Revolutionary Discovery at Bose Institute Challenges Decades-Old Bacterial Transcription Paradigm

In a groundbreaking study published just weeks ago, researchers at Bose Institute in Kolkata have upended a foundational model of bacterial gene expression that has stood for over 50 years. The work focuses on Mycobacterium tuberculosis (Mtb), the pathogen behind tuberculosis (TB), revealing that the behavior of sigma factors—key proteins in transcription initiation—varies dramatically depending on the factor involved. This finding not only rewrites textbook knowledge but also opens fresh avenues for tackling one of India's most pressing public health challenges.

The sigma cycle model, long assumed universal across bacteria, posits that sigma factors bind to RNA polymerase (RNAP), the enzyme responsible for transcribing DNA into RNA, to start gene expression, then detach during the elongation phase to allow recycling for other genes. However, the Bose team demonstrated that while some sigma factors follow this pattern, others like σF cling tenaciously to RNAP throughout transcription, ensuring persistent expression of survival genes under stress.

The TB Menace in India: A National Priority

India bears a staggering 25% of the global TB burden, with approximately 2.7 million active cases reported in 2025 alone, translating to an incidence rate of 187 per lakh population in 2024—down 21% from 237 in 2015. Despite progress, multidrug-resistant TB (MDR-TB) accounts for 32% of global cases here, with 1.3-1.5 lakh new DR-TB instances emerging yearly, claiming nearly half a million lives annually. Mtb's ability to persist in hostile host environments, like lung macrophages, hinges on precise gene regulation, making transcription a prime target for innovation.

This crisis underscores the urgency of basic research at institutions like Bose Institute, India's oldest biomedical research center established in 1917, which continues to drive higher education and scientific excellence.

Demystifying Bacterial Transcription: From DNA to Action

Transcription is the first step in gene expression, where RNAP, guided by sigma factors, reads DNA promoters to synthesize messenger RNA (mRNA), which is then translated into proteins. Sigma factors confer promoter specificity; bacteria like Mtb have 13, including principal σA for housekeeping genes, stress-responsive σE (extracytoplasmic function, ECF group), and σF for stationary phase survival.

In the classic model, sigma binds RNAP's core (comprising subunits α2ββ'ω), forms the holoenzyme, initiates at -10/-35 promoter boxes via sigma's region 2 and 4, then releases post-promoter clearance to free sigma for reuse. But Mtb, adapted for persistence, defies this uniformity.

The Bose Institute Pioneers: Meet the Research Team

Led by Dr. Jayanta Mukhopadhyay, Professor in the Department of Chemical Sciences, and first author Dr. Nilanjana Hazra, the team leveraged Bose Institute's state-of-the-art facilities. Dr. Mukhopadhyay's lab specializes in prokaryotic transcription, particularly RNAP-sigma-regulator interactions in Mtb, building on prior work identifying SigA regulons.

Bose Institute, an autonomous DST entity, fosters interdisciplinary higher education through PhD programs and collaborations, nurturing talent amid India's research ecosystem.

Photo by Mihai Dragomirescu on Unsplash

Unpacking the Methodology: Rigorous Science at Work

The study employed multifaceted approaches:

• In vitro assays: Purified Mtb RNAP core, σA/σE/σF from E. coli, fluorescent labeling (DyLight488 on RNAP β', TMR on sigma).
• Electrophoretic mobility shift assay (EMSA): Monitored sigma occupancy from open promoter complex (RPo) to initial transcribing complex (RPitc) and elongation complex (TEC).
• Fluorescence anisotropy/FRET: Quantified binding dynamics and domain rearrangements (σ2/σ3 stable in σF, σ4 displaced).
• In vivo ChIP-qPCR: In M. smegmatis overexpressing Mtb sigmas, confirming promoter-to-gene body occupancy gradients.

Initiation factors like NusA enhanced σA release at certain promoters (e.g., sinP3, rrnAP3), but not σE/σF.

Key Findings: Sigma Behaviors Decoded

σF's lack of region 1.1 enables σ2/σ3 anchoring in TEC, sustaining stress gene transcription crucial for Mtb latency.Published in Nucleic Acids Research, this challenges the 'universal' sigma cycle.

Targeting Persistent TB: Therapeutic Horizons

Mtb's dormancy evades standard antibiotics; σF retention ensures survival genes stay active. Disrupting σF-RNAP or NusA-σA interfaces could sensitize persisters. Sigma factors influence drug resistance; prior studies link them to efflux pumps. This positions sigma dynamics as novel targets, sidestepping active site resistance like rifampicin.DST highlights antimicrobial potential.

In India, where MDR-TB looms, such insights align with Ni-kshay Poshan Yojana and national elimination goals postponed to 2030.

Bose Institute's Legacy in TB Research

Bose has pioneered Mtb studies, from SigA promoters via genomic SELEX to CarD/RbpA roles. Dr. Mukhopadhyay's group advances understanding of mycobacterial RNAP uniqueness, training PhDs for India's research pipeline.

Photo by White Field Photo on Unsplash

Global Ripples and Future Outlook

This revises bacterial models beyond Mtb, aiding broad-spectrum antimicrobials. Ongoing Bose work explores sigma regulons; collaborations with IITs amplify impact. With India's R&D investments, expect sigma-targeted inhibitors in trials soon.NDTV coverage.

Stakeholders—from ICMR to pharma—eye translation, bolstering India's higher ed research stature.

Stakeholder Views and Challenges Ahead

• Govt/Policy: DST funding vital; integrate into End-TB Strategy.
• Clinicians: Faster diagnostics/treatments needed for DR-TB.
• Researchers: Domain-specific inhibitors promising but validation required.

Cultural context: TB stigma delays care; community education key.