Nuclear organization and transcriptional dynamics in Dictyostelium

Deformability and collision-induced reorientation enhance cell topotaxis in dense microenvironments

In vivo, cells navigate through complex environments filled with obstacles such as other cells and the extracellular matrix. Recently, the term "topotaxis" has been introduced for navigation along topographic cues such as obstacle density gradients. Experimental and mathematical efforts have analyzed topotaxis of single cells in pillared grids with pillar density gradients. A previous model based on active Brownian particles (ABPs) has shown that ABPs perform topotaxis, i.e., drift toward lower pillar densities, due to decreased effective persistence lengths at high pillar densities. The ABP model predicted topotactic drifts of up to 1% of the instantaneous speed, whereas drifts of up to 5% have been observed experimentally. We hypothesized that the discrepancy between the ABP and the experimental observations could be in 1) cell deformability and 2) more complex cell-pillar interactions. Here, we introduce a more detailed model of topotaxis based on the cellular Potts model (CPM). To model persistent cells we use the Act model, which mimics actin-polymerization-driven motility, and a hybrid CPM-ABP model. Model parameters were fitted to simulate the experimentally found motion of Dictyostelium discoideum on a flat surface. For starved D. discoideum, the topotactic drifts predicted by both CPM variants are closer to the experimental results than the previous ABP model due to a larger decrease in persistence length. Furthermore, the Act model outperformed the hybrid model in terms of topotactic efficiency, as it shows a larger reduction in effective persistence time in dense pillar grids. Also pillar adhesion can slow down cells and decrease topotaxis. For slow and less-persistent vegetative D. discoideum cells, both CPMs predicted a similar small topotactic drift. We conclude that deformable cell volume results in higher topotactic drift compared with ABPs, and that feedback of cell-pillar collisions on cell persistence increases drift only in highly persistent cells.

Linking DNA repair and cell cycle progression through serine ADP-ribosylation of histones

Although serine ADP-ribosylation (Ser-ADPr) by Poly(ADP-ribose)-polymerases is a cornerstone of the DNA damage response, how this regulates DNA repair and genome stability is unknown. Here, we exploit the ability to manipulate histone genes in Dictyostelium to identify that ADPr of the histone variant H3b at S10 and S28 maintains genome stability by integrating double strand break (DSB) repair with mitotic entry. Given the critical requirement for mitotic H3S10/28 phosphorylation, we develop separation of function mutations that maintain S10 phosphorylation whilst disrupting ADPr. Mechanistically, this reveals a requirement for H3bS10/28 ADPr in non-homologous end-joining by recruiting Ku to DSBs. Moreover, this also identifies H3bS10/S28 ADPr is critical to prevent premature mitotic entry with unresolved DNA damage, thus maintaining genome stability. Together, these data demonstrate how serine ADPr of histones coordinates DNA repair with cell cycle progression to maintain genome stability.

Moving the Research Forward: The Best of British Biology Using the Tractable Model System Dictyostelium discoideum

The social amoeba Dictyostelium discoideum provides an excellent model for research across a broad range of disciplines within biology. The organism diverged from the plant, yeast, fungi and animal kingdoms around 1 billion years ago but retains common aspects found in these kingdoms. Dictyostelium has a low level of genetic complexity and provides a range of molecular, cellular, biochemical and developmental biology experimental techniques, enabling multidisciplinary studies to be carried out in a wide range of areas, leading to research breakthroughs. Numerous laboratories within the United Kingdom employ Dictyostelium as their core research model. This review introduces Dictyostelium and then highlights research from several leading British research laboratories, covering their distinct areas of research, the benefits of using the model, and the breakthroughs that have arisen due to the use of Dictyostelium as a tractable model system.

Dictyostelium discoideum as a Model to Assess Genome Stability Through DNA Repair

Preserving genome integrity through repair of DNA damage is critical for human health and defects in these pathways lead to a variety of pathologies, most notably cancer. The social amoeba Dictyostelium discoideum is remarkably resistant to DNA damaging agents and genome analysis reveals it contains orthologs of several DNA repair pathway components otherwise limited to vertebrates. These include the Fanconi Anemia DNA inter-strand crosslink and DNA strand break repair pathways. Loss of function of these not only results in malignancy, but also neurodegeneration, immune-deficiencies and congenital abnormalities. Additionally, D. discoideum displays remarkable conservations of DNA repair factors that are targets in cancer and other therapies, including poly(ADP-ribose) polymerases that are targeted to treat breast and ovarian cancers. This, taken together with the genetic tractability of D. discoideum, make it an attractive model to assess the mechanistic basis of DNA repair to provide novel insights into how these pathways can be targeted to treat a variety of pathologies. Here we describe progress in understanding the mechanisms of DNA repair in D. discoideum, and how these impact on genome stability with implications for understanding development of malignancy.

