- ID: EG10870
- Name: rplI (polypeptide: 50S ribosomal subunit protein L9)
- Organism: E. coli
- UniProt ID: P0A7R1
Overview & Function: This protein is part of the 50S subunit of the ribosome (EcoCyc). There is only one copy of it in each chromosome. L9 is considered to be a large ribosomal protein that is found in all eubacteria even though it is not essential to life. This protein has been found to be responsible for keeping track of the reading frame when there is a pause during the translation process. It is especially efficient in preventing "ribosomal hopping" during translation. Strains that do not contain this protein have higher indices of stalled ribosome, frameshifting, and stop-hopping (EcoCyc).
Location: This protein is found on the surface of the ribosome and binds to the 23S rRNA. It is the first reconstitution intermediate of its subunit. Sequence similarities have been found between this protein and other proteins which has led to it's inclusion in a family of ribosomal proteins (InterPro).
Proposed Models: Multiple models of L9 have been proposed. Some have the show that L9 is in contact with other ribosome subunits such as the 30S. Other show that it consists of N-terminal and C-terminal that are joined by alpha helical domains. Depending on the state of the tRNA there can be crosslinking of tRNA in the A site of the ribosome to L9.
Studies: There have been in depth studies on L9 and they have found that when this protein is removed or lost there is a decrease in translation fidelity. To perform these studies they identified pathways that were affected by L9 and identified which mutants of E. coli required L9 to sustain life. Studies have found a second type of mutations that are dependant on L9 that significantly reduce or inactivate the elongation factor P which is a prokaryotic protein translation factor that is necessary for the synthesis of peptide bonds in ribosomes (Wikipedia). Even further studies suggest that there are mutant cases in which L9 replenishes monosomes and lowers the amount of immature rRNA in 30S particles. Scientists have also found that L9 makes the 16S maturation in wild=type cells work much more effectively (LOPS).
- DNA Length: 600 base pairs.
- DNA sequence:
ATG CAG GTT ATC CTG CTT GAC AAA GTC GCT AAC CTG GGC TCC CTG GGC GAT CAG GTT AAT GTC AAG GCG GGG TAT GCC CGT AAC TTT TTA GTT CCA CAA GGA AAG GCT GTC CCT GCC ACC AAG AAA AAC ATT GAG TTT TTT GAG GCG CGG CGG GCA GAA TTA GAG GCT AAG CTG GCT GAG GTC TTG GCA GCC GCT AAC GCG CGG GCA GAA AAG ATA AAC GCA TTA GAA ACC GTC ACC ATT GCC AGC AAG GCG GGA GAT GAA GGT AAG CTT TTT GGA TCA ATC GGC ACT CGT GAT ATC GCT GAT GCC GTA ACT GCT GCG GGT GTG GAG GTG GCT AAG AGC GAG GTC CGG TTG CCT AAC GGA GTC CTT AGA ACA ACG GGT GAA CAT GAG GTA AGC TTC CAG GTT CAC TCG GAA GTG TTC GCA AAA GTA ATT GTG AAC GTG GTG GCT GAG TAG
- Amino Acid length: 164 amino acids.
- Amino Acid sequence:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGKL FGSIGTRDIA DAVTAAGVEV AKSEVRLPNG VLRTTGEHEV SFQVHSEVFA KVIVNVVAE
Function and Homologs
- Functional Category: Translation
- Product: 50S subunit of the ribosome involved in transcription fidelity.
- Module: Part of the Ribosome (largest ribosomal protein).
- 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).
- 50S ribosomal protein L9 [Shigella sp. SF-2015], Max score: 291 /Query Cover: 100% /E-Value: 1e-99 /Ident: 99%, WP_001196064.1
- 50S ribosomal protein L9 [Shigella dysenteriae], Max score: 291 /Query Cover: 100% /E-Value: 1e-99 /Ident: 99%, WP_001196060.1
- 50S ribosomal protein L9 [Salmonella enterica subsp. enterica], Max Score: 219 /Query Cover: 100% /E-Value: 2e-99 /Ident: 99%, KSU45648.1
- Equivalent JCVI functional protein: MMSYN1_0833.
- Expression Level: High.
- Expression Level Hypothesis: I hypothesis that it has a high level of expression because this protein is a ribosome protein. Thus, it's probably really important because it's a necessary component of the ribosome and the ribosome is in charge of protein synthesis! If it's very important, its expression level must be high.
- 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: We expect the gene will be expressed at the beginning because in order for anything else to happen in the cell we need translation to already be occurring. Since this is a ribosomal protein, without it, translation cannot occur. It seems logical to have all the ribosomes created right at the beginning so that you can later on make everything else at a faster rate (the more ribosomes that you have, the more efficient your cell will be).
- Expression Time References and Description: The ribosome is essential for translation which begins to occur during interphase. Interphase happens right at the beginning. After talking to TAs in OH and discussing possibilities, I concluded that the expression of this protein should be at the beginning so that the cell can properly develop.
- Logic: no ribosome subunits ==> no ribosome ==> no translation ==> no cell life (kind of a chicken or egg dilemma, what came first; translation or ribosome?!)
- Information of translation occuring during interphase
- Other Components: L6_bact: ribosomal protein L6 EG10869
- 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 Elongation (specifically transcription fidelity)
- 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