The effects of illumination and trophic strategy on gene expression in Chlamydomonas reinhardtii

Abstract

Microalgae are of substantial biotechnological interest due their polyphyletic nature which grants them access to a wide array of high-value metabolites. The inherent genetic diversity of microalgae combined with their metabolic plasticity when grown using different trophic and illumination strategies necessitate the establishment of a reference knowledge base. In the present study we present a detailed characterisation of the combined effects of wavelength selection and trophic strategy on the growth kinetics and gene expression profile of the model microalgae Chlamydomonas reinhardtii grown under moderate to high light intensity (400 μmol ph m − 2 ⋅s − 1 ). The aim is twofold: (a) to establish a list of reliable housekeeping genes valid for quantitative comparisons across several combinations of different wavelengths and trophic strategies and (b) to enable the investigation of the response of central carbon metabolic pathways under these process conditions. White, blue and red light emitting diodes (LEDs) were used to grow pH controlled photo-and mixo-trophic cultures over a period of 136 h in batch mode. A panel of 10 candidate genes, along with biomass growth rate and pigment content were dynamically monitored across all conditions. Statistical analysis identified genes (acetyl-CoA carboxylase subunit α and photosystem I reaction centre subunit II) with less variability observed in their expression levels across the entirety of conditions evaluated compared to housekeeping genes often referred to in literature (receptor of activated protein kinase C and ribosomal protein (large subunit) 19). Further analysis of gene expression profiles revealed substantial differences in response to changes in both wavelength selection (upregulation of ribulose bisphosphate carboxylase small subunit under red phototrophic growth) and trophic strategy (upregulation of malate synthase from phototrophic to mixotrophic conditions). The systematic approach used to establish reliable reference genes presented herein enables robust comparisons of cellular responses across different conditions to better understand algal metabolism and improve process performance.

Effects of Trophic Acclimation on Growth and Expression Profiles of Genes Encoding Enzymes of Primary Metabolism and Plastid Transporters of Chlamydomonas reinhardtii

“…Appeared biochemical trophic adjustments include complex alterations in the various pathways of central metabolism such as carbon fixation, sugar metabolism, TCA, and lipid and starch deposition [ 2 , 7 , 10 , 34 , 35 ]. These alterations are closely related to a shift in the expression of genes encoding the involved enzymes [ 4 , 6 , 36 ], which results in a redirection in metabolic fluxes [ 27 , 37 , 38 ]. The assumption is that current algae growth and metabolism would have the effect of previous trophic conditions.…”

“…It defines the balance between synthesis and catabolism in algal cells [ 2 , 3 ]. The effect of trophic conditions on C. reinhardtii growth and metabolism has been studied at genetic, biochemical, and physiological levels through newly developed transcriptomic [ 4 , 5 , 6 ], proteomic [ 7 , 8 , 9 ], and metabolomic [ 7 , 10 , 11 ] approaches. Nevertheless, in comparison with other types of adaptation strategies [ 12 , 13 ], many processes involved in tropic adaptation are still far from known.…”

Molecular mechanisms of long-term light adaptation of an extremophilic alga Cyanidioschyzon merolae

“…Varying light quality and quantity influences the balance between solar energy capture and utilisation in photosynthesis, affecting concomitantly the downstream processes of central carbon and nitrogen metabolism as well as cellular growth and division. High light stress often results in metabolic flux imbalances, photo-oxidative stress and/or slower development of plants or inhibition of microalgal cell division (Foyer and Noctor, 2005; Li et al, 2009b; Miyagishima and Tanaka, 2021; Sanchez-Tarre and Kiparissides, 2021).…”

“…This suggests that for the maintenance of the highest photosynthetic performance in C. merolae cells exposed to long-term RL illumination, no metabolic energy investment is allocated to de novo synthesis of light harvesting components. In contrast to C. merolae , long-term application of varying light quantity and quality of Chlamydomonas reinhardtii cells has led to upregulation of the RuBisCo small subunit under red phototrophic growth, implying an increased demand for energy generation in this green microalga required to establish a shorter cell cycle and maintain a rapid duplication rate in conjunction with increased photosynthetic efficiency as well as reduced mutual shading across the light path (Sanchez-Tarre and Kiparissides, 2021). The same study showed that metabolic energy investment is based on transcriptomic upregulation of fatty acid biosynthesis and cell cycle components, which ensures shortening of the cell cycle and maintenance of a rapid duplication rate (Sanchez-Tarre and Kiparissides, 2021).…”

“…In contrast to C. merolae , long-term application of varying light quantity and quality of Chlamydomonas reinhardtii cells has led to upregulation of the RuBisCo small subunit under red phototrophic growth, implying an increased demand for energy generation in this green microalga required to establish a shorter cell cycle and maintain a rapid duplication rate in conjunction with increased photosynthetic efficiency as well as reduced mutual shading across the light path (Sanchez-Tarre and Kiparissides, 2021). The same study showed that metabolic energy investment is based on transcriptomic upregulation of fatty acid biosynthesis and cell cycle components, which ensures shortening of the cell cycle and maintenance of a rapid duplication rate (Sanchez-Tarre and Kiparissides, 2021). In our work, transcriptomic upregulation of fatty acid biosynthesis and cell cycle enzymes was observed for eHL adaptation rather than adaptation to light preferentially absorbed by PSII (RL), indicating the subtle regulatory differences between these two groups of evolutionary distant microalgae.…”