29 January 2018

Histidine signalling seems to be just as important as other routes

Underestimated communication channel in cell exposed

A specimen of Escherichia coli, the type of bacteria that was the subject of this study

Communication and signalling within cells is controlled by minute changes to the proteins involved. Scientists have already studied three of these communication channels in detail, but a fourth, using phosphorylation of histidine, could as yet not be monitored experimentally. Now researchers at Utrecht University have developed a method to do exactly that. The first, unexpected insight gained from the technique is that histidine phosphorylation seems to be just as important as the other three communication channels. The results of their research were published in Nature Methods on 29 January.

Scientists had long thought that histidine phosphorylation was a signalling route that only occurred to a limited extent in simple organisms, such as bacteria. The other three communication channels, using phosphorylation of serine, threonine or tyrosine, were thought to be more important in higher organisms. However, recently an increasing amount of evidence is accumulating revealing that the phosphorylation of histidine definitely plays a role in higher organisms, including humans, as well. “It’s therefore fascinating that we can finally conduct research in this area”, explains research leader Simone Lemeer from Utrecht University.

Action as reaction to changes

Simone Lemeer

The four above-mentioned communication channels are used to react to changes in the environment through actions within the cell, Lemeer explains. In cell biology, these actions are therefore called ‘signalling routes’. These signals include viral infections, medications, or changes in the individual’s DNA that cause cancer. The phosphorylation of one or more types of proteins then starts a chain reaction, which leads to changes in the cell’s activities, such as cell division, migration or death.

Needle in a haystack

The phosphorylation of histidine was discovered in 1962, but proved extremely difficult to study. “It was like looking for a needle in a haystack”, says Lemeer. The percentage of proteins involved in this signalling route in humans is smaller than in the other routes. In addition, they are unstable under the conditions under which protein research is normally conducted. As a result, the methods used to study the other signalling routes are not applicable to the phosphorylation of histidine.

Completely unexpected

Het kweken van de Escherichia coli op een voedingsbodem

Doing a bacterial culture

The researchers therefore decided to first develop a method for studying the histidine communication channel in bacteria (the Escherichia coli, see image), because they have fewer proteins and enzymes. They also created the optimal conditions for obtaining the highest possible percentage of proteins in which histidine was phosphorylated. “These analyses show that histidine phosphorylation may be just as important as the other signalling routes. That was completely unexpected”, tells Lemeer.

Culture medium influences signalling route

The researchers also showed that differences in the environment, and hence in signals, do indeed influence the histidine signalling route. To study this, they compared the phosphorylation and bacteria growth for different culture mediums. These proved to lead to differences in both the signalling and metabolism.

Further research into antibiotics resistance

“In our subsequent research, we will look at how histidine phosphorylation can be related to antibiotics resistance. This could lead to a new path towards dealing with resistance”, according to co-author Albert Heck from Utrecht University.

This research was funded in part by NWO (Vidi grant for Simone Lemeer, and the Roadmap Initiative Proteins@Work), and the European Union Horizon 2020 programme (MSmed programme).

Publication

Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry based proteomics
Nature Methods, DOI 10.1038/nmeth.4580, 29 January 2018
Clement M Potel, Miao-Hsia Lin, Albert J R Heck en Simone Lemeer*
* All authors are affiliated with Utrecht University