Discrepancy between mRNA and protein abundance: insight from information retrieval process in computers

Area of Science:

• Systems Biology
• Computational Biology
• Molecular Biology

Background:

• The discrepancy between RNA and protein abundance is a common observation in molecular biology.
• Existing theoretical frameworks struggle to explain this phenomenon, often attributing it to technical issues.

Purpose of the Study:

• To explore the gene expression process by drawing parallels with computer information flow.
• To develop a theoretical understanding of the RNA-protein abundance discrepancy using principles from computer system design.

Main Methods:

• Comparative analysis of cellular genetic information flow with computer information processing (storage to execution).
• Identification of functional similarities in architecture and retrieval processes between cellular systems (ribonome, proteome) and computer memory systems (primary, cache).
• Examination of regulatory techniques in computer systems and their cellular counterparts to optimize network performance.

Main Results:

• Functional analogies were identified between the ribonome/proteome and computer memory hierarchies.
• Similarities were found in how both systems support dynamic networks (biochemical vs. virtual).
• Computer system design principles offer a framework to understand gene expression regulation and efficiency.

Conclusions:

• The discrepancy between protein and RNA abundance is a logical consequence of optimizing cellular regulatory network efficiency.
• Interpreting this discrepancy through a systems-level perspective can reveal underlying regulatory logic.
• Computer science principles provide valuable insights into biological system design and function.