Lipid production and molecular dynamics simulation for regulation of acc D gene in cyanobacteria under different N and P regimes

Abstract

Background: Microalgae grown under different nutrient deficient conditions present a good source of natural lipids with applications for several types of biofuels. The expression of acetyl-CoA carboxylase gene can further provide an insight to the mechanisms leading to enhanced lipid production under such stresses. In this study, two nutrients viz. nitrogen and phosphorus were modulated to see its effect on lipid productivity in selected cyanobacteria and its correlation with Accase followed by molecular dynamics simulation.

Results: Selected cyanobacteria viz. Oscillatoria sp. (SP8), Anabaena sp. (SP12), Anabaena sp. (SP13), Microcoleus sp. (SP18), and Nostoc sp. (SP20) varied in their ability to accumulate lipids which ranged from a lowest of 0.13% in Anabaena sp. (SP13) to the maximum of 7.24% in Microcoleus sp. (SP18). Microcoleus sp. (SP18) also recorded highest lipid accumulation at both N (6 mM NaNO₃) and P (0.20 mM K₂HPO₄) limiting conditions. The overall expression of accD was found to be upregulated in both Oscillatoria sp. (SP8) and Microcoleus sp. (SP18) for all nitrogen concentrations but was differentially regulated with both positive and negative induction under phosphorus stress conditions. Maximum induction was observed in Microcoleus sp. (SP18) at 0.20 mM K₂HPO₄. The obtained 3D structure of SP8 protein (21.8 kDa) showed six alpha helices, while SP18 protein (16.7 kDa) exhibited four alpha helices and four beta sheets. The phi (ϕ)/psi(ψ) angles of the amino acid residues observed in Ramachandran plot analysis showed that both SP8 and SP18 proteins were highly stable with more than 90% amino acids in allowed regions. The molecular dynamics simulation results also indicated the stability of ligand-bound protein complexes.

Conclusion: It has been demonstrated that cyanobacterial isolates are affected differently by nutrient limitation leading to variation in their lipid productivity. The same has been revealed by the behavior of accD gene expression which was regulated more by nutrients concentrations rather than the organism. However, the ligand-bound protein complexes were stable throughout MD simulations.

Keywords: Cyanobacteria; Lipid production; Nitrogen; Phosphorus limitation; accD gene expression.

Fig. 1

Total lipid production in selected cyanobacteria grown under different nitrogen (NaNO₃) regimes after 28 and 35 days of incubation

Fig. 2

Total lipid production in selected cyanobacteria under different phosphorous (K₂HPO₄) regimes after 28 and 35 days of incubation

Fig. 3

Real-time expression profile of Acetyl-CoA carboxylase gene under nutritional stress (nitrogen and phosphorus). a Oscillatoria sp. (SP8) under NaNO₃ stress, b Microcoleus sp. (SP18) under NaNO₃ stress, c Oscillatoria sp. (SP8) under K₂HPO₄ stress, d Microcoleus sp. (SP18) under K₂HPO₄ stress

Fig. 4

Comparison between 3D models of SP8 and SP18 proteins. a Ball and stick models. b Ribbon models. c Ball and stick models with different color

Fig. 5

Ramachandran plot designed from the amino acid sequence of (a) SP8 protein and (b) SP18 protein

Fig. 6

Predicted 3D models of a biotin ligand and ACC proteins of b Oscillatoria sp. (SP8) and c Microcoleus sp. (SP18)

Fig. 7

Docking of predicted 3D models. a Docking of ACC proteins of Oscillatoria sp. (SP8) and b Docking of ACC proteins of Microcoleus sp. (SP18) subjected with Biotin ligand protein

Fig. 8

Root mean square fluctuation of atoms during the simulation process of protein ligand complex

Fig. 9

Root mean square deviation of protein ligand complex