EG10857

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Author Information

Sruti Arulmani

Basic Information

  • ID: EG10857
  • Name: Ribonuclease III
  • Organism: E. coli
  • Description: RNase III digests double stranded RNA and is used in the cell for the purpose of processing rRNA precursors, viral transcripts, some mRNAs and some tRNA (in particular, metY - a particular type of Met-tRNA). The function of this gene is to encode ribonuclease III (RNase III)- the primary purpose of RNase III is to digest double stranded DNA and process primary rRNA (ribosomal RNA) transcripts into the precursors of large and small rRNAs. The RNase cleaves the primary transcripts at these specific sites (to produce these specific lengths) to convert them into a more mature RNA form (an intermediate of the final rRNA that will be functional). These RNAs mostly play a role in ribosomal function. (Uniprot) Ultimately, the main role that RNase III plays in the bacterial cells is to refine the RNA components that are vital for other protein synthesis machinery. The 23S rRNA that is cleaved to correct size by RNase III is the center of peptidyl transferase activity in 50S subunit of the bacterial ribosome - this type peptidyl transferase action is what allows amino acids to join during translation by the ribosome. (Beringer et al., 2007) Similarly, 16S rRNA (which is also cleaved into the right size by RNase III) plays a significant role in ribosomal activity - this short rRNA binds to the Shine-Dalgarno sequence of the mRNA that is to be translated (allowing the ribosome to be correctly positioned). Both of these mature rRNAs are cleaved to the correct size by RNase III. However, RNase III can also be involved in the refinement of other RNAs as well -it also processes mRNAs and tRNAs that are encoded within the rRNA operon in the genome as well. If the organism has type II CRISPR loci in the organism, RNase III also processes the corresponding pre-crRNA and tracRNA. (Zamore, 2001)
  • DNA Length: 681
  • DNA sequence:

ATGAACCCCA TCGTAATTAA TCGGCTTCAA CGGAAGCTGG GCTACACTTT TAATCATCAG GAACTGTTGC AGCAGGCATT AACTCATCGT AGTGCCAGCA GTAAACATAA CGAGCGTTTA GAATTTTTAG GCGACTCTAT TCTGAGCTAC GTTATCGCCA ATGCGCTTTA TCACCGTTTC CCTCGTGTGG ATGAAGGCGA TATGAGCCGG ATGCGCGCCA CGCTGGTCCG TGGCAATACG CTGGCGGAAC TGGCGCGCGA ATTTGAGTTA GGCGAGTGCT TACGTTTAGG GCCAGGTGAA CTTAAAAGCG GTGGATTTCG TCGTGAGTCA ATTCTCGCCG ACACCGTCGA AGCATTAATT GGTGGCGTAT TCCTCGACAG TGATATTCAA ACCGTCGAGA AATTAATCCT CAACTGGTAT CAAACTCGTT TGGACGAAAT TAGCCCAGGC GATAAACAAA AAGATCCGAA AACGCGCTTG CAAGAATATT TGCAGGGTCG CCATCTGCCG CTGCCGACTT ATCTGGTAGT CCAGGTACGT GGCGAAGCGC ACGATCAGGA ATTTACTATC CACTGCCAGG TCAGCGGCCT GAGTGAACCG GTGGTTGGCA CAGGTTCAAG CCGTCGTAAG GCTGAGCAGG CTGCCGCCGA ACAGGCGTTG AAAAAACTGG AGCTGGAATG A

  • Amino Acid length: 226
  • Amino Acid sequence:

MNPIVINRLQ RKLGYTFNHQ ELLQQALTHR SASSKHNERL EFLGDSILSY VIANALYHRF PRVDEGDMSR MRATLVRGNT LAELAREFEL GECLRLGPGE LKSGGFRRES ILADTVEALI GGVFLDSDIQ TVEKLILNWY QTRLDEISPG DKQKDPKTRL QEYLQGRHLP LPTYLVVQVR GEAHDQEFTI HCQVSGLSEP VVGTGSSRRK AEQAAAEQAL KKLELE

Function and Homologs

  • Product: Ribonuclease III
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Ribonuclease III [Shigella boydii], 462/100%/2e-170/100, WP_078166985.1
    • Ribonuclease III [Enterobacteriaceae], 458/100/83-169/98%, WP_003037579.1
    • Ribonuclease III [Pluralibacter gergoviae], 458/100/9e-169/, WP_048285700.1
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0418

Expression

  • Expression Level: High
  • Expression Level Hypothesis: The expression level may be high since RNase III is involved in cleaving rRNAs and the met-tRNA that starts every polypeptide chain - the prevalence of these components must be really high (which requires a high level of RNase activity.)
  • Expression Level References and Description: The expression level is annotated as high in the database File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: Right at the beginning, but perhaps also continued throughout cell development
  • Expression Level Hypothesis: The function of RNase III is necessary in both early ribosomal biogenesis, but also continued through protein translation later in the cell's development as well.
  • Expression Time References and Description: [[1]]

Gene Context

  • Other Components: No other functional modules are required for RNase III to be fully functional and cleave rRNAs - however, rRNAs and tRNAs do require other functional modules to achieve their final mature state. E.g. EG10270 operates in the same functional module of producing mature ribosome subunit RNA components such as 16S rRNA.
  • Possible Dependencies: Though RNase III itself doesn't require other components to complete it's function of cleaving RNA, it does require that RNA is already made before it operates. Transcription must take prior to the cleaving process, suggesting that RNA polymerase module is operating first.
  • Process: Ribosome biogenesis is the process that RNase III partakes in - cleaving rRNA 16S and 23S that will be incorporated into ribosome subunits. The inputs are RNA and the outputs are rRNA for RNase III. Once the rRNA is functional and operating in the ribosome, the input of the system is RNA and the output is polypeptide chains.
    • Inputs: 16S rRNA, 23S rRNA, met-tRNA
    • Outputs: Mature 16S rRNA, Cleaved 23S rRNA, cleaved met-tRNA

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