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Mpev Is the Lyase Isomerase for the Doubly-Linked Phycourobilin On MpeV is the lyase isomerase for the doubly-linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus Lyndsay Carrigee, Jacob Frick, Jonathan Karty, Laurence Garczarek, Frédéric Partensky, Wendy Schluchter To cite this version: Lyndsay Carrigee, Jacob Frick, Jonathan Karty, Laurence Garczarek, Frédéric Partensky, et al.. MpeV is the lyase isomerase for the doubly-linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2020. hal-03038224 HAL Id: hal-03038224 https://hal.archives-ouvertes.fr/hal-03038224 Submitted on 3 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. MpeV is the lyase isomerase for the doubly-linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus Lyndsay A. Carrigee1, Jacob P. Frick1, Jonathan A. Karty2, Laurence Garczarek3, Frédéric Partensky3, and Wendy M. Schluchter1* 1 Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA 2 Department of Chemistry, Indiana University, Bloomington, IN 47405, USA 3Sorbonne Université & CNRS, UMR 7144, Ecology of Marine Plankton (ECOMAP) Team, Station Biologique, 29688 Roscoff, France *Corresponding author: Dr. Wendy M. Schluchter Phone (504) 280-7194; fax (504) 280-6121; email: [email protected] Running title: MpeV attaches doubly-linked phycourobilin to CpeB and MpeB Keywords: bilin lyase, cyanobacteria, lyase isomerase, phycoerythrobilin, phycobilisome, phycourobilin, post-translational modification 1 Abstract which chlorophyll absorbs poorly (2-4). Marine isolates of Synechococcus have a complex PBS Synechococcus cyanobacteria are widespread in the structure comprised of up to four highly pigmented marine environment due to their extensive pigment phycobiliproteins (PBP). The PBS core is made of diversity within their light-harvesting allophycocyanin and is surrounded by 6 to 8 rods phycobilisomes, enabling them to utilize various made of phycocyanin and up to two types of wavelengths of light for photosynthesis. phycoerythrin (PEI and PEII). These extended rod Phycobilisomes of Synechococcus sp. RS9916 structures increase the spectral range of the PBS contain two forms of phycoerythrin (PEI and PEII), light harvesting capabilities (Figure 1) (1,3,5-7). each binding two types of chromophores, green- PEI and PEII are homologous PBP, each composed light absorbing phycoerythrobilin and blue-light of an α- and a β-subunit arranged in a hetero- absorbing phycourobilin. These chromophores are hexameric (αβ)6 torus and stacked with the help of ligated to specific cysteines by bilin lyases. Some linker polypeptides to form the distal portion of the members of this enzyme family, called lyase- rods (Figure 1) (4,8,9). The large pigment diversity isomerases, attach phycoerythrobilin and of the PBS is not only due to its variable PBP simultaneously isomerize it to phycourobilin. content but also to the variable proportion of MpeV is a putative lyase-isomerase whose role in covalently bound linear tetrapyrrole bilins, post- PEI and PEII biosynthesis was examined in translationally added to PBP. Highly conserved RS9916 using recombinant protein expression, cysteine (C) residues of PEI and PEII serve as the absorbance and fluorescence spectroscopy and sites for covalent attachment of bilins via the tandem mass spectrometry. Our results show that activity of specialized enzymes known as bilin MpeV is a lyase-isomerase that covalently attaches lyases. a doubly-linked phycourobilin to two cysteine residues (C50, C61) on the β-subunit of PEI Based on sequence similarities, three major groups (CpeB). MpeV activity requires that CpeB is first or clans of bilin lyases have been characterized: chromophorylated by the lyase CpeS (which adds CpcS/U type, CpcT type, and CpcE/F type, (10-14). phycoerythrobilin to CpeB-C82). Its activity is Each clan differs from one another in primary further enhanced in the presence of CpeZ (a amino acid sequence and structure as well as bilin homolog of a chaperone-like protein first chromophore and attachment site specificity. characterized in Fremyella diplosiphon). Activity Solved crystal structures for members of the of MpeV on the β-subunit of PEII (MpeB) was distantly related CpcS/U (Protein Data Bank, analyzed, and phycourobilin ligation was also (PDB): 3BDR; (4,15-18)) and CpcT (PDB: 4O4O; detected at MpeB-C50, C61 residues. MpeV (19,20)) lyase families show that they adopt a showed no detectable activity on the a-subunits of similar antiparallel beta-barrel structure. CpcS-type PEI or PEII. The mechanism by which MpeV links lyases are hypothesized to have evolved first the A and D rings of phycourobilin to C50 and C61 because they recognize the central C82-equivalent of CpeB was explored using site-directed