Team:LCG-UNAM-Mexico:WTM

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WILD-TYPE MOLECULAR MODEL

Simbiology ® diagram of WTM

WTM simulate crucial reactions and events in the life cycle of phage T7:


  • Insertion and translocation of phage's DNA at different times


Entry of T7 DNA into the host cell occurs in several distinct stages.
Phage's DNA is arranged in three classes of genes depending on their positions, it is translocated into the cell between 6 to 10 minutes after attachment, so this order and timing drives the phage's development. This phenomenon of DNA translocation is modeled here taking into account reported insertion speeds [REFERENCE].


  • Trancription of different T7 DNA segments into polycistronic mRNAs


It has been shown that T7 genes are expressed in overlapped polycistronic mRNAs.
Transcription of T7 polycistronic mRNAs occurs only if its coding DNA segment is available in the cell, for example early phage mRNAs are present before late mRNAs given that DNA responsible for them is inserted at early stages.


  • Degradation of phage's mRNAs.


We assume the same degradation rate for all T7 polycistronic mRNAs. Until now impact of this phenomenon had not been studied. It has been found that phage messengers are stabler than Bacterial mRNAs [REFERENCE].


  • Translation of phage's mRNAs into proteins


In this model, translation is simulated assuming an environment of unlimited amino acids and ribosomes. We also assume that the rate at which ribosomes incorporate amino acids is constant over all T7 mRNA.
We define a set of translation rates for every protein taking into account a constant ribosome elongation rate and the length of the protein.


  • T7 DNA replication


DNA synthesis is simulated by taking elongation of T7 DNA polymerase as the rate-limiting step.
We assume an environment of limited free nucleotides so we can set a maximum number of T7 genomes produced in a single infection taking into account the size of the host genome (and this includes bacterial chromosomes, plasmids and other sources of free nucleotides).


  • Procapsid Assembly
  • DNA packaging and final assembly
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