EG10504

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Author Information

Paola Martinez

Basic Information

  • Name: infA (polypeptide: Translation initiation factor IF-1)
  • Organism: E. coli
  • Description:

Overview and Function: The major function of this gene remains unknown however some small functions have been linked to it. It has been discovered that it is really important for viability and is known to be one of the three translation initiation factors. It has been discovered that IF-1 improves the dissociation rate of 70s ribosomes through the incitation of IF-3 activity EcoCyc. It is also known that IF-1 is taken apart from the ribosome during 30S and 50S subunit association. It has also been discovered that IF-1 helps control mRNA selection which then leads the creation of the 10S pre-initiation complex UniProt. A lot of mutants have been created in efforts to figure out what it does, but so far the results have not yielded significant information. One plausible conclusion that scientists have arrived to is that IF-1, along with IF-3 may be responsible for the minimization of the ribosomes that are lacking an initiator tRNA.

IF-1 is believed to be involved in translation fidelity because it binds to the ribosomal A site and helps stabilize the binding of IF-2 and IF-3 so that N-formylmethionyl-tRNA(fMet) can bind after that. Nonetheless, these are simply speculations since the results are still not clear enough to reach that conclusion with 100% certainty EcoCyc.

Proposed Models: Fortunately, the IF-1 solution structure has been discovered and the residues that get left behind in interactions with the 30S ribosomal subunit are identified as well. When analyzing the structure, there are strong resemblances to the oligomer-binding old family of proteins EcoCyc.

Studies: In an IF-1 study, multiple mutants of the gene were created and some showed slower growth rates (makes scientists wonder in tIF-1 is important for growth rate), especially when placed in cold temperatures. Studies has also concluded that IF-1 is not involved in the recognition of the +2 codons that are found right after the start codon Stolckholms University.

  • DNA Length: 292 base pairs.
  • DNA sequence:

ATG GCA AAG GAA GAC AAT ATC GAA ATG CAA GGA ACC GTC CTT GAA ACT CTG CCC AAT ACA ATG TTT CGC GTA GAG CTG GAG AAT GGG CAC GTA GTG ACA GCA CAC ATC AGT GGC AAA ATG CGG AAA AAT TAT ATC AGA ATC TTG ACT GGC GAT AAG GTA ACC GTT GAA TTG ACT CCT TAT GAT TTG TCT AAG GGT CGT ATA GTC TTC CGG TCG AGA TAG

  • Amino Acid length: 80 amino acids.
  • Amino Acid sequence:

MAKEDNIEMQ GTVLETLPNT MFRVELENGH VVTAHISGKM RKNYIRILTG DKVTVELTPY DLSKGRIVFR SR

Function and Homologs

  • Product: Main purpose of gene remains unknown. No product has been clearly identified (look at "Description" under "Basic Information" for further details on what has been researched).
  • Module: Ribosome (binds to the ribosomal A site)
  • Closest homologous proteins: Note that since the protein itself belongs to e. coli, e. coli was excluded from the search. Multispecies Proteobacteria was also excluded because that's the top hit, but that is the protein itself (it is obviously homologous to itself).
    • translation initiation factor IF-1 [Leminorella grimontii], Max score: 147 /Query Cover: 100% /E-Value: 3e-45 /Ident: 97%, WP_027274492.1
    • translation initiation factor IF-1 [Salmonella enterica], Max score: 147 /Query Cover: 100% /E-Value: 4e-45 /Ident: 99%, WP_001040186.1
    • MULTISPECIES: translation initiation factor IF-1 [Shewanella], Max score: 147 /Query Cover: 100% /E-Value: 4e-45 /Ident: 97%, WP_005500725.1

Expression

  • Expression Level: High
  • Expression Level Hypothesis: Although the gene's function isn't totally clear, they suspect that it helps minimize the errors created when tRNA is lacking. Thus, it must have a high expression level because it must always be present in order to prevent this error from occurring (I hypothesize that the reason why scientists aren't 100% sure this is the protein's function is because this error doesn't occur frequently and thus it isn't immediately evident in mutants that don't have this gene).
  • Expression Level References and Description: The expression level information was available on the file File:EcoliProteomicExpressionData.xlsx.
  • Expression Time: Right at beginning
  • Expression Level Hypothesis: This makes sense with my gene's function because this protein is a part of the ribosome which is involved in translation. Translation begins to occur during interphase (beginning) and then continues to occur throughout the rest of the cells life. Even though it isn't a major component of the ribosome, it is probably developed when all the subunits of the ribosome are developed.
  • Expression Time References and Description: After talking to TAs in OH and discussing possibilities, I concluded that the expression of this protein should be at the beginning because it's part of the ribosome and I researched that translation occurs during interphase (the beginning) and in order for the translation to occur some ribosomes must have already been created.

Gene Context

  • Other Components: L6_bact: ribosomal protein L6 MMSYN1 0656
  • Possible Dependencies: The ribosome depends on RNA polymerase because if RNA polymerase doesn't translate the DNA into mRNA, the ribosome won't have any codons to translate to create proteins.
  • Process: Translation Initiation
    • Inputs: (catalyzed by a start codon) mRNA, tRNA (together they will form the initiation complex), GTP, other initiation factors
    • Outputs: Fully formed initiation complex
    • Resources: SparkNotes, Khan Academy

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