Nomenclature of Phycobilin lyases and related proteins

• All phycobilin lyases and related proteins This list allows users to retrieve any sequence from any organism included in the database by its locus tag/orf id or Genbank number when available.
• S/U clan The X-ray structure of one member of this phycobilin lyase group was determined at 2.8 Å resolution : CpcS-III from Thermosynechococcus elongatus BP1 (Kuzin et al., 2007; Kupka et al., 2009; Schluchter el al., 2010; PDB: 3BDR). CpcS-III is structurally related to the calyx-shaped lipocalin family (InterPro IPR002345). It possesses a 8-stranded anti-parallel, β-barrel structure with an α-helix. Searches using Phyre2 show that all members of the S/U clan have the same fold.
• S/U clan - Phycobilin lyases Members of this group encompass characterized phycobilin lyases as well as enzymes that are uncharacterized so far.
• CpcS family Two members of the CpcS family were biochemically characterized: Nostoc sp. PCC7120 CpcS-III (Zhao et al. 2007b) and Synechococcus sp. PCC 7002 CpcS-I (Saunée et al. 2008, Shen et al. 2008). Both bind a PCB at Cys-82 (consensus numbering) of alpha and beta-allophycocyanin (ApcA, B, D, F), beta-phycocyanin (CpcB/RpcB and beta-phycoerythrocyanin (PecB) in vivo (Zhao et al., 2007a,b). In vitro, CpcS can also catalyze the attachment of PEB to Cys-84 of alpha and beta-PEI (CpeA-B) and is thus is a nearly universal lyase with respect to apoproteins but is highly specific of this binding site (Zhao et al. 2007a).
• CpcS-I subfamily Classification proposed by Shen et al. (2008) and Schluchter et al. (2010). CpcS-I forms a heterodimer with CpcU-I in Synechococcus sp. PCC 7002 (Saunée et al., 2008; Shen et al., 2008). All strains containing a CpcS-I homolog also possess a CpcU-I homolog, except Synechococcus sp. PCC 7335 (see phyletic profiles).
• CpcS-II subfamily Classification proposed by Shen et al. (2008) and Schluchter et al. (2010). This subfamily contain only marine Synechococcus and Cyanobium. Co-occurrence with CpcU-II in phyletic profiles suggests that CpcS-II form an heterodimer with CpcU-II .
• CpcS-III subfamily Classification proposed by Shen et al. (2008) and Schluchter et al. (2010). None of the strains possessing the cpcS-III gene, including all PEC-containing strains, contains a cpcU-like gene (see phyletic profiles). The X-ray structure of CpcS-III from Thermosynechococcus elongatus BP1 (Tll1699) is available (PDB: 3BDR) and was crystallized as a homodimer. CpcS-III was erroneously called "CpeS1" by Zhao et al. (2007a) and Tu et al. (2008).
• CpcU family CpcU proteins form heterodimers with some CpcS types
• CpcU-I subfamily CpcU-I forms a heterodimer with CpcS-I, as shown in Synechococcus sp. PCC7002 (Saunée et al, 2008; Shen et al, 2008).
• CpcU-II subfamily Present only in marine Synechococcus and in Cyanobium spp. Not formally characterized yet but it likely forms a heterodimer with CpcS-II. Indeed, CpcU-II sequences are most closely related to CpcU-I and they have the same phyletic profile as CpcS-II.
• CpeS family Two members of this family were characterized biochemically : the "CpeS Pro HL" of Prochlorococcus marinus MED4 (Wiethaus et al 2010) and the CpeS-I of Fremyella diplosiphon Fd33/UTEX481/PCC7601 (Biswas et al., 2011).
• CpeS-I subfamily The CpeS-I from Fremyella diplosiphon strain UTEX481 was characterized as a PEB:Cys-80 beta-PE lyase (Biswas et al., 2011). This subfamily contains all PE-containing cyanobacteria outside the marine Synechococcus/Prochlorococcus branch
• CpeS-II subfamily All marine picocyanobacteria possess this gene, except high-light adapted (HL) Prochlorococcus ecotypes, the derived CpeS sequence of which was classified into a different subfamily (CpeS-ProHL).
• CpeS-ProHL subfamily This subfamily contains only the sequences of Prochlorococcus marinus HL ecotypes. CpeS sequence is the sole phycobilin lyase present in these genomes and was biochemically characterized in strain MED4 as a PEB:Cys-82 beta-PEIII (PpeB) lyase (Wiethaus et al., 2010a). PpeB is also the sole PBP present in this (and other Prochlorococcus HL) strain.
