Decoding cell signals

In order to create a symphony, an orchestra requires the subtle contribution of dozens of different musicians, each individual playing the right part at the right moment. Such collective synergy, too, is required by cell-signaling cascades, the complex and interconnected series of pathways through which cells receive and interpret information about their surroundings.

A team of Yale biologists has begun to elucidate, in unprecedented detail, the protein interactions that compose cell-signaling pathways in the plant Arabidopsis thaliana. Using high-throughput microarray technology, the study reports the discovery of over 1,000 targets of a group of cell-signaling proteins called MAPKs. Until this study, only a handful of these proteins had been previously identified.

“Protein kinases regulate virtually every biological process,” said Michael Snyder, professor of molecular, cellular, and developmental biology and of molecular biophysics and biochemistry. “But unfortunately, the protein targets of these kinases are largely unknown.”

MAPK cascades relay information through a pathway by phosphorylating target proteins — a process that either activates or deactivates its targets. The cascade concludes with the phosphorylation of an ultimate target protein, which carries out some cellular task. Within a single cell, hundreds of MAPK cascades occur simultaneously, regulating essential cellular processes such as cell division and development, response to environmental stress, and even cell death.

MAPKs can have many different targets, and some target proteins are activated by multiple MAPKs.

It is not surprising, therefore, that researchers have yet to completely understand the organization and targets of cell-signaling cascades.

“Only a few targets of MAPK [had been] identified by traditional methods because people study these one at a time,” Savithramma Dinesh-Kumar, associate professor of molecular, cellular, and developmental biology, said.

That is where high-throughput microarrays come into the picture.

“Our method allows us to identify over a thousand targets of a number of very important plant protein kinases for the first time,” Snyder said.

Each microarray contains over 2,000 different proteins, deposited onto specially coated microscope slides. The microarray can be screened using an upstream MAPK probe, and analyzed to reveal its target proteins.

Unlike traditional methods in which MAPKs and their targets must be studied one at a time, microarrays allow researchers to streamline a once-tedious process.

“The protein microarray technology provides a robust and convenient platform for the simultaneous analysis of thousands of individual protein samples,” Dinesh-Kumar said.

Although the Yale researchers have only studied signaling pathways in the model organism Arabidopsis thaliana, MAPK cascades are fairly common in many species of plants and animals — all the way up to humans. In fact, some cancers can be linked to defects in MAPK activity.

“Although directly the targets identified in this study may not be same between plants and other organisms, mechanistically they convey similar type of signaling system,” Dinesh-Kumar said.

Most importantly, the current study lays some important groundwork, “Our analysis of signaling cascades … should provide the basis for further studies of the MAPK signaling components,” the authors wrote in their paper.

Snyder said the lab will continue to clarify the molecular nature of MAPK cascades; while the scientists may have shed light on the kinase targets, the mechanisms by which they are controlled, for example, remain unknown.

The study was published in the most recent issue of the journal Genes and Development.

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