Team:OUC-China/polycistron

Team OUC-China: Main

polycistron

In our miniToe polycistron system, we build a coupled transcription-translation model considering several events in prokaryotes to get a deep understanding of polycistron. Then we simplify this model into a more flexible model to predict how the miniToe structure changes the relative expression level in polycistron.

1.Current model for polycistron expression system

Before we modeling our system, we firstly give a short review on model of polycistron expression system. For the common model, they believe that the mRNA of different cistrons in different positions has the same abundance and if they have the same translation rate, the protein which produced by different cistrons is equal. But in the truth, the natural polycistron has many strategies in regulate the protein abundance such as the overleap or hairpin in 3’. And for the synthetic polycistron, many things just like the transcription polarity and translation coupling paly an important roles. Many of them control the protein by control the mRNA abundance. So a more precise model for polycistron is needed.

2.The coupled transcription-translation model for monocistron

In this part we will present a coupled transcription-translation model for the polycistron in prokaryotes. The model is based on the Andre S Riberio’s work, he presents a coupled transcription-translation model for monocistron. We have done some works to extend the model to use in the polycistron.

2.1 The origin model for monocistron

The origin model build by Andre S Riberio is a stochastic delayed differential equation model in sequence-level, and it can be divided into two mian part: the transcriptional part and the translational part. The transcriptional part can be described by the following events:
(1)Initiation and promoter complex formation:

\Pr o + R N A p \overset{}{\to} R N A p \cdot \Pr o (τ_{O C})

(2)Promoter clearance:

R N A p \cdot \Pr o + U_{[1, △ R N A p + 1]} \overset{}{\to} O_{1} + \Pr o

(3)Elongation:

A_{n} + U_{n + △ R N A p + 1} \overset{}{\to} O_{n + 1} + U_{n - △ R N A p} + U^{R}_{n - △ R N A p}

(4)Activation:

O_{n} \overset{}{\to} A_{n}

(5)Pausing:

\begin{array}{l} O_{n} \overset{k_{p}}{\to} O_{n_{p}} \\ O_{n} \overset{1 / τ_{p}}{\leftarrow} O_{n_{p}} \end{array}

(6)Pause release due to collision:

O_{n_{p}} + A_{n - 2 △ R N A p - 1} \overset{0.8 k_{m}}{\to} O_{n} + A_{n - 2 △ R N A p - 1} i

(7) Pause release by collision

O_{n_{p}} + A_{n - 2 △ R N A p - 1} \overset{0.2 k_{m}}{\to} O_{n} + A_{n - 2 △ R N A p - 1_{p}}

(8)Arrest:

\begin{array}{l} O_{n} \overset{k_{a r}}{\to} O_{n_{a r}} \\ O_{n} \overset{1 / τ_{a r}}{\leftarrow} O_{n_{a r}} \end{array}

(9)Editing:

\begin{array}{l} O_{n} \overset{k_{e c}}{\to} O_{n_{c o r r e c t i n g}} \\ O_{n} \overset{1 / τ_{c}}{\leftarrow} O_{n_{c o r r e c t i n g}} \end{array}

(10)Premature termination:

O_{n} \overset{k_{p r e}}{\to} R N A p + U_{[n - △ R N A p, n + △ R N A p]}

(11)Pyrophosporolysis:

O_{n} + U_{n - △ R N A p - 1} + U^{R}_{n - △ R N A p - 1} \overset{k_{p y r o}}{\to} O_{n - 1} + U_{n + △ R N A p - 1}

(12)Completion:

A_{n_{l a s t}} \overset{k_{f}}{\to} R N A p + U_{[n_{l a s t}, n_{l a s t} - △ R N A p]}

(13) mRNA degradation:

A_{n_{l a s t}} \overset{k_{d r}}{\to} ϕ

Fig.1-1 The working process of miniToe system

All the reactions happened in our first system, miniToe, can be described chronologically by following five main steps[1]: