Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum

Abstract

BackgroundPhysarum polycephalum is a free-living amoebozoan protist displaying a complex life cycle, including alternation between single- and multinucleate stages through sporulation, a simple form of cell differentiation. Sporulation in Physarum can be experimentally induced by several external factors, and Physarum displays many biochemical features typical for metazoan cells, including metazoan-type signaling pathways, which makes this organism a model to study cell cycle, cell differentiation and cellular reprogramming.ResultsIn order to identify the genes associated to the light-induced sporulation in Physarum, especially those related to signal transduction, we isolated RNA before and after photoinduction from sporulation- competent cells, and used these RNAs to synthesize cDNAs, which were then analyzed using the 454 sequencing technology. We obtained 16,669 cDNAs that were annotated at every computational level. 13,169 transcripts included hit count data, from which 2,772 displayed significant differential expression (upregulated: 1,623; downregulated: 1,149). Transcripts with valid annotations and significant differential expression were later integrated into putative networks using interaction information from orthologs.ConclusionsGene ontology analysis suggested that most significantly downregulated genes are linked to DNA repair, cell division, inhibition of cell migration, and calcium release, while highly upregulated genes were involved in cell death, cell polarization, maintenance of integrity, and differentiation. In addition, cell death- associated transcripts were overrepresented between the upregulated transcripts. These changes are associated to a network of actin-binding proteins encoded by genes that are differentially regulated before and after light induction.

A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes

“…18 We initially identified sequences encoding a DYW domain in three ESTs obtained in an early transcriptome study. 19 Our initial observation prompted us to scan preliminary genome assemblies of the ongoing Physarum polycephalum sequencing project (http:// genome.wustl.edu/genomes/detail/physarum-polycephalum), which revealed additional occurrences of loci encoding DYW domains. The existing contigs in the Physarum genome database are relatively small, largely due to the repetitive nature of the genome and recombination.…”

“…[16][17][18][19][20] in Physarum and predict that the total number of PPR proteins, i.e., including those lacking a DYW domain, will likely exceed 100 in this myxomycete (Fig. 2).…”

A Next-Generation Sequencing Approach to Study the Transcriptomic Changes during the Differentiation of Physarum at the Single-Cell Level

“…Replicate data distributions were 1.85 and 1.82 Gb corresponding to the starved plasmodium (cDNA library replicates D1 and D2), and 1.67 and 1.78 Gb for the cells collected 6 hours after photoinduction (libraries L1 and L2; Table 1). Therefore, assuming a 10% of protein-encoding genes, we obtained a 237.32x coverage for the 300 Mb genome of Physarum 13. Later, from the de novo assembly of the trimmed sequencing output, we obtained 909,505 sequences, with a N50 contig size of 371 bp.…”

“…Well-established Mendelian genetics and the occurrence of naturally synchronous macroscopic cells as source of homogeneous cell material for biochemical analyses have made Physarum an attractive model organism for studying the regulatory control of cell differentiation. Recent advances in sequencing technologies motivated detailed analyses of transcriptome dynamics during the life cycle of Physarum 12,13. These studies were performed using RNA isolated from cell populations.…”

Conductivity patterning with Physarum polycephalum: natural growth and deflecting

“…Physarum polycephalum belongs to the Physarales species, once defined as fungi, today simply slime mold [3][4][5]. It is a unicellular organism made by a myriad of nuclei dispersed in the cytoplasm.…”