EG12098 jsdeng

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Author Information

Shelly Deng

Basic Information

  • ID: EG12098
  • Name: Ribosomal Large Subunit Pseudouridine Synthase D
  • Organism: E.Coli
  • Description: In E.Coli, ribosomal large subunit pseudouridine synthase D catalyze the synthesis of pseudouridine from uracil, a nucleobase in RNA at positions 1911, 1915, and 1917 in helix 69 (H69) of the 23S ribosomal RNA, resulting in three pseudouridines clustered at those locations [1]. In the absence of this gene in E. Coli, severe growth inhibition results [2] because the loss of pseudouridylation at those three positions (1911, 1915, and 1917 in 23S rRNA) resulted in defect in ribosome assembly, biogenesis, and function [3]. Without the pseudouridine synthase D, 70S ribosomes decreased, 50S and 30S subunits which make up the 70S ribosome increase, and 62S and 39S particles newly appeared. 62S is derived from the breakdown of unstable 70S ribosomes, and 39S particles are immature precursors of 50S subunits [4]. This shows that the pseudouridine synthase D is important for the assembly of 70S ribosomes.
  • DNA Length: 981 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 326 amino acids.
  • Amino Acid sequence:

MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL

Function and Homologs

  • Product: Pseudouridine Synthase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: ribosomal large subunit pseudouridine synthase D [Proteobacteria], 666/ 100%/0.0/100%, WP_000079100.1
    • MULTISPECIES: ribosomal large subunit pseudouridine synthase D [Enterobacteriaceae], 665/100%/0.0/99%, WP_000079112.1
    • ribosomal large subunit pseudouridine synthase D [Shigella flexneri], 664/100%/0.0/99%, WP_000079121.1
  • Equivalent JCVI functional protein: MMSYN1 0416 (Please note that MMSYN1 0416 is an unknown gene that share few similarities with this rluD gene. They are not exactly equivalence.)

Expression

  • Expression Level: Medium
    • Expression Level Hypothesis: The rluD gene plays an important role in the assembly of 70S ribosomes in E. coli. Since ribosomes are present in sizable quantity in E. coli, it makes sense that this rluD-like gene has medium expression level to make sure that the ribosomes assemble without defects.
    • Expression Level References and Description: E. coli proteimic expression data was referenced, and the cited sources from the description section provided necessary knowledge to make this hypothesis.
  • Expression Time: Early
    • Expression Level Hypothesis: Ribosomes are much needed early on for protein production, thus this gene/protein which potentially aids with the assembly of ribosomes should be expressed early.
    • Expression Time References and Description: The cited sources from the description section provided necessary knowledge to make this hypothesis.

Gene Context

  • Other Components: None in this module
  • Possible Dependencies: Transcription of DNA into rRNA (DNA must be first transcribed by RNA Polymerase to rRNA, more specifically 23S rRNA, which will provide the source of uridine[5][6].
  • Process: Catalysis of pseudouridine synthesis from uridine [7]

Construct

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  • 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