Bacterial Protein Universe is Much Larger Than Expected

The bacterium Mycoplasma pneumoniae, one of the smallest known microbes and a mild disease-causing human pathogen, has 43% more genes than previously thought, according to the findings of a study published in the journal Nature Communications. The findings were made by researchers at the Centre for Genomic Regulation (CRG) in Barcelona.

“Given that M. pneumoniae is of the most well-studied living organisms in biology, it’s a surprise to find it has an entire hidden universe of proteins that was waiting to be discovered. E. coli, another well-known bacterium, has around four thousand protein-coding genes in its genome, while humans have twenty thousand. Both these numbers could be a significant underestimate,” explains Dr. Samuel Miravet Verde, first author of the paper.

The researchers were able to expand the known list of genes by developing a technique which can detect stretches of DNA which code for any protein, regardless of its size. Traditional methods are usually only good at detecting proteins which are at least 100 amino acids long. Small proteins which fall under this size are often overlooked in research because of these limitations.

The technique, called ProTInSeq, works by using DNA sequences which can move around in the genome, also known as transposons. The researchers engineered transposons to express a marker only if they insert into a part of the genome that's being used to make a protein. When combined with a method which can read huge amounts of DNA very quickly and accurately, researchers can see where the transposons have inserted themselves.

When combining traditional methods with the new technique and applying these to M. pneumoniae, the researchers identified most known genes and also revealed 302 new ones, all of which coded for small proteins. A quarter of the newly identified genes code for proteins with potential antimicrobial properties. These types of proteins offer a different mechanism of action against pathogens compared to traditional antibiotics, opening new avenues for tackling antibiotic resistance.

“With antibiotic resistance on the rise, finding new targets for antibiotic action is more critical than ever. The small proteins with antimicrobial properties we report are one way of tackling this emerging threat. Applying ProTInSeq to other types of bacteria could significantly accelerate the discovery process,” says Dr. Miravet Verde.

The study adds to the growing body of evidence of the tiny but mighty role exerted by small proteins in biology. “Small protein-coding genes are like dark matter. One is essential for the structure of the cosmos, the other for the intricate complexity of life. They are both found in abundance yet are largely overlooked because they evade standard detection methods. By pushing the boundaries of technology, we’ve been able to explore the hidden realms in the genome in comprehensive detail. What we have yet to discover might outweigh what we currently understand,” concludes Dr. Luis Serrano, co-author of the paper and Director of the Centre for Genomic Regulation.

Imagen: Scanning electron microscope image of Mycoplasma pneumoniae cells. Credit: María Lluch/Center for Genomic Regulation