What does gene expression have to do with CCD?

Review: Johnson et al. (2009). Proceedings of the National Academy of Science, 106: 14790-14795

Written: October 7, 2009

Posted: 10/07/09

Word count: 749

Question: What does gene expression have to do with CCD?

Answer: Some novel insights into the possible mode of action

In case you’ve been sailing around the world for the last three years or otherwise have been without any human or media contact, honey bees have been facing some serious problems lately. Most notorious of these is a largely mysterious ailment termed Colony Collapse Disorder, or CCD, since the hallmark symptom is a rapid depopulation of the adult worker force. Purported culprits abound, but none has yet to really emerge as the front runner. Scientists have therefore been busily working on trying to find the underlying cause or causes, using various approaches that range from beekeeper surveys to colony bioassays. Another approach that several groups have taken is a genetic approach, since genes are a large part of what bees are.

Genes are something that we inherit from our parents, encoded in our DNA. Each gene codes for a protein, and the combination of all of these gene products is what makes us what we are. The pathway to making proteins from DNA is the central dogma of genetics: DNA is transcribed into RNA, and then RNA is translated into proteins. The place where RNA translation takes place, the “protein factories” in us all, are called ribosomes (more on that later). Following this process of transcription and translation, genes can be highly regulated, each being turned on or off or tuned up or down, depending on the needs of the organism. You can imagine, therefore, that the entire genome of any living thing is like a huge panel of toggle switches that get flicked on and off to deal with whatever challenges a critter might face.

Patterns of gene expression—this panel of toggle switches—can be a powerful tool to understand the effect that something has on an organism (such as disease, toxins, etc…). It is this genomic approach that a research team from the University of Illinois, lead by Reed Johnson, took to elucidate the effects of CCD on bees across all of their genes. They tested three sets of bees—one sampled from the East coast (which included both healthy and CCD bees), one sampled from the West coast (which also included both healthy and CCD bees), and one “historical” sample collected prior to the onset of CCD (which were presumably all healthy). They then compared which genes were up- or down-regulated as a consequence of being in these various groups.

The researchers found considerable variation in the different sources of bees. In other words, there were many differences in gene expression just simply based on whether the bees were from the East, West, or Historical. But, when accounting for the geographic differences, they were able to isolate 65 genes that might be potential markers for CCD (and therefore provide clues as to what might be causing it). Of that gene set, few were genes associated with detoxification enzymes, which suggests that there isn’t much of a connection with pesticide exposure with the expression of CCD. Similarly, there was no clear trend in genes associated with immune response, which suggests that there was no clear connection with any one disease agent and CCD.

Johnson and his colleagues, however, did find something unusual. They detected many small fragments of ribosomal RNA, the skeletal structure of the “protein factories” that translate RNA into protein. They speculate that these fragments might be caused by some of the viruses that infect bees, including Deformed Wing Virus (the calling card of varroa mites) and Israeli Acute Paralysis Virus, which can interfere with protein production by breaking up ribosomes. Thus these findings suggest a potential mode of action for CCD, namely viruses causing protein production and colony ill health.

While this study is more of a starting point than a conclusion, it does illustrate the power of looking at the whole genome to determine mechanism. Of course, more work will need to be done to verify this putative link. To paraphrase one of the authors in a media interview, this may not be the smoking gun, but it just might be the bullet wound.