mutants. position present in a and b subunits of This analysis revealed that linkage at the A ring to allophycocyanin, b-phycocyanin, and b-PE C50 is a critical step in chromophore attachment, (4,10,11,15,19-22). Unrelated to the other clans, the isomerization and stability. CpcE/F lyase clan members display a high specificity for a single bilin and a single binding site Introduction on a particular PBP (PDB 5N3U; (13,14,23,24)). These lyases contain five to six HEAT-repeat Marine cyanobacteria in the genus Synechococcus motifs (thought to facilitate protein-protein are the second most abundant oxygenic phototrophs interactions) coupled with Armadillo repeats (25- and contribute significantly to global ocean primary 28) (Figure S1) (4,22,29). This CpcE/F group also productivity and carbon cycling (1). Synechococcus includes enzymes that have both bilin isomerase are widespread in part because of their efficiency at and ligase activity (lyase-isomerases), proteins with harvesting available light using their antenna, or chaperone-like functions, and proteins with the phycobilisome (PBS), which is tuned to absorb capability to remove bilins (13,14,30-34). To date, light colors from portions of the visible spectrum in the crystal structure of only one CpcE/F type lyase 2 has been solved and was found to adopt an alpha In F. diplosiphon, CpeS is the PEB lyase for C82 helical solenoid shape (29). on CpeB and CpeF is the PEB lyase for the doubly ligated PEB at C50,61, and both of these enzymes The marine Synechococcus sp. strain RS9916 require the chaperone-like protein CpeZ to keep the possesses the ability to alter the ratio of the blue CpeB substrate soluble (34,46). In these recent light-absorbing chromophore phycourobilin (PUB) studies, Kronfel et al. also characterized the [absorbance maximum (λmax) ~495 nm] and the chromophorylation pattern for the doubly-linked green light-absorbing chromophore PEB at C50, 61 in F. diplosiphon CpeB by CpeF phycoerythrobilin (PEB) (λmax ~545 nm) on the and demonstrated that linkage along the A ring distal portion of the PBS rods, a phenomenon likely occurs first and is important for subsequent known as type IV chromatic acclimation (CA4) attachment to the D ring (46). The closest homolog (3,6,35-39). During CA4, the PUB to PEB ratio to the cpeF gene from F. diplosiphon in RS9916 is (PUB:PEB) is adjusted to be higher in blue light mpeV, first described in the genome of marine and lower in green light in order to optimize light Synechococcus strain WH8020 (47), though capture in changing light color environments WH8020 MpeV has not yet been characterized. (3,31,35,36,39,40). All CA4 strains contain one of However, the presence of a PUB chromophore at the two genomic island configurations, CA4-A or the C50, 61 position of the β-subunits of both PEI CA4-B, each encoding transcritional activators and and PEII in RS9916 (31) led us to question the a lyase or a lyase-isomerase (36). Although PEB is function of this gene. Here, we demonstrate that readily produced in cyanobacteria as a free RS9916 MpeV is the lyase-isomerase responsible precursor molecule (41), the bilin PUB is produced for the doubly-linked PUB on RS9916 β-PEI through the activity of specialized bilin lyase- (CpeB) and β-PEII (MpeB) and its activity requires isomerases that attach PEB while simultaneously ligation of PEB at C82 by CpeS and is enhanced by isomerizing it to PUB (Figure 2) (31,42). Increased CpeZ. We also show that linkage of C50 to the A- PUB content in PBS allows these organisms to ring is required for bilin isomerization to occur. better absorb the blue light available in deeper water (43). Results In RS9916, there are five possible sites for bilin Structural prediction attachment on PEI, two on the α-subunit (CpeA) and three on the β-subunit (CpeB), and six possible The putative lyase MpeV of the marine sites on PEII, three each on the α-subunit (MpeA) Synechococcus strain RS9916 shares sequence and β-subunit (MpeB) (31). It is hypothesized that similarity (54.9%) with the recently characterized a bilin lyase is responsible for ligation of a given CpeF lyase from the freshwater cyanobacterium F. bilin at each individual site. Thus far, only four PE diplosiphon and a structural prediction analysis lyases (all members of the CpcE/CpcF clan) have using Phyre2 shows that they have similar predicted been characterized for RS9916 in the literature structures (Figure S1; closest characterized (31,38,43,44). During CA4, MpeY (PEB lyase) and structure PDB: bgfp-a) (48), suggesting that these MpeZ (PUB lyase-isomerase) chromophorylate the enzymes may have a similar substrate specificity C83 position of MpeA in green or blue light, for b-PE subunits.
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