Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae.

Bahman Panahi,Mohammad Amin Hejazi,Mohammad Farhadian,O Roger Anderson

doi:10.1371/journal.pone.0225677

Abstract

Heterotrophic growth mode is among the most promising strategies put forth to overcome the low biomass and secondary metabolites productivity challenge. To shedding light on the underlying molecular mechanisms, transcriptome meta-analysis was integrated with weighted gene co-expression network analysis (WGCNA), connectivity analysis, functional enrichment, and hubs identification. Meta-analysis and Functional enrichment analysis demonstrated that most of the biological processes are up-regulated at heterotrophic growth condition, which leads to change of genetic architectures and phenotypic outcomes. WGNCA analysis of meta-genes also resulted four significant functional modules across logarithmic (LG), transition (TR), and production peak (PR) phases. The expression pattern and connectivity characteristics of the brown module as a non-preserved module vary across LG, TR, and PR phases. Functional analysis identified Carotenoid biosynthesis, Fatty acid metabolism and Methane metabolism as enriched pathways in the non-preserved module. Our integrated approach was applied here, identified some hubs, such as a serine hydroxymethyltransferase (SHMT1), which is the best candidate for development of metabolites accumulating strains in microalgae. Current study provided a new insight into underlying metabolite accumulation mechanisms and opens new avenue for the future applied studies in the microalgae field.

Highlights

Microalgae have become attractive sources for metabolites, such as lipids, enzymes, polymers, toxins, and pigments production
Dual-culture systems comprising heterotrophic growth followed by photoautotrophic cultivation are proposed as an effective issue for secondary metabolites production in some microalgae [29]
It has been established that the integration of transcriptome meta-analysis with weighted co-expression network analysis is effective approach to shed light on complexity of biological processes

Summary

Introduction

Microalgae have become attractive sources for metabolites, such as lipids, enzymes, polymers, toxins, and pigments production. To overcome the poor biomass accumulation, open ponds that mimic natural environments of the microalgae are alternative option for the most commercial microalgae [5] These cultivation systems present relatively lower construction and operating costs and large ones can be constructed on nonagricultural lands [6]. Differential accumulation patterns of lipids and carotenoids after the transition from photoautotrophic to heterotrophic cultures have been documented in the large body of research [4]. We integrated meta-analysis with weighted gene co-expression network to identify functionally enriched pathways and network-centric genes associated with secondary metabolites production after transition to the heterotrophic growth condition in Chlorella microalgae

Materials and methods

Results and discussion

Conclusion