The sequence of regulatory events in the sporulation control network of Physarum polycephalum analysed by time-resolved somatic complementation of mutants

Mitochondrial numbers increase during glucose deprivation in the slime mold Physarum polycephalum

Glucose deprivation in the slime mold Physarum polycephalum leads to a specific morphotype, a highly motile mesoplasmodium. We investigated the ultrastructure of both mesoplasmodia and non-starved plasmodia and found significantly increased numbers of mitochondria in glucose-deprived mesoplasmodia. The volume of individual mitochondria was the same in both growth forms. We conjecture that the number of mitochondria correlates with the metabolic state of the cell: When glucose is absent, the slime mold is forced to switch to different metabolic pathways, which occur inside mitochondria. Furthermore, a catabolic cue (such as AMP-activated protein kinase (AMPK)) could stimulate mitochondrial biogenesis.

A lumped parameter model of endoplasm flow in Physarum polycephalum explains migration and polarization-induced asymmetry during the onset of locomotion

The plasmodial slime mold Physarum polycephalum exhibits strong, periodic flow of cytoplasm through the veins of its network. In the special case of mesoplasmodia, a newly described starvation-induced, shape-constant morphotype, this periodic endoplasm streaming is the basis of locomotion. Furthermore, we presume that cytoplasm flow is also involved in signal transmission and signal processing. Mesoplasmodia motility resembles amoeboid locomotion. In contrast to other amoebae, however, mesoplasmodia move without extending pseudopods and retain a coherent, fan-shaped morphology throughout their steady locomotion. Attaining sizes of up to 2 mm², mesoplasmodia are also much bigger than other amoebae. We characterize this particular type of locomotion and identify patterns of movement. By using the analogy between pulsatile fluid flow through a network of elastic tubes and electrical circuits, we build a lumped model that explains observed fluid flow patterns. Essentially, the mesoplasmodium acts as a low-pass filter, permitting only low-frequency oscillations to propagate from back to front. This frequency selection serves to optimize flow and reduces power dissipation. Furthermore, we introduce a distributed element into the lumped model to explain cell polarization during the onset of chemotaxis: Biochemical cues (internal or external) lead to a local softening of the actin cortex, which in turn causes an increased flow of cytoplasm into that area and, thus, a net forward movement. We conclude that the internal actin-enclosed vein network gives the slime mold a high measure of control over fluid transport, especially by softening or hardening, which in turn leads to polarization and net movement.

Patterns of cell thickness oscillations during directional migration of Physarum polycephalum

The functional relationship between the velocity of cell locomotion and intracellular spatial patterns of thickness oscillations in the acellular slime mould Physarum polycephalum was studied. The freely migrating plasmodial cells of 300-800 µm length were tadpole-shaped and displayed thickness oscillations along their longitudinal (body) axis. Two distinct patterns of intracellular thickness oscillations were observed in dependence on the locomotive velocity. The first mode consisted of a single travelling wave that propagated from the rear to the front of the cell. This pattern occurred when the plasmodium migrated slowly. The second mode was a multinodal standing wave that was found during events of fast propagation. Transitions between these two types of cell thickness oscillation patterns took place in narrow propagation velocity intervals. We discuss the possible mechanism leading to these patterns, which are conjectured to modulate both the intracellular pressure and the velocity of free locomotion of the cell.

Switch-like reprogramming of gene expression after fusion of multinucleate plasmodial cells of two Physarum polycephalum sporulation mutants

Nonlinear dynamic processes involving the differential regulation of transcription factors are considered to impact the reprogramming of stem cells, germ cells, and somatic cells. Here, we fused two multinucleate plasmodial cells of Physarum polycephalum mutants defective in different sporulation control genes while being in different physiological states. The resulting heterokaryons established one of two significantly different expression patterns of marker genes while the plasmodial halves that were fused to each other synchronized spontaneously. Spontaneous synchronization suggests that switch-like control mechanisms spread over and finally control the entire plasmodium as a result of cytoplasmic mixing. Regulatory molecules due to the large volume of the vigorously streaming cytoplasm will define concentrations in acting on the population of nuclei and in the global setting of switches. Mixing of a large cytoplasmic volume is expected to damp stochasticity when individual nuclei deliver certain RNAs at low copy number into the cytoplasm. We conclude that spontaneous synchronization, the damping of molecular noise in gene expression by the large cytoplasmic volume, and the option to take multiple macroscopic samples from the same plasmodium provide unique options for studying the dynamics of cellular reprogramming at the single cell level.

Futile attempts to differentiate provide molecular evidence for individual differences within a population of cells during cellular reprogramming

The heterogeneity of cell populations and the influence of stochastic noise might be important issues for the molecular analysis of cellular reprogramming at the system level. Here, we show that in Physarum polycephalum, the expression patterns of marker genes correlate with the fate decision of individual multinucleate plasmodial cells that had been exposed to a differentiation-inducing photostimulus. For several hours after stimulation, the expression kinetics of PI-3-kinase, piwi, and pumilio orthologs and other marker genes were qualitatively similar in all stimulated cells but quantitatively different in those cells that subsequently maintained their proliferative potential and failed to differentiate accordingly. The results suggest that the population of nuclei in an individual plasmodium behaves synchronously in terms of gene regulation to an extent that the plasmodium provides a source for macroscopic amounts of homogeneous single-cell material for analysing the dynamic processes of cellular reprogramming. Based on the experimental findings, we predict that circuits with switch-like behaviour that control the cell fate decision of a multinucleate plasmodium operate through continuous changes in the concentration of cellular regulators because the nuclear population suspended in a large cytoplasmic volume damps stochastic noise.

