Scientists at IOCB Prague have discovered a new molecular mechanism involved in the initiation of gene transcription. The research, published in Nature Chemical Biology, details how certain molecules known as alarmones can initiate the process by which genetic information is transcribed from DNA into RNA.
Alarmones are present in many organisms and their levels typically rise when cells are under stress. These molecules can serve as non-standard "caps" at one end of an RNA strand, offering protection during times of cellular threat. While canonical RNA caps are well understood for their role in stability and regulation, the formation and attachment mechanisms for these alternative caps have remained unclear.
The study, led by Dr. Hana Cahová and her team, focused on how bacterial RNA polymerase uses dinucleoside polyphosphates (NpNs)—a type of alarmone—to start transcription instead of conventional building blocks. For the first time, researchers described at the atomic level how RNA with an alarmone cap is created directly at the onset of gene transcription. They also found that NpNs interact through a different base pairing than usual.
Valentina Serianni from Cahová's team demonstrated that dinucleoside polyphosphates could initiate gene transcription. Jana Škerlová contributed structural analysis using cryogenic electron microscopy (cryo-EM) to show precisely how these molecules bind within the active site of RNA polymerase.
Hana Cahová stated: "We're describing something that truly occurs in cells and that we're now able to observe directly at the level of individual molecules. This allows us to answer fundamental questions about cellular processes, such as how cells adapt to stress. RNA plays a central role in this, as it carries the cascade of information underlying any cellular response – for example, to threatening conditions caused by nutrient deprivation or temperature shock."
Dr. Tomáš Kouba led the cryo-EM component of the project. He explained: "Cryogenic electron microscopy allows us to freeze biological molecules in a state very close to their natural form and then determine their three-dimensional structure. This makes it possible to look directly into the active centers of enzymes and observe their function down to the atomic level."
In 2025, IOCB Prague opened a new cryo-EM center designed specifically for advanced structural biology research, enabling scientists to examine biological processes with high precision.
