Low CO₂ Responsive Gene Co-Expression Network Identifies Regulators Facilitating Photosynthetic Growth of...

Cyanobacteria operate a photosynthetic CO₂ concentrating mechanism (CCM) to cope with the low inorganic carbon (Ci) concentration in natural aquatic environment. Unlike in higher plants, transcription factors (TF) identified to improve photosynthesis and growth or to participate in the regulation of CCM are relatively limited. In this work, we constructed a gene co-expression network (GCN) with transcriptome data from multi-timepoint treatments under varied CO₂ concentrations in Synechocystis sp. PCC 6803, to systematically identify CO₂ responsive regulators. New regulatory factors of CCM components (including Ci transporters, CO₂ uptake systems, and NDH complex) were identified, and subsequent functional validation revealed that overexpression of slr6040 or sll5097 could facilitate the photosynthetic growth of Synechocystis 6803, especially under low Ci conditions. Gene expression analysis in overexpressing strains showed that elevated Slr6040 or Sll5097 could up-regulate the expression of CCM related genes. Yeast one-hybrid and EMSA assays indicated direct regulation of target gene by Slr6040 in a metabolite coregulator dependent manner. Our full-scale CO₂-responsive regulatory network provided resources for further mining putative regulatory modules of cyanobacteria CCM in future studies, as well as for exploring the potential of engineering cyanobacteria with more efficient assimilation of CO₂ and improved productivities.