Methylation-directed acetylation of histone H3 regulates developmental sensitivity to histone deacetylase inhibition

Hydroxamate-based lysine deacetylase inhibitors (KDACis) are approved for clinical use against certain cancers. However, intrinsic and acquired resistance presents a major problem. Treatment of cells with hydroxamates such as trichostatin A (TSA) leads to rapid preferential acetylation of histone H3 already trimethylated on lysine 4 (H3K4me3), although the importance of this H3K4me3-directed acetylation in the biological consequences of KDACi treatment is not known. We address this utilizing Dictyostelium discoideum strains lacking H3K4me3 due to disruption of the gene encoding the Set1 methyltransferase or mutations in endogenous H3 genes. Loss of H3K4me3 confers resistance to TSA-induced developmental inhibition and delays accumulation of H3K9Ac and H3K14Ac. H3K4me3-directed H3Ac is mediated by Sgf29, a subunit of the SAGA acetyltransferase complex that interacts with H3K4me3 via a tandem tudor domain (TTD). We identify an Sgf29 orthologue in Dictyostelium with a TTD that specifically recognizes the H3K4me3 modification. Disruption of the gene encoding Sgf29 delays accumulation of H3K9Ac and abrogates H3K4me3-directed H3Ac. Either loss or overexpression of Sgf29 confers developmental resistance to TSA. Our results demonstrate that rapid acetylation of H3K4me3 histones regulates developmental sensitivity to TSA. Levels of H3K4me3 or Sgf29 will provide useful biomarkers for sensitivity to this class of chemotherapeutic drug.

Role of epigenetics in unicellular to multicellular transition in Dictyostelium

BACKGROUND

The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth between both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity.

RESULTS

While transitioning to multicellular states, patterns of H3K4 methylation and H3K27 acetylation significantly change. By combining transcriptomics, epigenomics, chromatin accessibility, and orthologous gene analyses with other unicellular and multicellular organisms, we identify 52 conserved genes, which are specifically accessible and expressed during multicellular states. We validated that four of these genes, including the H3K27 deacetylase hdaD, are necessary and that an SMC-like gene, smcl1, is sufficient for multicellularity in Dictyostelium.

CONCLUSIONS

These results highlight the importance of epigenetics in reorganizing chromatin architecture to facilitate multicellularity in Dictyostelium discoideum and raise exciting possibilities about the role of epigenetics in the evolution of multicellularity more broadly.

Effects of spatial confinement on migratory properties of Dictyostelium discoideum cells

Migratory environments of various eukaryotic cells, such as amoeba, leukocytes and cancer cells, typically involve spatial confinement. Numerous studies have recently emerged, aimed to develop experimental platforms that better recapitulate the characteristics of the cellular microenvironment. Using microfluidic technologies, we show that increasing confinement of Dictyostelium discoideum cells into narrower micro-channels resulted in a significant change in the mode of migration and associated arrangement of the actomyosin cytoskeleton. We observed that cells tended to migrate at constant speed, the magnitude of which was dependent on the size of the channels, as was the locomotory strategy adopted by each cell. Two different migration modes were observed, pseudopod-based and bleb-based migration, with bleb based migration being more frequent with increasing confinement and leading to slower migration. Beside the migration mode, we found that the major determinants of cell speed are its protrusion rate, the amount of F-actin at its leading edge and the number of actin foci. Our results highlighted the impact of the microenvironments on cell behavior. Furthermore, we developed a novel quantitative movement analysis platform for mono-dimensional cell migration that allows for standardization and simplification of the experimental conditions and aids investigation of the complex and dynamic processes occurring at the single-cell level.

Dictyostelium as a Model to Assess Site-Specific ADP-Ribosylation Events

The amoeba Dictyostelium discoideum is a single-cell organism that can undergo a simple developmental program, making it an excellent model to study the molecular mechanisms of cell motility, signal transduction, and cell-type differentiation. A variety of human genes that are absent or show limited conservation in other invertebrate models have been identified in this organism. This includes ADP-ribosyltransferases, also known as poly-ADP-ribose polymerases (PARPs), a family of proteins that catalyze the addition of single or poly-ADP-ribose moieties onto target proteins. The genetic tractability of Dictyostelium and its relatively simple genome structure makes it possible to disrupt PARP gene combinations, in addition to specific ADP-ribosylation sites at endogenous loci. Together, this makes Dictyostelium an attractive model to assess how ADP-ribosylation regulates a variety of cellular processes including DNA repair, transcription, and cell-type specification. Here we describe a range of techniques to study ADP-ribosylation in Dictyostelium, including analysis of ADP-ribosylation events in vitro and in vivo, in addition to approaches to assess the functional roles of this modification in vivo.

