Gene expression characterizes different nutritional strategies among three mixotrophic protists

Abstract

Mixotrophic protists, i.e. protists that can carry out both phototrophy and heterotrophy, are a group of organisms with a wide range of nutritional strategies. The ecological and biogeochemical importance of these species has recently been recognized. In this study, we investigated and compared the gene expression of three mixotrophic protists, Prymnesium parvum, Dinobyron sp. and Ochromonas sp. under light and dark conditions in the presence of prey using RNA-Seq. Gene expression of the obligately phototrophic P. parvum and Dinobryon sp. changed significantly between light and dark treatments, while that of primarily heterotrophic Ochromonas sp. was largely unchanged. Gene expression of P. parvum and Dinobryon sp. shared many similarities, especially in the expression patterns of genes related to reproduction. However, key genes involved in central carbon metabolism and phagotrophy had different expression patterns between these two species, suggesting differences in prey consumption and heterotrophic nutrition in the dark. Transcriptomic data also offered clues to other physiological traits of these organisms such as preference of nitrogen sources and photo-oxidative stress. These results provide potential target genes for further exploration of the mechanisms of mixotrophic physiology and demonstrate the potential usefulness of molecular approaches in characterizing the nutritional modes of mixotrophic protists.

Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

“…In our study we also tested such a sequence based method but in contrast to the results of Liu et al (2016) and Koid et al (2014) we could not identify a higher number of core genes. Genome based studies of related lineages also range from 1,666 to 3,063 core genes (Bowler et al 2008, Radakovits et al 2012.…”

“…This seems low but is similar in size to core transcriptomes reported for prymnesiophytes (Koid et al 2014: 1,433 core genes) and diatoms (Di Dato et al 2015: 1,370 core genes); all these estimates are based on functionally assignable genes. Sequence based methods for the identification of core genes are independent from the necessity of functional assignment and resulted in previous studies in approximately 3,000 core genes (Liu et al 2016, Koid et al 2014). …”

“…the transcriptome, investigations of core genes are scarce. Estimates on the core transcriptome within a lineage to date indicate a core set of at least 1,400 to 3,000 genes (Koid et al 2014, Beisser et al 2017, Liu et al 2016). Here we focus on the comparative transcriptomics of members of Ochromonadales (Chrysophyceae) aiming at the genetic repertoire essential for chrysophytes.…”

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

“…It is accompanied by an enhanced glycolysis, oxidative pentose phosphate pathway as well as tricarboxylic acid cycle during heterotrophic growth. A recent study on mixotrophic chrysophytes with a primarily phototrophic mode of nutrition also shows alterations in the expression level of genes involved in carbon utilization pathways under light and dark conditions [63]. Although, P. malhamensis does not grow but sustains cell metabolism with the help of light-derived energy when organic carbon sources are limited [28], the high amount of differentially expressed proteins suggest a heavy usage of the photosynthesis apparatus to generate energy and storage molecules.…”

“…Particularly, photosynthesis and calvin cycle are increased in light to generate energy via photosynthesis for primary production. If photosynthesis is the main carbon source, glycerate-3-phosphate will be produced as an intermediate to enter glycolysis/gluconeogenesis [63]. The energy surplus allows the storage of glucose by gluconeogenesis.…”