1. Modeling the involvement of Rpb4/7 in the mRNA biogenesis and degradation with Object-Process Methodology
Dov Dori and Mordechai Choder
Technion - Israel Institute of Technology
August 2005
We use Object-Process Methodology to model specific biological pathways at the molecular and cellular levels.
In this study we model biogenesis and degradation of messenger RNA (mRNA) and its transport between cellular compartments.
Our aim is to gain conceptual understanding of the role various factors play in this process, focusing on currently studied Rpb4/7.
The combination of formal yet intuitive graphics and automatically-generated equivalent natural language clarifies how experimental findings fit together and raises ideas for new research where gaps in knowledge exist.

2. OPM in a nutshell: Bread Baking and Eating example
Objects (green boxes) can have states (brown rounded corner rectangles): “Person can be hungry or satisfied.” Processes (ellipse, e.g., Baking) transform objects by:
Consuming : Baking consumes Dough.
Generating: “Baking yields Bread.”
Changing their state: “Eating changes Person from hungry to satisfied.”
Oven is instrument for Baking: “Baking requires Oven.”
Dough has parts: “Dough consists of Flour, Water, and Salt.”
Temperature is an attribute of water: “Water exhibits Temperature.”
The text to the left, Object-Process Language (OPL) is a subset of English generated automatically and is fully equivalent to the OPD.
The inverse action is also possible: One can write OPL sentences and the OPD will be updated automatically accordingly.

3. The basic cellular compartments
The list above shows the hierarchy of Object-Process Diagrams (OPDs) describing the system.
The OPD (top right) zooms into the Cytoplasm showing the structure of cellular compartments.
The text below, Object-Process Language (OPL) is a subset of English generated automatically and is fully equivalent to the OPD.

4. The transcription process: mRNA synthesis
The Transcription processes consumes Ribo-nucleotides to generate mRNA within the Chromosome using the DNA and the RNA Polymerase II as instruments.
Compare the OPD with the automatically generated OPL text below.

5. Composition of RNA Polymerase II
The OPD can schematically show (as done here) the spatial arrangement of the components that comprise the RNA Polymerase II.
We propose to enhance OPCAT with spatial animation (see last slide) for enhanced visualization.

6. mRNA transport between cellular compartments
Red links indicate that some of the proposed functions of Rpb4/7in the mRNA Transport & Decay process are hypothetical.
Path names are recorded along arrows:
nc = nucleus to cytoplasm
cr = cytoplasm to ribosome
rP = ribosome to P-body
They help define the localization of mRNA-Rb4/7 Complex.

7. Rpb4/7 recruitment of Pat1
Our unpublished results suggest that Rpb4/7 is involved in translation. In OPL it means that in the Ribosome the mRNA Rpb4/7 Complex enables the Translation process, which consumes Amino Acid and yields Protein. Red links indicate uncertainty.
We also propose that
Pat1 undergoes Pat1 Recruitment by Rpb4 and Rpb7 to yield the mRNA Rpb4/7 Pat1 Complex. The red instrument links from Rpb4 and Rpb7 to Pat1 Recruitment denote that the involvement of Rpb4 and Rpb7 still needs to be experimentally verified.
Rpb4/7 recruitment of Pat1

8. Details of mRNA transport & decay
Like objects, processes can also be zoomed in.
Here we zoom into the mRNA transport & decay process.
Complete OPL text is in the next slide.
Red indicates uncertainty as to: (1) whether Ribo-nucleotides from Degradation of Bulk mRNA undergo Transport To Nucleus. RASING THIS QUESTION IS A DIRECT RESULT OF MODELING! (2) whether Deadenylation occurs only in P-body, and (3) whether Rpb4/7 participates in all these processes.

9. Details of mRNA transport & decay: The complete OPL text
This is the complete OPL text of the OPD in the previous slide.

10. Rpb4/7-dependent mRNA degradation in the P-body
Note that mRNA Transport & Decay was modeled earlier as a multi-step process. Here we zoom in the P-body and the OPD shows only the relevant steps that take place in this compartment: Decapping and Degradation.

11. mRNA transport & decay: OPCAT animated simulation example
Here we see mRNA Transport & Decay occurring with the sub-processes happen in a top-to-bottom order. We define Ribosome Entry as a process that changes Localization of mRNA from cytoplasm to ribosome: When OPCAT package is practiced, the red dots move along the arrows, the brown color of cytoplasm fades, while ribosome color is getting brown. This helps visualizing the process dynamics and finding “bugs” if one does not introduce data correctly.
OPCAT can simulate the system by animating occurrence of processes, generation and consumption of objects, and change of their states. This cannot be performed with PowerPoint and requires OPCAT to be installed.

12. adenilate cyclase complementation term:
Free text definition of Adenylate cyclase from the
Protein-Protein Interaction Ontology
adenilate cyclase complementation
term:
MI:0014
goid:
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex.
definition:
PMID:
definition_reference:

13. The translation of the textual definition of
Adenylate cyclase in previous slide to OPL script
Adenylate Cyclase consists of Catalytic Domain. Adenylate Cyclase is encoded by CyaA. Ternary Complex consists of T25, T18, and Calmodulin.             T18 and T25 are compelementary.             Calmodulin triggers Association. CyaA is a Gene . Proteolytical Cleavage consumes Catalytic Domain . Proteolytical Cleavage yields T18 and T25. Association consumes T18, T25, and Calmodulin.

14. The automatically generated OPD (top)
that is equivalent in its knowledge content to the OPL scrip (bottom),
also listed in previous slide