News from CRG
There is a type of very small proteins, with less than 100 amino acids, that are essential to understanding how living things work, and about which we know virtually nothing, since merely identifying them is a veritable technological challenge.
Now, however, investigators from the Centre for Genomic Regulation (CRG) of Barcelona, led by the ICREA Research Professor Luis Serrano, head of the Design of Biological Systems group, have developed a technique that can predict and classify these proteins based on a new bioinformatics tool into which they fed multiple -omic data. This enabled them to discover that these small proteins account for at least 16% of the bacterial genome.
Recent studies have shed some light on the importance of these small proteins, such as the antimicrobial peptides secreted by insects, animals, plants and even human beings in response to infection. These small proteins have also been shown to communicate with other bacteria in the environment and also with the host, such as our organism. In fact, they may play a very important role in having a balanced microbiota.
Hitherto, when a genome was annotated, only DNA segments which following transcription and translation could yield proteins with more than 100 amino acids were taken into account. Anything below this number was disregarded because of the technological challenge involved, since the usual approaches used to identify proteins are not possible precisely because they are so small. This is further complicated by the fact that these proteins tend to have a very short life, they are not abundant or they even present tissue- and time-specific expression patterns that render them even more difficult to detect.
In this research, the investigators conducted a preliminary study in 109 bacterial genomes in which they tried to classify or assign functions to these proteins. To this end, they applied algorithms already used in other settings, into which they input parameters related to the nature of a protein. They subsequently validated their findings by using proteins already identified in other bacterial species.
The technique they developed is universal and may be applied to different bacterial species.
Samuel Miravet-Verde, Tony Ferrar, Guadalupe Espadas-García, Rocco Mazzolini, Anas Gharrab, Eduard Sabido, Luis Serrano & Maria Lluch-Senar (2019). Unraveling the hidden universe of small proteins in bacterial genomes. Molecular Systems Biology 15: e8290. doi.org/10.15252/msb.20188290