Bacteria as Computers: Formalizing Transcriptional Regulatory Networks by Way of Digital Logic Circuits

摘要

Bacteria display a number of qualities that are typically associated to computers. These include not only the distinct interplay between their hardware (i.e. their molecular machinery and cell structure) and the software (the information and instructions encoded in their DNA). Also, microorganisms recognize a large number of external (e.g. environmental conditions,nutrients,stress) and internal (e.g.NADH, ATP.ppGpp levels) signals as inputs that are then deterministically processed and translated into specific output responses (e.g. protein expression, growth, motility). Such a frame has opened the possibility of rcprogramming living organism for addressing a range of fundamental questions -as well as developing remarkably new biotechnological applications. In this article we discuss and ultimately advocate the adoption of Boolean formalisms and digital logic gates as a phenomenal tool for making sense of the extant architecture of transcriptional regulatory networks as well as for engineering new properties in thereby designed bacteria.