Design patterns of biological cells

• Published in: BioEssays Vol. 46; no. 3; pp. e2300188 - n/a
• Main Authors: Andrews, Steven S., Wiley, H. Steven, Sauro, Herbert M.
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.03.2024; Wiley
• Subjects: BASIC BIOLOGICAL SCIENCES; cell biology; cell biology modeling; cell signaling; Design; design principles; E coli; Escherichia coli - genetics; Escherichia coli - metabolism; Metabolic Networks and Pathways; metabolism; Models, Biological; reaction network; Signal Transduction; systems biology; Yeasts; systems biology; cell biology modeling; metabolism; cell signaling
• ISSN: 0265-9247; 1521-1878
• DOI: 10.1002/bies.202300188

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of ion for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems. The chemical reaction networks that animate cell biology can be ed into a set of design patterns, each of which is a generalized solution to a frequently recurring problem. We present a catalog of 21 such patterns that describe cellular biosynthesis, reaction network structure, and reaction network function.