UvA-DARE ( Digital Academic Repository ) Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Single cell profiling was performed to assess differences in RNA accumulation in neighboring hyphae of the fungus Aspergillus niger. A protocol was developed to isolate and amplify RNA from single hyphae or parts thereof. Microarray analysis resulted in a present call for 4 to 7% of the A. niger genes, of which 12% showed heterogeneous RNA levels. These genes belonged to a wide range of gene categories. Background Cellular heterogeneity within an isogenic cell population is a widespread event in both prokaryotic and eukaryotic organisms. Heterogeneity of cells can be beneficial for the organism in many ways. Many documented cases of phenotypic variability in microorganisms relate to responses to environmental stress. This suggests that phenotypic variation aids in the survival of cells under adverse conditions and therefore may be an evolvable trait [1,2]. It has been shown that mycelia of filamentous fungi are also heterogeneous. For instance, protein secretion [3-5] and gene expression [6-9] are heterogeneous between zones of fungal colonies. These differences were explained by the availability of carbon source and by spatial and temporal differentiation [7]. Heterogeneous gene expression can even be found within a zone of a colony. In fact, expression of the glucoamylase gene glaA, the acid amylase gene aamA, the a-glucuronidase gene aguA, and the feruloyl esterase gene faeA is heterogeneous between neighboring hyphae at the periphery of the colony of Aspergillus niger [10,11]. Co-expression studies showed that hyphae that highly express one of these genes also highly express the other genes encoding secreted proteins [11]. Moreover, these hyphae highly express the glyceraldehyde-3-phosphate dehydrogenase gene gpdA, and are characterized by a high 18S rRNA content. Taken together, it was concluded that at least two subpopulations of hyphae exist within the outer zone of the mycelium of A. niger. These subpopulations are characterized by a high and a low transcriptional activity, respectively [11]. The data implied also that the translational activity may be different in the two populations of hyphae. Transcriptome analysis of single cells is an important tool to understand the extent of cellular heterogeneity and its underlying mechanisms. So far, whole genome expression analysis has been reported of an individual neuron and a single blastomere [12,13]. Here, we performed for the first time a single cell transcriptome analysis in a microbe. It is shown that the RNA composition of neighboring hyphae at the periphery of an A. niger mycelium is heterogeneous. Heterogeneity can be found in all functional gene classes (FunCats) as well as in rRNAs and tRNAs.