6/18/2026 Jeni Bushman for Illinois Grainger Engineering
New research from The Grainger College of Engineering has uncovered a general principle for understanding diverse gene expression strategies, challenging long held assumptions within the field.
Written by Jeni Bushman for Illinois Grainger Engineering
New research from The Grainger College of Engineering has uncovered a general principle for understanding diverse gene expression strategies, challenging long held assumptions within the field.
Gene expression is one of the most fundamental processes in life, converting genetic information from DNA into functional outputs like protein. Its ubiquitous two-step sequence — transcription and translation—appears on the first page of introductory biology textbooks as a central dogma. In bacteria, these processes were long believed to be tightly coordinated, or coupled. However, new research from The Grainger College of Engineering at the University of Illinois Urbana-Champaign shows that this picture is incomplete. Reported in Nature Microbiology, their findings reveal insight into the distinct coordination strategies driving bacterial gene expression.
While the assumption of universal coupling has been considered a core tenet of the field, its intricacies remained largely unexamined — an ambiguity that vexed Sangjin Kim, an assistant professor of biological physics whose lab studies gene expression using experimental, imaging, and computational approaches.
“There has been no rule to say whether coupling and uncoupling can happen in all kinds of genes, or if there can be exceptions,” Kim said. “From our perspective as physicists, we like to establish a principle that can explain everything: both the majority and the exceptions.”
Seeking to understand the inner workings of the mRNA lifecycle and its variances across bacterial species, Kim and her colleagues began by examining three species of bacteria. Their findings revealed that bacterial gene expression was governed not by a single universal mode of coordination, but by two physical variables — timing and location.
The Illinois Grainger physicists noticed that in frequently translated genes, where ribosome binding was most active, transcription and translation tended to remain closely coordinated. But when ribosome binding was infrequent, premature transcription termination was more prevalent, indicating that the transcription process often does not reach completion. This reinforced the idea that transcription-translation coupling depends on translational frequency.
Next, the researchers zeroed in on an important factor in the cell’s spatial arrangement. In E. coli, a major RNA-degrading enzyme called RNase E is located at the cell membrane, while many mRNAs are produced in the cell center. This physical separation explained why coupling between transcription and RNA degradation was rare for many transcripts. This finding also elucidated an important exception: transcripts encoding membrane proteins could experience degradation during transcription, likely due to their transcription happening at the membrane.
To determine whether these principles were specific to E. coli or reflected a broader bacterial design rule, the researchers compared evolutionarily distant species including Bacillus subtilis and Caulobacter crescentus. Their results revealed that bacteria do not universally rely on the same gene-expression strategy. Instead, each species operates with its own kinetic and spatial architecture, shaped by variables such as transcription speed, translation frequency, and RNA localization.
For engineers designing synthetic biological systems, these findings point to a new way of thinking about gene output: not as a simple linear sequence of events, but as a dynamic and spatially organized kinetic system—one whose exceptions can be understood through common physical principles.
“I think this is definitely going to change the textbook material,” Kim said.