In a discovery that could reshape our understanding of bacterial biology — and possibly the future of antibiotics — scientists have overturned a central model that has been taught in textbooks for nearly half a century.

A collaborative team from Kolkata’s Bose Institute and Rutgers University has revealed that a long-accepted mechanism of how bacteria regulate their genes may not actually apply to many bacterial species. Their findings, published in the prestigious Proceedings of the National Academy of Sciences (PNAS), challenge the well-known “sigma cycle,” a model that has shaped molecular biology since the 1970s.

For decades, students and scientists believed that bacteria turn their genes on through special proteins called sigma factors. These factors were thought to latch onto RNA polymerase — the enzyme that reads DNA — simply to kick-start the process, and then detach once transcription begins. This idea was built around observations from the bacterium E. coli, specifically its sigma factor known as σ70.

But the new study shows that this system is not universal.

The researchers found that in Bacillus subtilis, a common soil bacterium, the main sigma factor called σA doesn’t leave after initiating transcription. Instead, it stays attached to RNA polymerase throughout the entire process. Even more surprisingly, a modified version of the E. coli σ70 behaves the same way.

“Our work shows that in Bacillus subtilis, the sigma factor stays attached all the way through,” said Dr. Jayanta Mukhopadhyay of the Bose Institute. “This fundamentally changes how we think about bacterial transcription and gene regulation.”

To uncover this, the team used an advanced mix of biochemical tests, chromatin immunoprecipitation, and cutting-edge fluorescence imaging — effectively allowing them to “watch” bacterial transcription in real time. What they saw was unmistakable: the classical sigma cycle doesn’t hold true for all bacteria.

Co-author Aniruddha Tewari said the discovery opens new pathways for research. “These findings show that the long-accepted sigma cycle is not universal. It gives us fresh directions to explore how bacteria regulate genes and how these systems evolved.”

Why does this matter?

Understanding how bacteria control their genes is crucial for everything from treating infections to engineering bacteria for useful purposes. If different bacteria use different strategies, it could dramatically impact how scientists design antibiotics to block harmful microbes. It may even help create engineered bacteria capable of producing biofuels, plastics, medicines, or other valuable compounds more efficiently.

The implications extend far beyond academic curiosity — they could influence how the world tackles antibiotic resistance, develops new drugs, and harnesses microbial power for industry.

The study was led by Dr. Mukhopadhyay and Dr. Tewari from the Bose Institute, with contributions from Shreya Sengupta, Soumya Mukherjee, and Nilanjana Hazra, as well as renowned researchers Yon W. Ebright and Richard H. Ebright from Rutgers University.

Their message is clear: it’s time to rethink what we thought we knew about bacteria.