Molecular and structural characterization of the C-phycocyanin β-subunit in native cyanobacteria from temple ponds: implications for biopigment yield and function.

C-phycocyanin (C-PC) is a high-value blue phycobiliprotein extensively utilized as a natural colorant and multifunctional bioactive compound. This study employed a polyphasic framework to characterize eleven native cyanobacterial isolates (NTBN series) from temple ponds in Tamil Nadu, India, with the aim of quantifying extractable C-PC and correlating pigment yield with molecular traits of the C-PC β-subunit. All isolates were cultivated under identical, non-optimized conditions (BG-11 medium, 25 ± 2 °C, 16:8 h light: dark, ~ 50 µmol photons m⁻² s⁻¹, 21 days, n = 3). Crude pigments were extracted and quantified spectrophotometrically, while cpcB sequences were subjected to homology modeling and physicochemical profiling (GRAVY, aliphatic index, instability index). Among the isolates, NTBN-07 and NTBN-15 exhibited the highest extractable C-PC content. Strains with lower GRAVY values (greater hydrophilicity) and moderate aliphatic indices consistently showed higher pigment productivity, as supported by multivariate analyses (heatmap and PCA). Homology models revealed conserved chromophore-binding residues with subtle tertiary conformational variations potentially influencing pigment stability and extractability. Although several native isolates yielded more C-PC than the laboratory reference Synechocystis sp. PCC 6803 under uniform, non-optimized conditions, their yields remained lower than those reported for optimized Arthrospira cultures. Study limitations include the use of crude extracts and reliance on in silico predictions pending protein-level validation. Overall, this work identifies temple-pond cyanobacteria as promising native bioresources for predictive strain selection, downstream process optimization, and sustainable pigment biotechnology.