Model for the phycobilisome rod with interlocking disks based on domain-weighted linker-polypeptide sequence homologies of Mastigocladus laminosus

The 8 linker-polypeptides from the cyanobacterium Mastigocladus laminosus were examined by comparative amino-acid sequence analysis for the predicted domain structure reported in the literatur (Glauser 1991, Esteban 1993) in detail using split sequences for the rod, rod-core and for the repeats from the core-membrane linker-polypeptide (Lcm). This analysis gives two distinct domains, where domain 1 (∼ 22 kDa, identity between 31 and 70%) is present in the N-terminal two thirds of the class II linkers (∼ 30 kDa) and in the repeats of the Lcm, and domain 2 (∼ 10 kDa, identity between 28 and 41%) in the C-terminal part of the class II rod linkers (Lr and Lr) and in the two capping linkers (Lc and Lr). Based on these data, X-ray structure analysis from phycobiliproteins and proteolysis experiments, an interlocking model for the phycobilisome rod organization is proposed, with linkers protruding from one phycobilisome disk into the neighbouring one. Abbreviations: APC= allophycocyanin (encoded by apcA and apcB, for the αand β-subunits, respectively), apc= gene locus of allophycocyanin, cpc= gene locus of phycocyanin, L= linkerpolypeptide [the superscripts denote the molecular weights, according to protein sequence calculation, the subscripts give the location denoted as r (rod), rc (rod-core), c (core), and cm (core-membrane)], the correspondance of genes and the derived linker polypeptides are as follows: Lr(cpcD), Lr (cpcC), Lr (pecC), Lrc (cpcG1), Lrc (cpcG2), Lrc (cpcG3), Lc (apcC) and Lcm (apcE), M.= Mastigocladus, PBS= phycobilisome, PC= phycocyanin (encoded by cpcB and cpcA, for the βand α-subunits), PE= phycoerythrin, PEC= phycoerythrocyanin (encoded by pecB and pecA, for the βand α-subunits), pec= gene locus from phycoerythrocyanin.