Thompson Lab Dictyostelium Research

The social amoeba Dictyostelium discoideum provides a simple model system to investigate cell and developmental biology processes that are seen in more complex animals or associated with human disease. A key strength of Dictyostelium is that its relative simplicity and advanced molecular genetics, enables us to address several major scientific questions relevant to human biology.

How can random differentiation be harnessed during embryonic development?

The remarkable similarity of genetically identical twins illustrates the precise reproducibility of embryonic development. Any variation is thought to lead to errors, which can have disastrous consequences. Researchers have long sought to understand the molecular mechanisms underlying embryonic development and have generally assumed them to be exact.

However, recent observations challenge this idea with noise and stochasticity resulting in extensive cell-cell variation and heterogeneous gene network activity. In normal development, do cells ignore this variation, or use it to their advantage? For example, in stem cell cultures, all cells receive the same amount of signal, yet few cells respond.

Although, this inefficiency represents one of the greatest challenges in stem cell based regenerative medicine, in normal development, this variation could ensure a continuous supply of stem cells. Furthermore, it is now becoming apparent that embryonic pattern can begin with seemingly chaotic salt and pepper differentiation, followed by sorting out into ordered patterns.

Our work seeks to understand the molecular basis of this variation using genetic manipulation, biochemical analysis, mathematical modelling and live imaging in a simple developmental system, the social amoeba D. discoideum. Our studies will have major implications on our understanding of stem cell differentiation and developmental patterning.

Cheaters and the evolution of cooperation

‘Survival of the fittest’ is central to our understanding of evolution. However, understanding the evolution of cooperative behaviour remains a challenge. This is because the evolution of ‘cheaters’ that pay fewer costs than cooperating altruists should be favored.

We believe that identifying the genes and pathways regulating cooperative behaviors will help solve this problem, since some genetic changes might result in gains that are offset by other fitness costs. To test this we are using D. discoideum, which forms fruiting bodies consisting of hardy spores supported by dead stalk cells.

Stalk cells sacrifice themselves to enable the dispersal of spores, raising the question of why selection does not lead to ‘cheater’ strains that do not become stalk cells. We have recently found that D. discoideum strains recognise one another and can change their social ‘cheating’ strategies.

We are now trying to understand the molecular or genetic pathways underpinning these behaviours. These data will allow us to develop a better theoretical understanding of how cooperative behaviour is maintained.

Functional Genomics in Dictyostelium

A strength of Dictyostelium is its advanced molecular genetics, and this took a large stepforward with the completion of the whole Dictyostelium genome sequence in 2005. However, akey challenge remains: understanding the function of each gene. One way to addressthis is to study mutant Dictyostelium strains in which a single gene has been removed.

However, the creation of a genome-wide mutant bank has, to date, been impossible. To overcome this limitation we are employing a new technique, REMI-seq. REMI-seq combines Restriction Enzyme Mediated Insertional (REMI) mutagenesis with Next Generation Sequencing (NGS) to generate large numbers of mutants and then identify the disrupted gene by NGS.

Each mutation position will be mapped onto the genome sequence, and be searchable on-line via the existing Dictyostelium genomic resource, dictyBase. Individual, groups and even large pools of mutants will be available to the research community via the linked Dicty Stock Center. Most importantly, this allows researchers to screen for mutants that exhibit changes in fitness when challenged (e.g. in developmental signalling or drug sensitivity).

This is because within a mixed population of multiple mutants, the number of reads of each unique sequence tag (or “barcode”) provides a quantitative measure of the relative abundance of that mutant. When these populations are subjected to selection conditions, mutants that increase or decrease their frequency can be identified by changes in barcode read counts. This new mutant resource will produce a step change in Dictyostelium genetics