Structural models of the different trimers present in the core of phycobilisomes from Gracilaria chilensis based on crystal structures and sequences

Abstract

Phycobilisomes (PBS) are accessory light harvesting protein complexes that directionally transfer energy towards photosystems. Phycobilisomes are organized in a central core and rods radiating from it. Components of phycobilisomes in Gracilaria chilensis (Gch) are Phycobiliproteins (PBPs), Phycoerythrin (PE), and Phycocyanin (PC) in the rods, while Allophycocyanin (APC) is found in the core, and linker proteins (L). The function of such complexes depends on the structure of each component and their interaction. The core of PBS from cyanobacteria is mainly composed by cylinders of trimers of α and β subunits forming heterodimers of Allophycocyanin, and other components of the core including subunits αII and β18. As for the linkers, Linker core (LC) and Linker core membrane (LCM) are essential for the final emission towards photoreaction centers. Since we have previously focused our studies on the rods of the PBS, in the present article we investigated the components of the core in the phycobilisome from the eukaryotic algae, Gracilaria chilensis and their organization into trimers. Transmission electron microscopy provided the information for a three cylinders core, while the three dimensional structure of Allophycocyanin purified from Gch was determined by X-ray diffraction method and the biological unit was determined as a trimer by size exclusion chromatography. The protein sequences of all the components of the core were obtained by sequencing the corresponding genes and their expression confirmed by transcriptomic analysis. These subunits have seldom been reported in red algae, but not in Gracilaria chilensis. The subunits not present in the crystallographic structure were modeled to build the different composition of trimers. This article proposes structural models for the different types of trimers present in the core of phycobilisomes of Gch as a first step towards the final model for energy transfer in this system.

Fig 1. Characterization of phycobilisomes of Gracilaria chilensis.

A) Absorption(-) and emission(..) spectra. B) Transmission electron micrograph of purified phycobilisomes.The inserts show amplified images. Schematic drawings of PBS are also shown.

Fig 2. Spectroscopic characterization and oligomerization state of Allophycocyanin.

A) Absorption (-) and emission (--) spectra of purified Allophycocyanin. B) Molecular sieve chromatogram; the standards and the sample are indicated.

Fig 3. Sequence comparison between α and α^II (ApcA and ApcD), β and β¹⁸ (Apcb and ApcF) and α and the PB_domain of the L_CM (ApcA and ApcE).

Chromophore binding region are enclosed in green rectangles, and the conserved residues are highlighted in green. The cysteine residues that bind the chromophores are shown in red background. The PB-loop sequence is enclosed in blue lines.

Fig 4. Crystallographic structure of Allophycocyanin from Gracilaria chilensis.

A) Ribbon representation of the asymmetric unit, the heterodimer. B) A section of the |2F-Fo| omit electron density map is shown for phycocyanobilin in α subunit. The residues interacting with the chromophore are also shown.

Fig 5. Binding sites of phycocynobilin.

A) Sticks representation of binding site of phycocyanobilin in α subunit of 5TJF (this paper), α^II and the PB domain in APC_3. The chromophores are represented in green. B) Sticks representation of β subunit in 5TJF and β¹⁸ in APC_3. The chromophores are also in green.

Fig 6. Structural models proposed for each trimer of Allophycocyanin.

A) Schematic representation of the different composition trimers. B) Structure of APC, APC_1, APC_2, and APC_3.