Global transcriptional regulation by small non-coding RNAs is required for the response to injury of a filamentous fungus

The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring fine tuned regulation by small RNAs for adequate healing of the wounded area. We previously reported that in response to injury, the filamentous fungus Trichoderma atroviride uses molecular mechanisms very similar to those of plants and animals. These processes lead to the formation of new hyphae and the development of asexual reproduction structures (conidiophores). Here we show that regulation by sRNAs of nitrogen metabolic processes and the cellular redox balance is necessary to carry out the correct response to injury. We further discover microRNA-like RNAs (milRNAs) related with the development of conidiophores. Finally, using a loss-of-function and transcriptomic approach, we demonstrate that a milRNA plays a central role in growth and hyphal regeneration in the filamentous fungus T. atroviride, which regulates signaling and cell proliferation at the transcriptional level. Although many classes of small RNAs have been profiled in fungi, and showed to be important for contending with different types of stress, this is the first report showing a physiological function of a milRNA in fungi.