Coordinated alterations in gene expression and metabolomic profiles of Chlamydomonas reinhardtii during batch autotrophic culturing

Roman Puzanskiy,Daria Romanyuk,Maria Shishova

doi:10.21638/spbu03.2018.110

Abstract

Chlamydomonas reinhardtii was grown under autotrophic batch culturing, which is known to be a widely applicable method for both fundamental research and applied purposes. This type of cultivation results in elevation of cell density and fast exhaustion of nutrient resources. We expected the revealed metabolic adaptation to be triggered at the transcriptional level. This investigation focuses on analyzing expression of the genes encoding enzymes involved in primary metabolism and plastid transporters during the exponential phase of C. reinhardtii autotrophic batch culture. About two-thirds of the tested genes demonstrated differential expression during algae growth. Patterns of expression were clustered into 5 groups. Most of the genes were gathered in two large clusters, characterized by peaks of expression at early or later exponential growth (EG). Genes which showed maximal expression in early EG were OMT1, HXK1, AMYB1, ACK1,2, CHLREDRAFT_123419, APE2, PCK1, CHLREDRAFT_195672, CIS2, TPT2 and ACLA1. Among the genes with maximal expression in later EG were SBE3, TPIC, CHLREDRAFT_137300, CHLREDRAFT_111372, PPT1 and CHLREDRAFT_122970. There were no genes detected with maximal expression at the cessation of proliferation. PCA showed that the expression profiles in the beginning EG were similar, and profiles changed drastically in the middle of exponential growth. PLS-DA revealed the difference between the beginning of EG and later periods linked to PC1 (44 %), between late EG and early stationary linked to PC2 (23 %) and finally between two points at the beginning of growth linked to PC3 (10 %). Mapping of genes and metabolites according to their correlation revealed a graph with two clusters. The first, smaller cluster contains genes that encode plastid exporters, enzymes of starch and carbohydrates metabolism. The expression level of these genes peaked later in EG. These genes are mainly associated with metabolites such as carbohydrates, acylglycerols and fatty acids metabolism. The second cluster is larger and more diverse. It combines genes with maximum expression in the beginning of EG. The core of this cluster is formed by genes encoding enzymes of fatty acids synthesis, energy and plastic pathways, and plastid transporters. This cluster included the majority of amino acids, carboxylic acids and many fatty acids.

Highlights

Batch culturing is a common method of growing microalgae
One of the reasons for acidification is that photosynthesis assimilates CO2 and produces hydroxyl ions, which leads to a pH shift (Mandalam and Pallson, 1995; Kim et al, 2013)
Samples were collected during C. reinhardtii autotrophic culture development: three times during the exponential growth phase, and at the beginning of the stationary phase (Fig. 1)

Summary

Introduction

Batch culturing is a common method of growing microalgae. The essence of this method is cultivation in a certain volume of incubation media, which is not renewed and not supplied with nutrients. The advantages of this culture are universality, simplicity, reliability and scalability (Perez-Garcia and Bashan, 2015). Mineral nutrients assimilation during cell growth causes media depletion, which significantly modulates the physiological activity of cells. Due to the elevation of cell density and intensive microalgae metabolism, the content of Ci and O2 in the media varies. The absorption of ammonium might promote acidification of the media (Pratt and Fong, 1940)

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Conclusion