Rapid Adaptation of Cyanobacteria to Environmental Perturbations Is Achieved Through Structural Remodeling of the Proteome

Dynamic environments require cyanobacteria to rapidly respond to fluctuating light conditions on timescales faster than transcription-translation processes allow, which is possible through immediate regulation of protein function via molecular and conformational adjustments. Traditional abundance-based proteomics cannot capture these rapid structural changes, creating a critical gap in understanding cellular adaptation mechanisms. We hypothesized that application of alternative structural proteomics approaches would enable identification of immediate structural remodeling across the cyanobacterial proteome triggered by environmental perturbations, potentially driving functional adaptations invisible to conventional abundance-based methods. We interrogated three complementary techniques-limited proteolysis-based mass spectrometry, thermal proteome profiling, and redox proteomics-for their capacity to unveil structural reorganization within the model cyanobacterium Synechococcus elongatus PCC 7942 during physiologically relevant light transitions. Within 30 min of increased light exposure, we detected structural changes in 753 proteins (limited proteolysis-based mass spectrometry), thermal stability shifts in 600 proteins (thermal proteome profiling), and cysteine oxidation in 1887 sites, while only 145 proteins changed in abundance. All three techniques consistently revealed coordinated remodeling of photosynthetic machinery, ribosomal complexes, and carbon metabolism, exemplified by cytochrome f stabilization modulating electron transport efficiency. Remarkably, <10% of proteins overlapped between methods, demonstrating that each technique captures distinct molecular dimensions of environmental adaptation. This structural proteomics framework demonstrates how alternative techniques can reveal hidden facets of proteome dynamics underlying cellular processes, offering new methodological approaches for understanding environmental responses and informing biotechnological applications.