MMSYN1 0418

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Author Information

Sruti Arulmani

Basic Information

  • ID: MMSYN1_0418
  • Name: Ribonuclease III (rnc)
  • Organism: JCVI-Syn3.0
  • Description: 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 (23S and 16S rRNAs). The RNase cleaves the primary transcripts at these specific sites (to produce these specific lengths) to convert them into their mature RNA forms. These mature 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 of 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: 699
  • DNA sequence:

ATG AAT ATT AAG AAC TTT TTT GAG AAG TAC AAT ATC AAA ATC AAC AAC GAG AAG CTG TTC AAT GAG GCC TTA ACG CAC AAC AGT TAT GCC AAT GAG CAC AAG CTT AAA TAT TCC TAC CAA CGC TTA GAA TTC CTG GGA GAT GCC ATC TTA CAA ATG TAT GTC TCG CGC TTT CTT TTC TTC AAT TAC TCA AAA CTT TCA GAG GGC GAG CTG ACT CGC CTT CGC GCG AGC ACT GTA CGC GAG GAA ACA TTG TTC CGC GTA GCC AAA GAC ATC AAT TTG GGT GCG CTG GTA AAA TTG GGA CAC GGA GAA TAC ATC ACT AAG GGG TAC GAG AAA CCA TCG ATC CTT GCC GAC GTA TTT GAA GCG CTG ACT GCA GCG ATT TAT CTT GAC CAG AAA GAA GAC GGT TTA GTA ACG TGG TTG GAT CAA ACA TTA TTC AAG TAT ATC AAA GAT TCT AAT TTC ATC AAT GAC ACT AAA GAT TTT AAG AGT GAG CTG CAA GAA CTG TTG CAA TCG GAG AAA CGC TCG GAC TTA AAA TAC ATC ATT GAG AAA GAA GAT TTT TTT GCC AAC GAA AAT AAG ATC CTT TAT ACA GTA TCT GTA AAC TTG AAC GGA CAA AAG TTC GGA GTT GGA AAG GGC TTC TCT AAA CAG GAA GCA GAA CAA AAT GCC GCA AGT GAT TGC TTA AGC AAA CTG AAA AAA CCA ACC AAC AAC TGA

  • Amino Acid length: 232
  • Amino Acid sequence:

MNIKNFFEKYNIKINNEKLFNEALTHNSYANEHKLKYSYQRLEFLGDAILQMYVSRFLFFNYSKLSEGELTRLRASTVREETLFRVAKDINLGALVKLGHGEYITKGYEKPSILADVFEALTAAIYLDQKEDGLVTWLDQTLFKYIKDSNFINDTKDFKSELQELLQSEKRSDLKYIIEKEDFFANENKILYTVSVNLNGQKFGVGKGFSKQEAEQNAASDCLSKLKKPTNN

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 [Mycoplasma mycoides], 467/100%/4e-172/99%, WP_013729583.1
    • Ribonuclease III [Mycoplasma feriruminatoris], 432/100%/4e-158/90%, WP_008363954.1
    • RIbonuclease III [Mycoplasma capricolum], 402/100%/3e-146/83%, WP_036431888.1
  • Equivalent E. coli / JCVI functional protein: EG10857

Expression

  • Expression Level: Low
  • Expression Level Hypothesis: RNase III is required to cleave mainly two types of rRNAs (meant to serve functions in ribosomes) - since they won't be processing a large quantity of RNA (relative to other RNAs), it does make sense that the expression level is fairly low.
  • Expression Level References and Description: The M. genitalium database supports the low expression level.
  • Expression Time: Beginning
  • Expression Level Hypothesis: The expression should be at the beginning of the cell's development- RNase III is required to mature the rRNA required for ribosomal function. Ribosomes and other machinery required to develop other cellular proteins (thus, RNase III function would occur at the very beginning of the cell's development).
  • Expression Time References and Description: [[1]]

Gene Context

  • Other Components: Though no other functional modules are required for RNase III to be fully functional and cleave rRNAs, rRNAs and tRNAs also require other RNases to help achieve their final mature state. e.g. MMSYN1 0257 & MMSYN1 0403 are part of the same functional module to process components such as 16S rRNAs.
  • Possible Dependencies: Transcription 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
    • Outputs: Mature 16S rRNA, Cleaved 23S rRNA

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