Common proteins and different genes

Earth’s species have more in common than previously believed, but tomatoes are really quite different.

That’s the fascinating – and actually not contradictory – take-home message from two recent studies.

In the first, an international team analysed the proteins found in 100 different species – from bacteria and archaea to plants and humans – and learned that they have a number of common characteristics. 

In the second, analysis of genetic variation among tomatoes uncovered 230,000 previously hidden large-scale differences in DNA between varieties.

The protein project, a major collaboration between Denmark’s University of Copenhagen and the Max Planck Institute of Biochemistry in Germany, is described in a paper in the journal Nature.

To date, the authors say, researchers have mainly focussed on the DNA of organisms, but with advancements in the technology used for studying these organisms at the molecular level, they have turned to proteins as “the workhorses of the cell”.

“A common characteristic of all these life forms is the fact that a high percentage of their proteomes focus on maintaining a sort of balance, what is called as homeostasis,” says co-author Alberto Santos Delgado.

“Another common characteristic is the fact that a large share of the proteins help to generate energy, even though the ways in which this is done differ – from photosynthesis to carbohydrate burning.”

Previous research has predicted how many and which proteins exist based on the genetic code and bioinformatic calculations. The new mapping provided data on the existence of a very large number of new proteins, doubling the number confirmed experimentally.

“Our work connecting quantitative mass spectrometry-based proteomics with database resources has resulted in a data set of eight million data points with 53 million interconnections,” says co-author Johannes Mueller. The data have been made publicly available.

The second study, led by Cold Spring Harbor Laboratory (CSHL) and Johns Hopkins University in the US and published in the journal Cell, is, the authors say, the most comprehensive analysis to date of structural genome variation for a major crop.

Once again, new technology made it possible. Advances in DNA sequencing and genome editing allowed the researchers to detect structural variants and study how they affect crop traits. “There was a whole massive amount of natural genetic variation that we were blind to,” says co-author Xingang Wang from CSHL.

The group sequenced and compared the genomes of 100 different varieties of tomato, including robust varieties suitable for industrial agriculture, succulent heirlooms, and wild relatives of cultivated tomatoes.

Within those genomes, the team identified the more than 230,000 structural variants and discovered that thousands of genes were changed by these structural changes.