Written by Vic Nicolis at the James Hutton Institute. This is the report from a BSPP Grace Waterhouse Fellowship. Click here to read more/apply for one yourself.
Wheat is one of the major staple crops grown in South Africa, ranking second after maize. However, in the last two decades, the hectareage under wheat cultivation in South Africa has significantly dropped from 1.4 million hectares to about 600 000 hectares.
The high input costs and low returns cause farmers to favour cash crops over staple crops, while leaving South Africa with an enormous food security threat. One of the pests exacerbating the loss of wheat yields, not only in South Africa but worldwide, is the Russian wheat aphid (Diuraphis noxia), a specialist phloem feeding insect. While resistant cultivars are the most effective strategy for controlling Russian wheat aphid infestation, the genes responsible for resistance have yet to be identified. Our study on the differentially expressed microRNA during aphid infestation have resulted in a number of nucleotide binding leucine rich repeat (NLR) targets to be identified for further investigation. Of particular interest are those targets which have integrated domain fusions (NLR-IDs) where the integrated domains serve as a bait to detect effectors. In known NLR-IDs, the protein containing the integrated domain is in a receptor complex with a secondary NLR in planta that acts as the molecular switch. Initial data suggests that this NLR-ID plays a role in the resistance response against the Russian wheat aphid. Unfortunately, due to the limited genetic resources available for wheat, identifying the secondary NLR has proved difficult. One of the best established methods for identifying protein-protein interactions is through the use of a yeast two hybrid screen, although creating a good, complex library can be challenging.
My two month fellowship visit was hosted by Dr Ingo Hein and Dr Jorunn Bos, two researchers at the James Hutton Institute situated in Invergowrie, Scotland, who welcomed me with warm conversation over a cup of coffee. The main objectives of the fellowship were to gain experience in screening a yeast two hybrid library, under the supervision of Dr Bos, and to perform a phylogenetic analysis of NLR proteins under the supervision of Dr Hein. Dr Bos works on a generalist aphid system and has tremendous experience screening yeast two hybrid libraries. Initially, the yeast two hybrid screen was to be performed using an existing barley library. However, introduction of the full-length NLR-ID into the bait construct resulted in high levels of auto-activity and this library system could not be screened. Very generously, Dr Bos allowed me to create a new library from wheat, which I believe taught me a set of valuable skills that I would not have developed by simply screening an existing library. Unfortunately, due to time constraints, I was unable to screen the created library at the James Hutton Institute and we are in the process of creating our own yeast two hybrid library in South Africa with local cultivars. We will in future collaborate more with the lab of Dr Bos as the two libraries can be mined for both aphid interactions that the two groups work on.
My work with Dr Hein and Dr Katrin MacKenzie involved an HMM analysis of over 3 000 NLR protein sequences from wheat in order to search for an evolutionary relationship between a subset of NLRs that are targeted by a miRNA. While no clear relationship between the NLRs could be established this work taught me so much about using Linux command line and the use of various phylogenetic tools in order to accomplish the analysis.
Dundee is situated on the “sunshine” coast of Scotland, which meant that the weather was pleasant and allowed for some sightseeing outside of the lab and city. I had the opportunity to visit Edinburgh during the world renowned Fringe festival and even managed a quick escape to the Scottish highlands to see famous landmarks such as Ben Nevis and Loch Ness.
My visit to the James Hutton Institute has empowered me with new skills which I intend to share with others in my department at the University of Johannesburg and collaborators at other South African universities when we create and screen our own library using a South African wheat cultivar. Learning to work within the Linux operating system allowed me to explore the daunting world of computational biology with a little more confidence. These are skills I hope to continue practicing and building upon into the future.
I thoroughly enjoyed my trip to the James Hutton Institute and would like to thank Dr Bos, Dr Hein and Dr MacKenzie for their invaluable input and assistance in accomplishing my objectives. I would also like to thank everyone in the Bos lab for making me feel so welcome and for all of their assistance. I am truly grateful to the BSPP for giving me this opportunity to travel to the UK and allowing me to gain experience from such knowledgeable researchers which I am sure will help me progress in my scientific career.