• CpeU family No member of this putative phycobilin lyase has been fully biochemically characterized yet. Given its gene environment (see e.g. Grébert et al. 2022), this is probably a PEB:PEI lyase, but the cysteinyl residue chromophorylated by this enzyme is unknown yet. In marine Synechococcus pigment type 3 strains, it may also act on the corresponding site of PEII, at least in low-PUB strains.
• CpeU-I subfamily includes PE-containing cyanobacteria other than marine Synechococcus. Most sequences have multiple possible start codons. In Fremyella diplosiphon a ΔcpeU mutant had a similar phenotype to WT including similar peak profiles with slight decreases in PE levels in the mutant (Adhikari 2015).
• CpeU-II subfamily includes all PE-containing strains marine Synechococcus and Cyanobium.
• S/U clan-related proteins These proteins are related to characterized or probable phycobilin lyases but may have other metabolic functions.
• CpcS homologs family Unknown function. Present only in some PC- or PE-containing cyanobacteria but absent from marine picocyanobacteria.
• CpcV family Unknown function. A CpcV mutant had no discernable phenotype in Synechococcus sp. PCC 7002 (Shen et al., 2008)
• T clan The structure of CpcT of Nostoc sp. PCC7120 and its complex with phycocyanobilin was resolved at 1.95 and 2.50 Å resolution (Protein Data Bank ID: 4O4O), respectively. CpcT forms a dimer and adopts a calyx-shaped β-barrel fold (Zhou et al., 2014). The structure of the CpeT of the cyanophage P-HM1 was resolved at 1.8 Å (Protein Data Bank ID: 5HI8; Gasper et al., 2017).
• T clan - Phycobilin lyases
• CpcT family Characterized in Synechococcus sp. PCC 7002 and Nostoc sp. PCC7120 to attach a PCB at Cys-153 of beta-PC (Shen et al., 2006; Zhao et al., 2007a,b). Nostoc sp. PCC 7120 CpcT also attaches PCB to Cys 155 of PecB (i.e. beta-PEC; Zhao et al., 2007a,b). Crystal structures of CpcT from Nostoc sp. PCC7120 and its complex with phycocyanobilin, have been obtained at 1.95 and 2.50 Å resolution, respectively (Zhou et al. 2014). CpcT forms a dimer and adopts a calyx-shaped beta-barrel fold.
• CpeT family CpeT from the Prochlorococcus marinus MED4 cyanophage P-HM1 was biochemically characterized and its structure resolved at 1.8-Å (Protein Data Bank ID: 5HI8). It attaches a PEB at Cys-155 of beta-PEI (Gasper et al. 2017) and perhaps at the corresponding position in beta-PEII of marine Synechococcus cyanobacteria. CpeT was also characterized in the red alga Gracilariopsis lemaneiformis as a PEB:Cys-158 beta-phycoerythrin lyase (Cao et al. 2019).
• RpcT family Gene name proposed by Six et al. (2007). This enzyme is not formerly biochemically characterized yet, but indirect evidence suggests that it attaches a PEB at Cys-153 of beta-PC (Blot et al. 2009). RpcT is a paralog of CpcT, and they are located in different positions of the PBS rod region of marine Synechococcus spp. (Six et al. 2007, Grébert et al. 2022). Interestingly, strain RS9916 possesses both RpcT and CpcT, confirming the paralogy.
• T clan related proteins
• T homologs family Members of the T clan, but function unknown. Called T homologs by Schluchter et al. (2010) and CpcT2 by Zhao et al. (2007).
• E/F clan The crystal structure of the heterodimer of CpcE-I/F-I from Nostoc sp. PCC7120 was determined at a 1.89-Å resolution (Zhao et al., 2017; PDB: 5N3U). However, the crescent-shaped architecture described by these authors has recently been disputed after the resolution at 2.5-Å of the structure of the lyase-isomerase MpeQ from Synechococcus sp. A15-62 (Kumaraperruma et al. 2022). The latter authors posit that the E/F family of bilin lyases, including the single-chain and heterodimeric enzymes, share a common structural framework represented by the question-mark architecture of MpeQ (PDB: 7MC4 and 7MCH).
• E/F clan: subclan 1 All members of E/F subclan 1 form heteroduplexes or are fusion proteins (RpcG).