When Dicty Met Myco, a (Not So) Romantic Story about One Amoeba and Its Intracellular Pathogen

In recent years, Dictyostelium discoideum has become an important model organism to study the cell biology of professional phagocytes. This amoeba not only shares many molecular features with mammalian macrophages, but most of its fundamental signal transduction pathways are conserved in humans. The broad range of existing genetic and biochemical tools, together with its suitability for cell culture and live microscopy, make D. discoideum an ideal and versatile laboratory organism. In this review, we focus on the use of D. discoideum as a phagocyte model for the study of mycobacterial infections, in particular Mycobacterium marinum. We look in detail at the intracellular cycle of M. marinum, from its uptake by D. discoideum to its active or passive egress into the extracellular medium. In addition, we describe the molecular mechanisms that both the mycobacterial invader and the amoeboid host have developed to fight against each other, and compare and contrast with those developed by mammalian phagocytes. Finally, we introduce the methods and specific tools that have been used so far to monitor the D. discoideum-M. marinum interaction.

Site-specific ADP-ribosylation of histone H2B in response to DNA double strand breaks

ADP-ribosyltransferases (ARTs) modify proteins with single units or polymers of ADP-ribose to regulate DNA repair. However, the substrates for these enzymes are ill-defined. For example, although histones are modified by ARTs, the sites on these proteins ADP-ribosylated following DNA damage and the ARTs that catalyse these events are unknown. This, in part, is due to the lack of a eukaryotic model that contains ARTs, in addition to histone genes that can be manipulated to assess ADP-ribosylation events in vivo. Here we exploit the model Dictyostelium to identify site-specific histone ADP-ribosylation events in vivo and define the ARTs that mediate these modifications. Dictyostelium histones are modified in response to DNA double strand breaks (DSBs) in vivo by the ARTs Adprt1a and Adprt2. Adprt1a is a mono-ART that modifies H2BE18 in vitro, although disruption of this site allows ADP-ribosylation at H2BE19. Although redundancy between H2BE18 and H2BE19 ADP-ribosylation is also apparent following DSBs in vivo, by generating a strain with mutations at E18/E19 in the h2b locus we demonstrate these are the principal sites modified by Adprt1a/Adprt2. This identifies DNA damage induced histone mono-ADP-ribosylation sites by specific ARTs in vivo, providing a unique platform to assess how histone ADP-ribosylation regulates DNA repair.

Three-dimensional balance of cortical tension and axial contractility enables fast amoeboid migration

Fast amoeboid migration requires cells to apply mechanical forces on their surroundings via transient adhesions. However, the role these forces play in controlling cell migration speed remains largely unknown. We used three-dimensional force microscopy to measure the three-dimensional forces exerted by chemotaxing Dictyostelium cells, and examined wild-type cells as well as mutants with defects in contractility, internal F-actin crosslinking, and cortical integrity. We showed that cells pull on their substrate adhesions using two distinct, yet interconnected mechanisms: axial actomyosin contractility and cortical tension. We found that the migration speed increases when axial contractility overcomes cortical tension to produce the cell shape changes needed for locomotion. We demonstrated that the three-dimensional pulling forces generated by both mechanisms are internally balanced by an increase in cytoplasmic pressure that allows cells to push on their substrate without adhering to it, and which may be relevant for amoeboid migration in complex three-dimensional environments.

Robustness of self-organizing chemoattractant field arising from precise pulse induction of its breakdown enzyme: a single-cell level analysis of PDE expression in Dictyostelium

The oscillation of chemoattractant cyclic AMP (cAMP) in Dictyostelium discoideum is a collective phenomenon that occurs when the basal level of extracellular cAMP exceeds a threshold and invokes cooperative mutual excitation of cAMP synthesis and secretion. For pulses to be relayed from cell to cell repetitively, secreted cAMP must be cleared and brought down to the subthreshold level. One of the main determinants of the oscillatory behavior is thus how much extracellular cAMP is degraded by extracellular phosphodiesterase (PDE). To date, the exact nature of PDE gene regulation remains elusive. Here, we performed live imaging analysis of mRNA transcripts for pdsA--the gene encoding extracellular PDE. Our analysis revealed that pdsA is upregulated during the rising phase of cAMP oscillations. Furthermore, by analyzing isolated cells, we show that expression of pdsA is strictly dependent on the presence of extracellular cAMP. pdsA is induced only at ∼1 nM extracellular cAMP, which is almost identical to the threshold concentration for the cAMP relay response. The observed precise regulation of PDE expression together with degradation of extracellular cAMP by PDE form a dual positive and negative feedback circuit, and model analysis shows that this sets the cAMP level near the threshold concentration for the cAMP relay response for a wide range of adenylyl cyclase activity. The overlap of the thresholds could allow oscillations of chemoattractant cAMP to self-organize at various starving conditions, making its development robust to fluctuations in its environment.

