This is the report from a BSPP Undergraduate ‘Vacation’ Bursary.
Click here to read more/apply for one yourself.
The potato is one of the most popular vegetables in the UK, however the potato growing industry suffers losses in excess of £50M per year from potato blackleg disease. Blackleg disease is a soft rot disease whereby pathogenic bacteria such as the ones from the Pectobacterium spp. produce enzymes such as cellulases that allow them to degrade plant cell walls. While this capability of Pectobacterium is disastrous for the potato growing industry, it is quite interesting in terms of biotechnological applications. For example, food or paper mill waste contains high volumes of cellulose, which can be degraded using a process called anaerobic digestion and converted into renewable energy in the form of methane gas. In this process, the initial breakdown of cellulose is often the rate-limiting step which leads to poor methane yields. Therefore, by analysing the genomes of Pectobacterium species with a focus on metabolic processes such as complex carbon degradation, we can gain more understanding on how the species can degrade plant cell walls so easily while also assessing the potential of Pectobacterium for waste treatment processes.
I started the project by getting all publicly available Pectobacterium atrosepticum (Pba) and Pectobacterium parmentieri (Pbp) genomes from NCBI and adding additional Pba and Pbp genomes provided by the James Hutton Institute which were obtained from soft-rotting potato tubers. I then annotated all the Pba and Pbp genomes to identify all their coding and non-coding regions. Using this annotated assemblies, I then performed pan-genome analysis to gain a better picture about which genes are conserved and which are accesory in Pba and Pbp. The reason for this is that Pba and Pbp can easily acquire genes from other organisms which may promote the emergence of new metabolic pathways, increase virulence, or even provide the microbes resistance to drugs. From the pangenome data, I then recovered metabolic function profiles in the form of presence-absence tables with a particular focus on major biochemical pathways such as complex carbon degradation, nitrogen fixation, and other nutrient cycles.
I observed that complex carbon degrading functions are conserved among Pectobacterium species, with both Pba and Pbp having genes for degrading cellulose, chitin and other complex oligosaccharides. However, there was functional dissimilarity across genomes from the two species, explained by differences in functions such as beta-galactose degrading activity or perchlorate reduction, which were present in Pba but not in Pbp. Moreover, Pba genomes had a high number of genes involved in nitrogen fixation and nitrate reduction, which were almost completely absent in Pbp.
In the future, these data and results will be linked with metadata about the genomes such as strain, isolation source or sensitivity to bacteriocins, and pangenome association will be performed to compute associations between genes and phenotypical traits.
Working on this project was an amazing experience which gave me the chance to improve my bioinformatics skills and work with the latest tools and technologies, so I would like to thank the BSPP for providing me with this opportunity. Last but not least, I would like to thank Dr Ciara Keating and Dr Umer Ijaz for their guidance with scripting, running analysis, organising tutorials and catch-ups, and with providing me an amazing team to work in!
Alexandru-Nicolae Popescu
University of Glasgow
