Plant biologists at DBI use modern biotechnology methods to identify the molecular basis of fundamental plant processes. Their research is providing knowledge and resources for enhancing crop production and generating novel traits and products as well as enhancing understanding of all higher organisms.
DBI scientists have gotten back to the basics of plant genetics through their pioneering work on the stability of messenger RNA (mRNA) and its role in the regulation of gene expression. While knowing how mRNA is synthesized or transcribed is important to understanding gene expression, this research probes an equally significant question that, until recently, many believed inconsequential: How is mRNA degraded and how is this process controlled? It is now understood that this question is both fundamental and vital to understanding the way all genes are expressed not only in plants, but also in most organisms.
Research on this topic is led by Dr. Pamela Green, the Crawford H. Greenewalt Chair, Professor of Plant and Soil Sciences and of Marine Studies. Researchers in her team investigate the basic principles that control the stability – or rather the instability – of mRNA molecules in higher plants. They are examining the unstable mRNA transcripts that often encode regulatory proteins and are tackling three primary questions: How does the cell’s mRNA degradation machinery recognize unstable transcripts from the majority of relatively stable mRNAs? What role do RNA-degrading enzymes (ribonucleases) play in mRNA decay and other physiological processes? What is the purpose and function of non-coding RNA genes?
“When people think of how genes turn ‘on’ and ‘off’ they think of the first step in the process, which is the synthesis of mRNA from DNA, and that is an important process,” says Dr. Green. “The next step in many minds is the translation of the mRNA into protein. But there are other highly regulated processes along the way – such as the rate at which mRNA degrades —that can impact translation and are very important for switching genes ‘on’ and ‘off’ quickly.”
One way that Green’s team to investigates gene expression is by using microarrays, a method that allows them to look at nearly 14,000 distinct DNA at one time on a single microscope slide. These microarrays are then examined with fluorescent probes to identify expressed genes. Not only does this technology help the investigators look at thousands of genes at a time as opposed to examining them one by one, it also lets identify networks or clusters of those that are regulated in a similar way. Prior to joining DBI, Green led a consortium of investigators that carried out microarray experiments for the international community and deposited the data in a publicly available database at Stanford, giving researchers around the world access to the data for clustering and other applications. “Clustering allows us to make associations and form hypotheses we never could have done before because we couldn’t see all these data at once,” says Dr. Green. In the past year, this approach led Green’s group to link genes affected in an mRNA degradation mutant with regulation in response to day/night cycles. This work is being continued at the Genomics Facility at DBI, which is equipped with state-of-the-art microarray analysis equipment.
In other experiments, researchers in Dr. Green’s group have investigated some ribonucleases that are likely to degrade mRNAs inside the cell and some that are secreted outside the cell membrane, where RNA is not usually found. Their recent data has led them to a novel hypothesis about this phenomenon: These patrolling enzymes have a role in regulating the permeability or integrity of the cell membrane, a function that could have broad significance.
Along with these discoveries, the group has also uncovered the existence of what might be called hidden genes. These non-coding RNA genes produce RNA molecules that do not make protein and have been undetected in the past because traditional methods of searching look only for protein-coding molecules. Using novel techniques and software programs, Dr. Green and her colleagues are investigating these hidden genes that they believe may have tremendous impact on plant physiology.
The work of Dr. Janine Sherrier, also on the faculty of the University’s Department of Plant and Soil Sciences, explores plant microbe interactions, plant development and proteomics, the emerging area of biological tissue protein composition. Of particular interest to Dr. Sherrier and her fellow researchers is the close relationship between legumes, the soil microbe rhizobia, and the consequent nitrogen-fixing root nodule.