Isolation of Dictyostelium nuclei for light and electron microscopy

The significance of amoebae for studies of nuclear architecture has considerably increased in the recent years. The availability of a protocol for isolation of nuclei in a quality sufficient for high-resolution light and electron microscopy is a prerequisite for such studies. Here we present a protocol for high enrichment of nuclei by sucrose density-gradient centrifugation. Moreover, we describe how to use these isolated nuclei as specimens for immunofluorescence and immune-electron microscopy of ultrathin sections.

Imaging nascent RNA dynamics in Dictyostelium

Dictyostelium cells have great utility for live imaging of single gene transcriptional dynamics. The cells allow efficient molecular genetics, for targeting of RNA reporters and fluorescent proteins to individual, defined loci. Dictyostelium cells share many signalling, chromatin and nuclear characteristics of larger eukaryotes, yet the cells have a relatively simple scattered differentiation programme, allowing imaging of transcriptional events in the context of stochastic developmental choices. This review will detail the methods and considerations for imaging nascent RNA dynamics at single genes in living Dictyostelium cells.

Analysis of chromatin organization by deep sequencing technologies

Micrococcal nuclease (MNase) is an endonuclease that cleaves native DNA at high frequency, but is blocked in chromatin by sites of intimate DNA-protein interaction, including nucleosomal regions. Protection from MNase cleavage has often been used to map transcription factor binding sites and nucleosomal positions on a single-gene basis; however, by combining MNase digestion with high--throughput, paired-end DNA sequencing, it is now possible to simultaneously map DNA-protein interaction regions across the entire genome. Biochemical and bioinformatic protocols are detailed for global mono-nucleosome positioning at ~160 bp spacing coverage, but are applicable to mapping more broadly or for site-specific binding of transcription factors at ~50 bp resolution.

Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote

Dynamic acetylation of all lysine-4-trimethylated histone H3 is a complex phenomenon involved in Immediate-early gene induction in metazoan eukaryotes. Higher eukaryotes express repeated copies of three closely related H3 variants, inaccessible to genetic analysis. We demonstrate conservation of these phenomena in Dictyostelium which has three single-copy H3 variant genes. Although dynamic acetylation is targeted to two H3 variants which are K4-trimethylated, K9-acetylation is preferentially targeted to one. In cells lacking Set1 methyltransferase and any detectable K4-trimethylation, dynamic acetylation is lost demonstrating a direct link between the two. Gene replacement to express mutated H3 variants reveals a novel interaction between K4-trimethylation on different variants. Cells expressing only one variant show defects in growth, and in induction of a UV-inducible gene, demonstrating the functional importance of variant expression. These studies confirm that dynamic acetylation targeted to H3K4me3 arose early in evolution and reveal a very high level of specificity of histone variant utilization in a simple multicellular eukaryote.

Characterization of NE81, the first lamin-like nucleoskeleton protein in a unicellular organism

Dictyostelium NE81 is the first protein found in a lower eukaryote with properties justifying its denomination as a lamin-like protein. Knockout and overexpression mutants revealed an important role for NE81 in nuclear integrity, chromatin organization, and mechanical stability of cells.

Lamins build the nuclear lamina and are required for chromatin organization, gene expression, cell cycle progression, and mechanical stabilization. Despite these universal functions, lamins have so far been found only in metazoans. We have identified protein NE81 in Dictyostelium, which has properties that justify its denomination as a lamin-like protein in a lower eukaryote. This is based on its primary structure, subcellular localization, and regulation during mitosis, and its requirement of the C-terminal CaaX box as a posttranslational processing signal for proper localization. Our knockout and overexpression mutants revealed an important role for NE81 in nuclear integrity, chromatin organization, and mechanical stability of cells. All our results are in agreement with a role for NE81 in formation of a nuclear lamina. This function is corroborated by localization of Dictyostelium NE81 at the nuclear envelope in human cells. The discovery of a lamin-like protein in a unicellular organism is not only intriguing in light of evolution, it may also provide a simple experimental platform for studies of the molecular basis of laminopathies.