Inhibition of DNA methylation in P. soloecismus alters algae productivity

Steadman, Christina Rene; Banerjee, Shounak; Kunde, Yuliya A.; Sanders, Claire Kathleen; Marrone, Babetta Louise; Twary, Scott Nicholas

doi:10.3389/fgene.2020.560444

Title: Inhibition of DNA methylation in P. soloecismus alters algae productivity

Journal Article · Thu Oct 15 00:00:00 EDT 2020 · Frontiers in Genetics

DOI:https://doi.org/10.3389/fgene.2020.560444· OSTI ID:1726203

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Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism’s molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (~1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (~66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.

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Research Organization:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE). Bioenergy Technologies Office

Grant/Contract Number:: 89233218CNA000001; NL0026328

OSTI ID:: 1726203

Report Number(s):: LA-UR-20-23482

Journal Information:: Frontiers in Genetics, Vol. 11; ISSN 1664-8021

Publisher:: FrontiersCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biological science
algae
epigenetics
5-aza-2'-deoxycytidine
DNA methylation
lipid accumulation
fatty acid synthesis
bisulfite sequencing

Title: Inhibition of DNA methylation in P. soloecismus alters algae productivity

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