also functions in the post-transcriptional regulation of the ribosomal protein genes encoded in the L11 operon. Ribosomes lacking L1 show a lower translation activity than wild type and are defective in binding of aminoacylated tRNA. L1 has been identified within a 3-D map of the 70S ribosome constructed by cryo-electron microscopy. L1 interacts with a region in the 5' end of 23S rRNA. It also can be crosslinked to a region near the central fold of aminoacylated tRNA in the P and E site. L1 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center. L1 is a translational repressor of the synthesis of L11 and L1, the proteins encoded by the L11 operon. Synthesis of L1 is regulated by translational coupling to the synthesis of L11. The target site for L1 binding to the mRNA is near the translation initiation site of L11, and the presence of 23S rRNA relieves translational inhibition by L1. The predicted secondary structure of the L1 binding region within 23S rRNA and rplKA mRNA is similar and has been studied experimentally.

Both the growth rate control and stringent control of the synthesis of ribosomal proteins L11 and L1 are resulting from translational regulation by L1.

  • DNA Length: 681 base pairs.
  • DNA sequence:

ATG GCG AAG ATC TCA AAA CGC TTC AAG GAA GCT CTT AGC AAA GTC GAA AAA AAC AAA GTG TAT CCC CTG ACT CAG GCC CTG GAC TTG GCG AAG CAA ACAAGT ACA ACT AAG TTT GAC TCC ACC GTG GAA GTC GCC TTC AAT CTT AAT ATC GAC CCG CGC AAA GCG GAC CAA CAG ATT CGT GGC GCC GTA GTT TTA CCCGCT GGT ACG GGG AAA ACC CAG CGC GTG CTG GTC TTA ACG AAT ACT AAA ACC AAG GAG GCA GAG CAA GCA AAA GCA GAC ATC GTA GGG GGA GAA GAG CTGATT AAC CGC ATC AAG AAC GAA AAT TGG TTC GAC TTT GAC ATC ATC GTT GCT ACC CCG GAG ATG ATG GCG AAG CTG GGT GCT ATT GGA AAG ATT CTT GGGCCG AAA GGA CTG ATG CCT AAT CCG AAG ACG GGC ACT GTG ACC TTG GAC GTT GCT AAG GCG GTA GAT GAT ATC AAA AAA GGT AAA GTA GAA TAC CGC GCGGAT AAA GAG GGT AAC ATT CAC TTA ATC ATC GGA AAA GTT AGC TTT GAA ATC GAA AAG CTT GAG GAA AAT TTC AAG GCA GTT ATT GAT GAA ATC CGC CGTGTC AAA CCA CAA ACG GTG AAG GGG GAC TAT ATC AAG AAT GTG ACG CTT TCG ACG ACA ATG GGT CCT GGC ATC AAA GTA GAG TTC TAA

  • Amino Acid length: 226 amino acids.
  • Amino Acid sequence:

MAKISKRFKEALSKVEKNKVYPLTQALDLAKQTSTTKFDSTVEVAFNLNIDPRKADQQIRGAVVLPAGTGKTQRVLVLTNTKTKEAEQAKADIVGGEELINRIKNENWFDFDIIVATPEMMAKLGAIGKILGPKGLMPNPKTGTVTLDVAKAVDDIKKGKVEYRADKEGNIHLIIGKVSFEIEKLEENFKAVIDEIRRVKPQTVKGDYIKNVTLSTTMGPGIKVEF

Function and Homologs

  • Product: 50S ribosomal protein L1.
  • Closest homologous proteins: The top homologous proteins to this protein, as identified by BLAST searches.
    • 50S ribosomal protein L1 (Mycoplasma mycoides), 451/100%r/2e-160/99%, [2]
    • 50S ribosomal protein L1 (Mycoplasma feriruminatoris), 444/100%/8e-158/97%, [3]
    • 50S ribosomal protein L1 (Mycoplasma capricolum) 443/100%/2e-157/97%, [4]
  • Equivalent E. coli protein: EG10864.

Expression

  • Expression Level: High
  • Expression Level Hypothesis: The gene product is a component of the 50S ribosome subunit, so its expression level is a limiting factor for ribosome production. Because ribosomes are produced frequently in cells, the expression level is high.
  • Expression Level References and Description: Information from File:MgenitaliumSimProteinCounts.xlsx. There are 293 counts of this protein per bacterial cell, making its expression level high-- sure of this choice.
  • Expression Time: Right at beginning.
  • Expression Level Hypothesis: Cells must be able to produce proteins from the outset, and proteins cannot be created without ribosomes. Cells have ribosomes at the start of their life cycle, but more must by synthesized from the start in order to enable translation of other proteins.
  • Expression Time References and Description: Reasoning based on fact that translation is crucial to cells at any point in the life cycle.

Gene Context

  • Other Components in the functional module: MMSYN1_0663
  • Possible Dependencies: RNA Polymerase
  • Process: L1 is a translational repressor of the synthesis of L11 and L1, the proteins encoded by the L11 operon. Synthesis of L1 is regulated by translational coupling to the synthesis of L11. The target site for L1 binding to the mRNA is near the translation initiation site of L11, and the presence of 23S rRNA relieves translational inhibition by L1. [5]
    • Inputs: mRNA
    • Outputs: mRNA+L1

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