Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties

Ravi R Sonani,Mukesh Ghanshyam Chaubey,Rajesh Prasad Rastogi,Gagan D Gupta,Vinay Kumar,Stuti Nareshkumar Patel,Datta Madamwar,Niraj Kumar Singh

doi:10.1038/s41598-019-46288-4

Abstract

The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among α- and β-subunit (3 in α- and 9 in β-subunit). The phylogenetic analysis suggested that molecular evolution of α- and β-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in β-subunit, compared to α-subunit (relative divergence, 7.38 for α-subunit and 9.66 for β-subunit). Crystal structure of N-PC was solved at 2.35 Å resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two αβ-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in β-subunit may be involved in maintaining topology of β-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The β153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.

Highlights

Presence of phycocyanobilin (PCB) with N-PC subunits was confirmed by chromophore specific zinc acetate staining (Fig. 1A)
UV-visible absorbance profile of N-PC showed an absorption maximum at 611 nm (Fig. 1B), which is blue shifted as compared to reported PCs
Comparison of N-PC and ML-PC absorption components suggested that component 1 and 2 are blue-shifted by ~20 nm and ~11 nm, respectively, in N-PC as compared to ML-PC

Summary

Introduction

Phycobiliproteins (PBPs) are accessory light harvesting, water-soluble and fluorescence proteins present in cyanobacteria, red algae and cryptophyte[1]. In order to understand the fashion of spectral variation among PBPs of different origin, knowledge of the phycobilin-apoprotein interactions is crucial. Besides their role in cyanobacteria, PBPs have been widely documented to possess the antioxidant, hepatoprotective, neuroprotective, anti-inflammatory and anti-aging activity[11,12]. R76DM (N-PC) acquires distinct sequence feature and unique blue-shifted spectral properties The study provides structural implication of distinct sequence features, structural attributes responsible for N-PC’s unique spectral properties and possible correlation between them. The effect of distinct sequence features on an antioxidant activity of N-PC is accessed in-vitro and in-vivo

Methods

Results

Conclusion