Researchers at the Indian Institute of Science (IISc), in collaboration with the Institute of Mathematical Sciences (IMSc), have identified how a protein called Lsr2 helps Mycobacterium tuberculosis protect itself from foreign DNA that may be inserted into its genome. This discovery could inform future drug development targeting this protein, potentially aiding efforts to combat tuberculosis.
"This protein is interesting to study as it controls a large set of genes in the bacteria," said Mahipal Ganji, Assistant Professor at the Department of Biochemistry, IISc, and corresponding author of the study.
Previous research has established that Lsr2 is essential for Mtb to infect other organisms. In this recent work, researchers found that Lsr2 silences regions of Mtb DNA containing genetic material introduced by external sources such as viruses. If these foreign genes are expressed, they can disrupt normal cellular function, making it important for the bacterium to suppress their activity.
The mechanism involves Lsr2 binding to DNA segments rich in adenine (A) and thymine (T). When enough Lsr2 proteins are present near each other, they aggregate or condense on these regions. This condensation prevents the cell’s machinery from reading and transcribing these DNA segments—a unique method by which Lsr2 blocks potentially harmful gene expression.
To investigate this process, the team used single-molecule imaging, computer simulations, and microscopy to observe individual bacterial cells. They created various long strands of DNA with different base compositions to monitor how Lsr2 interacts with them. A technique developed by Ganji during his postdoctoral work at TU Delft enabled visualization of single DNA strands stretched over glass slides. "Very few labs around the world currently use this method," Ganji noted.
Through these approaches, researchers determined that one region of Lsr2 enables it to connect with other protein molecules while another region allows attachment to specific DNA sequences.
"The Mtb genome is highly GC (guanine and cytosine) rich. The foreign gene … is high in AT (adenine and thymine) content, which is why this protein silences these sections of the DNA," explained Prakshi Gaur, PhD student in Ganji's lab and one of the lead authors.
"If we can design some proteins that target these regions, we could stop Lsr2 from forming these condensates," added Thejas Satheesh, former Master's student and another lead author. The team suggests this strategy could help prevent Mtb from infecting hosts.
Further research will focus on understanding how these condensates halt transcription within the bacterium and how other proteins interact with and regulate Lsr2’s function.