• E/F subclan 1 - Phycobilin lyases All members of this subclan form heterodimers (E/F or Y/Z). CpcE/F are found in C-PC-containing strains (which has PCB chromophores at all binding sites) and RpcE/F in strains possessing R-PC (Ong and Glazer 1987, Six et al., 2007). CpcE/F and RpcE/F are mutually exclusive. CpeY/Z are present only in PE-containing strains.
• CpcE/RpcE family
• CpcE-I subfamily Forms a heterodimer with CpcF-I. The CpcE-I/CpcF-I complex attaches a PCB at cys-84 of alpha-PC (Fairchild et al., 1992; Swanson et al. 1992; Bhalerao et al. 1994). The crystal structure of the CpcE-I/CpEF-I heterodimer from Nostoc sp. PCC7120 was determined at 1.89-Å resolution (Zhao et al., 2017), but the crescent architecture described in this paper has recently been disputed and now thought to be a question-mark architecture (Kumaraperruma et al. 2022).
• CpcE-II subfamily Likely forms a heterodimer with CpcF-II. This subfamily is present only in marine Synechococcus and Cyanobium.
• RpcE subfamily Likely forms a heterodimer with RpcF. The activity of the RpcE/F complex was not formerly characterized but it is thought to attach a PEB at Cys-84 of alpha-PC-II in most PE-containing marine Synechococcus spp. RpcE and RpcF are closely related to CpcE and CpcF, respectively.
• CpcF/RpcF family
• CpcF-I subfamily Forms a heterodimer with CpcE-I. The CpcE-I/CpcF-I complex attaches a PCB at cys-84 of alpha-PC. The crystal structure of the heterodimer of CpcE-I/F-I
  from Nostoc sp. PCC7120 was determined at 1.89-Å resolution (Zhao et al., 2017).
• CpcF-II subfamily Likely forms a heterodimer with CpcE-II. This subfamily is present only in marine Synechococcus and Cyanobium.
• RpcF subfamily Likely forms a heterodimer with RpcE. The activity of the RpcE/F complex was not formerly characterized but it is thought to attach a PEB at cys-84 of alpha-PC-II in most PE-containing marine Synechococcus spp. RpcE and RpcF are closely related to CpcE and CpcF, respectively.
• E/F subclan 1 - Phycobilin lyases-isomerases This group gathers PecE/F, a PCB lyase isomerase found only in PEC-containing strains (Zhao et al., 2000, 2002, 2005; Storf et al., 2001) and RpcG, a fusion PEB lyase-isomerase found only in some PEII-containing marine strains (Synechococcus and Crocosphaera; Blot et al. 2009). In vitro, both PecE/F and RpcG can bind PCB and PEB on alpha-84 PC or PEI (Blot et al., 2009).
• PecE family Forms a heterodimer with PecF. The PecE/F complex attaches a PCB and isomerises it to PVB at Cys-84 of alpha-PEC.
• PecF family Forms a heterodimer with PecE. The PecE/F complex attaches a PCB and isomerises it to PVB at Cys-84 of alpha-PEC.
• RpcG family Fusion protein with C-terminal and N-terminal parts showing similarity to PecE and PecF, respectively, but with different function in vivo: RpcG attaches a PEB and isomerizes it to PUB at Cys-84 of alpha-PC (Blot et al. 2009). Found only in some marine cyanobacteria (Grébert et al. 2022).
• E/F clan: subclan 2 Most phycobilin lyase-isomerases of the E/F subclan 2 have been biochemically characterized. They do not seem to form heteroduplexes, thus members of this group might be monomers or homodimers. This group also contains several enzymes that have been characterized but are not phycobilin lyases (CpeZ, IaiH, NblB, etc.) and numerous homologs with unknown function.
• E/F subclan 2 - Phycobilin lyases and lyases-isomerases
• CpeF-MpeU-V-X superfamily The phylogeny of this lyase superfamily was described by Carrigee et al. (2021).
• CpeF family CpeF was biochemically characterized as the lyase that ligates the doubly linked PEB on Cys-48,59 of β-phycoerythrin in Fremyella diplosiphon (Kronfel et al. 2019). It is related to the Synechococcus-specific lyase-isomerases MpeU (Mahmoud et al. 2017) and MpeV (Carrigee et al. 2021) and the yet uncharacterized Prochlorococcus-specific lyase (or lyase-isomerase?) MpeX (Hess et al. 1999).
