MMSYN1 0656

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Author Information

Maria Gutierrez

Basic Information

  • ID: MMSYN1_0656
  • Name: L6_bact: ribosomal protein L6
  • Organism: JCVI-Syn3.0
  • Description: The gene that produces this protein is called rplF. This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Uniprot
  • DNA Length: 543
  • DNA sequence:

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

  • Amino Acid length: 180
  • Amino Acid sequence:

MSRIGNRLLQIPNGVEVKIAENNLITITGSKGTLSKQFSPLIKIEVEENKLITKRLNEQKHTKQLHGTTNSLLQGMLTGVSEGFKKELQITGVGYKAAVNGSKLNLSLGYSHPVEFEIPKGVEIQAVKPTELVITGIDKQLVGQVAANIRAYRKPEPYKGKGIKYKNETIIRKEGKAAGK

Function and Homologs

  • Product: 50S ribosomal protein L6
  • Module: Ribosome (This protein binds to the 23S rRNA, and is important in its secondary structure.)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 50S ribosomal protein L6 [Mycoplasma feriruminatoris], 347/100%/2e-120/97%, WP_008362505.1
    • Select seq ref|WP_036432211.1| 50S ribosomal protein L6 [Mycoplasma capricolum], 346/100%/2e-120/97%, WP_036432211.1
    • Select seq emb|CBV67384.1| 50S ribosomal protein L6 [Mycoplasma leachii 99/014/6], 331/95%/1e-114/97%, CBV67384.1
  • Equivalent E. coli / JCVI functional protein: EG10869.

Expression

  • Expression Level: High.
  • Expression Level Hypothesis: Because this protein is involved in translation, then it must be highly expressed in order for it to be of aid in all of the translation the cell needs to do. It is involved in the assembly of the subunits of the ribosome, and thus is required for every single translation that occurs within the cell, and thus, vital for all its functionality.
  • Expression Level References and Description: In general, I looked at the main websites that have previously been used in class such as NCBI, UniProt, EcoCyc. I also googled my gene and its expression level and arrived at different articles that describe how L6 is important for the assembly of the ribosomal subunit NCBI and thus its expression is high.
  • Expression Time: Right at the beginning.
  • Expression Level Hypothesis: L6 is used in translation, which occurs during interphase (the first stage of the cell cycle) and then throughout the life of the cell. Since it is required for assembly of the ribosome subunits, then I hypothesized it occurs right at the beginning because ribosomes are needed at all points of the cell's lifecycle.
  • Expression Time References and Description: Googling about when translation occurs in the cell I found it it's one of the main components of interphase as well as happening throughout the cell cycle. After discussing with teachers and peers, I came to the conclusion that since L6 is required to assemble the ribosome subunits, and ribosomes are necessary since the beginning of the lifecycle of the cell, its expression time starts since the beginning of the cell.

Gene Context

  • Other Components: rplI (polypeptide: 50S ribosomal protein L9) MMSYN1 0833
  • Possible Dependencies: RNA polymerase delta subunit is involved in transcribing DNA, and the ribosome then enters and transcribes what the RNA Polymerase created. Thus the ribosome depends on the RNA Polymerase doing its job in order to be able to transcribe the mRNA.
  • Process: Translation Initiation
    • Inputs: Charged tRNA, Ribosomal subunits, mRNA, GTP, Initiation factors (IF1, IF2, IF3)
    • Outputs: Initiation complex, GDP