Genomic and proteomic signatures of radiation adaptation in the Arthrospira genus and beyond

SCK•CEN Mentor

Janssen Paul, pjanssen@sckcen.be, +32 (0)14 33 21 29

Expert group

Microbiology

SCK•CEN Co-mentor

Goussarov Gleb , ggoussar@sckcen.be , +32 (0)14 33 28 18

Introduction

Arthrospira are cyanobacteria with a high protein content and rich in carbohydrates, essential fatty acids, and a variety of minerals, vitamins, and nutritional pigments such as beta-carotene. Hence, Arthrospira species have a long history of human consumption (now being commercialised under the name ‘Spirulina’) and are also used worldwide as feed for fish, poultry, and farm animals. Besides their nutritional value Arthrospira species are known for their clinical relevance (e.g. as antioxidants and immunity modulators), their potential in bioremediation and biosequestration, and their applied use in CO2 mitigation and biofuel technology. The Arthrospira sp. PCC 8005 strain was selected by the European Space Agency as an oxygen producer as well as a nutritional end-product for the life support system MELiSSA.

When we investigated the genomic stability of irradiated PCC 8005 cells (since this strain would be used in space missions hence subjected to cosmic radiation) we were surprised to find that this strain could withstand up to 5,000 Gray of gamma radiation. To put this in perspective, the average dose for 50% lethality (LD50) in mammals is about a thousand times less, or 5 Gy. This remarkable radioresistance in strain PCC 8005 was further investigated by whole-genome DNA sequencing and microarray-based gene expression analysis. We are currently also investigating two subtypes of this strain using RNAseq and a range of other molecular and biochemical approaches.

Objective

An extensive comparative genome analysis of oligonucleotide (OU), codon and aminoacid usage patterns will be undertaken within the genus Arthrospira in reference to  other prokaryote genomes. These composition-based approaches will help us to unravel the adaptive strategies employed by Arthrospira to survive extreme high doses of radiation.

In addition, for a wide range of prokaryotes adapted to ionising radiation (IR), a full catalogue of genes involved in all aspects of radioresistance will be made including genes that are, according to literature, involved in ROS-avoidance and –detoxification, general antioxidant functions,  metal ion homeostasis, oxygen transport, redox sensing, cell wall synthesis, cell division, SOS-response, and DNA-repair. Any other cellular processes reportedly affected by IR will be investigated. Based on this catalogue (which would entail building a database of protein sequences for all selected genes) a search will be undertaken for Arthrospira orthologs by performing a BLASTp operation of this database against the eight Arthrospira proteomes known sofar (Arthrospira platensis YZ, C1, and NIES-39, Arthrospira sp. TJSD091, Arthrospira maxima CS328, and  three subtypes of strain PCC 8005). In parallel, protein sequences corresponding to IR-affected PCC 8005 genes (fold change between 2 and 0.5) will be collected to form a protein sequence set that will be compared (by BLASTp) to the proteomes from a range of IR-sensitive and IR-resistant organisms. It is expected that these bioinformatic analyses will give first clues on the distribution of particular genes and their products across multiple organisms and may result in a broad correlation between the presence and absence of certain genes, or the differential expression of certain genes, in respect to IR-resistant and IR–sensitive phenotypes. In this way we also hope to identify protein signatures that allow the reliant discrimination between IR-sensitive and –resistant bacteria.

The minimum diploma level of the candidate needs to be

Academic bachelor

The candidate needs to have a background in

Informatics , Statistiek, Bioinformatica, Computationele Biologie

Estimated duration

4 maanden