Cross-Feeding between Cyanobacterium Synechococcus and Escherichia Coli in Artificial Autotrophic-Heterotrophic Co-Culture System Revealed by Integrated Omics Analysis
Authors: Ma Jiajia , Guo Taohong , Chen Lei , Song Xinyu , Zhang Weiwen 
Published: December 2021

Abstract
Background: The light-driven consortia consisted of sucrose-secreting cyanobacteria and heterotrophic species capable of producing valuable chemicals have recently attracted significant attention, and are considered as a promising strategy for green biomanufacturing. In a previous study (Zhang et al, 2020, Biotechnol Biofuel, 13:82), we achieved a one-step conversion of CO2 through sucrose derived from cyanobacteria to fine chemicals by constructing an artificial co-culture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analysis of the co-culture system showed that cyanobacterial cells were growing better than its corresponding axenic culture. To explore the underlaid mechanism and to identify the metabolic modules to further improve the co-culture system, an integrated metabolomics, transcriptomic and proteomic analysis was conducted.Results: We first explored the effect of reactive oxygen species (ROS) on cyanobacterial cell growth under co-culture system by supplementing additional ascorbic acid to scavenge ROS in CoBG-11 medium. The result showed cyanobacterial growth was obviously improved with additional 1 mM ascorbic acid under pure culture; however, cyanobacterial growth was still slower than that in the co-culture with E. coli, suggesting that the better growth of Synechococcus cscB+ might be caused by other factors more than just ROS quenching. We then investigated the intracellular metabolite levels in cyanobacteria using LC-MS based metabolomics analysis. The results showed that metabolites involved in central carbon metabolism were increased, suggesting more carbon sources were utilized by cyanobacteria in the co-culture system, which illuminating that enhanced photosynthesis attributes to the higher CO2 availability produced from co-cultivated heterotrophic partner. To further explore the interaction based on cross-feeding and metabolite exchange, quantitative transcriptomics and proteomics were applied to Synechococcus cscB+. Analysis of differentially regulated genes/proteins showed that the higher availability of carbon, nitrogen, phosphate, calcium, Cu2+, Fe3+ and co-factors was observed in co-cultivated Synechococcus cscB+ during co-cultivation, suggesting the heterotrophic partner in the system might be involved in supplementing CO2 and improving essential micronutrients necessary to maintain high photosynthetic growth of Synechococcus cscB+. Conclusion: Integrated omics analysis of the interaction mechanism between S. elongateus and E. coli showed metabolic changes such as enhanced photosynthesis, oxidative phosphorylation, essential micronutrients, and the ROS scavenging occurred at multiple levels of genes, proteins and metabolites, which might be together contributing to the better cell growth of Synechococcus cscB+ in co-cultivation. In addition, the results implicated that the co-culture system could be further improved by engineering the modules related to the ROS quenching, carbon metabolism, nitrogen metabolism, Pi transport, metal transport and co-factors biosynthesis. Finally, the light condition, which may influence the cross-feeding metabolites between phototrophic and heterotrophic species, and also affect the oxidative pressure on the E. coli strains due to the photosynthesis, could be further optimized to improve cell growth in the co-culture system, eventually leading to high productivity of value-added products.