Automatic reconstruction of molecular and genetic networks from discrete time series data

We apply a mathematical algorithm which processes discrete time series data to generate a complete list of Petri net structures containing the minimal number of nodes required to reproduce the data set. The completeness of the list as guaranteed by a mathematical proof allows to define a minimal set of experiments required to discriminate between alternative network structures. This in principle allows to prove all possible minimal network structures by disproving all alternative candidate structures. The dynamic behaviour of the networks in terms of a switching rule for the transitions of the Petri net is part of the result. In addition to network reconstruction, the algorithm can be used to determine how many yet undetected components at least must be involved in a certain process. The algorithm also reveals all alternative structural modifications of a network that are required to generate a predefined behaviour.

Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors

Phys (phytochromes) are a superfamily of photochromic photoreceptors that employ a bilin-type chromophore to sense red and far-red light. Although originally thought to be restricted to plants, accumulating genetic and genomic analyses now indicate that they are also prevalent among micro-organisms. By a combination of phylogenetic and biochemical studies, we have expanded the Phy superfamily and organized its members into distinct functional clades which include the phys (plant Phys), BphPs (bacteriophytochromes), Cphs (cyanobacterial Phys), Fphs (fungal Phys) and a collection of Phy-like sequences. All contain a signature GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA) domain, which houses the bilin lyase activity. A PHY domain (uppercase letters are used to denote the PHY domain specifically), which helps stabilize the Pfr form (far-red-light-absorbing form of Phy), is downstream of the GAF region in all but the Phy-like sequences. The phy, Cph, BphP and Fph families also include a PLD [N-terminal PAS (Per/Arnt/Sim)-like domain] upstream of the GAF domain. Site-directed mutagenesis of conserved residues within the GAF and PLD motifs supports their importance in chromophore binding and/or spectral activity. In agreement with Lamparter, Carrascal, Michael, Martinez, Rottwinkel and Abian [(2004) Biochemistry 43, 3659-3669], a conserved cysteine within the PLD of several BphPs was found to be necessary for binding the chromophore via the C-3 vinyl side chain on the bilin A ring. Phy-type sequences were also discovered in the actinobacterium Kineococcus radiotolerans and collections of microorganisms obtained from marine and extremely acidic environments, thus expanding further the range of these photoreceptors. Based on their organization and distribution, the evolution of the Phy superfamily into distinct photoreceptor types is proposed.

Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation

We reconstruct the regulatory network controlling commitment and sporulation of Physarum polycephalum from experimental results using a hierarchical Petri Net-based modelling and simulation framework. The stochastic Petri Net consistently describes the structure and simulates the dynamics of the molecular network as analysed by genetic, biochemical and physiological experiments within a single coherent model. The Petri Net then is extended to simulate time-resolved somatic complementation experiments performed by mixing the cytoplasms of mutants altered in the sporulation response, to systematically explore the network structure and to probe its dynamics. This reverse engineering approach presumably can be employed to explore other molecular or genetic signalling systems where the activity of genes or their products can be experimentally controlled in a time-resolved manner.

Detecting functional interactions in a gene and signaling network by time-resolved somatic complementation analysis

Somatic complementation by fusion of two mutant cells and mixing of their cytoplasms occurs when the genetic defect of one fusion partner is cured by the functional gene product provided by the other. We have found that complementation of mutational defects in the network mediating stimulus-induced commitment and sporulation of Physarum polycephalum may reflect time-dependent changes in the signaling state of its molecular building blocks. Network perturbation by fusion of mutant plasmodial cells in different states of activation, and the time-resolved analysis of somatic complementation effects can be used to systematically probe network structure and dynamics. Time-resolved somatic complementation quantitatively detects regulatory interactions between the functional modules of a network, independent of their biochemical composition or subcellular localization, and without being limited to direct physical interactions.

Theory of time-resolved somatic complementation and its use to explore the sporulation control network in Physarum polycephalum

Mutants of Physarum polycephalum can be complemented by fusion of plasmodial cells followed by cytoplasmic mixing. Complementation between strains carrying different mutational defects in the sporulation control network may depend on the signaling state of the network components. We have previously suggested that time-resolved somatic complementation (TRSC) analysis with such mutants may be used to probe network architecture and dynamics. By computer simulation it is now shown how and under which conditions the regulatory hierarchy of genes can be determined experimentally. A kinetic model of the sporulation control network is developed, which is then used to demonstrate how the mechanisms of TRSC can be understood and simulated at the kinetic level. On the basis of theoretical considerations, experimental parameters that determine whether functional complementation of two mutations will occur are identified. It is also shown how gene dosage-effect relationships can be employed for network analysis. The theoretical framework provided may be used to systematically analyze network structure and dynamics through time-resolved somatic complementation studies. The conclusions drawn are of general relevance in that they do not depend on the validity of the model from which they were derived.