• MpeU family Present only in PEII-containing marine Synechococcus, except low-PUB (pigment type 3a) strains (Six et al., 2007; Mahmoud et al., 2017; Grébert et al. 2022). Interruption of mpeU caused a reduction in PUB content, impaired phycobilisome assembly and reduced growth rate more strongly in blue than green light (Mahmoud et al.2017). MpeU is therefore important for adaptation of Synechococcus spp. to blue light but the site of this probable lyase-isomerase specificity remains to be established.
• MpeV family MpeV is present only in marine Synechococcus strains belonging to pigment type 3dA, one of the two kinds of type IV chromatic acclimaters. MpeV has been biochemically characterized as a PEB:Cys-50,61 β-PEI and β-PEII lyase-isomerase in Synechococcus strain RS9916 (Carrigee et et al. 2021). Of note, the Cys-50-61 β-PEI of another 3dA strain WH8020 binds a PEB and not a PUB (Ong & Glazer, 1991). This discrepancy has been associated with the occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916: this histidine was found to prevent the isomerization activity of MpeV (Carrigee et al. 2022).
• MpeX family MpeX is a yet uncharacterized member of the CpeF-MpeU-V-X superfamily found in low light-adapted Prochlorococcus strains, such as P. marinus strain SS120/CCMP1375 (Hess et al. 1999, Wiethaus et al. 2010b, Carrigee et al. 2021). Its predicted function is to bind a PEB or PUB at Cys-50,61 of beta-PEIII, but most likely a PUB given that the PUB:PEB ratio of PEIII is 3:1 (Steglich et al. 2003).
• CpeY-MpeQ-W-Y-Z superfamily The phylogeny of this lyase superfamily was described by Grébert et al. (2021).
• CpeY family CpeY was biochemically characterized as the lyase attaching PEB at Cys-82 alpha-PE (CpeA) from Fremyella diplosiphon strain UTEX 481. Its activity is enhanced by CpeZ. CpeY alone, but not CpeZ, can ligate PEB to CpeA, but with a reduced yield than CpeY and CpeZ together (Biswas et al. 2011). CpeY was also characterized in Synechococcus sp. RS9916 as a PEB:Cys-82 alpha-PEI in vitro in the presence or absence of CpeZ, but it was unable to attach PEB to Cys-83 alpha-PEII (Carrigee et al. 2020).
• MpeQ family The mpeQ gene is present in the "PEII subregion" of the "phycobilisome rod gene region" of all PEII-containing marine Synechococcus strains belonging to pigment types 3c and 3dB (Grébert et al. 2021, 2022); it is found at the same position as mpeY in pigment types 3a and 3dA (Grébert et al. 2021, 2022). MpeQ is related to MpeY, MpeW and MpeZ, and more distantly related to CpeY. It was biochemically characterized as a PEB:Cys-83 alpha-PEII lyase-isomerase in the pigment 3dB Synechococcus strain A15-62 (Grébert et al. 2021). In Synechococcus pigment type 3c strains, this site constitutively binds a PUB, whereas in pigment type 3dB strains, this site binds a PUB in blue light and a PEB in green light, as the result of a competition between the constitutively expressed mpeQ gene and the PEB lyase gene mpeW, which is strongly activated in green light but repressed in blue light (Humily et al. 2013; Grébert et al. 2021). The crystal structure of MpeQ has been described at 2.5-Å resolution and its "question mark" architecture is representative of all members of the E/F clan. (Kumarapperuma et al. 2022).
• MpeW family MpeW is specific of marine Synechococcus strains belonging to pigment type 3dB, one of the two kinds of type IV chromatic acclimaters. The mpeW gene is located in the CA4-B genomic island, also comprising the two transcriptional regulator genes fciA and fciB (Sanfilippo et al. 2016). The CA4-B island is localized in the middle of the phycobilisome rod region (Humily et al. 2013, Grébert et al. 2021, 2022). MpeW has been biochemically characterized as a PEB:Cys-83 alpha-PEII lyase in Synechococcus strain A15-62 (Grébert et al. 2021). In this and other pigment type 3dB strains, this site binds a PUB in blue light and a PEB in green light, as the result of a competition between the constitutively expressed mpeQ gene and the PEB lyase gene mpeW, which is strongly activated in green light but repressed in blue light (Humily et al. 2013; Grébert et al. 2021). Given its high specificity, the mpeW gene has also been used as a biomarker to study the abundance and distribution of pigment type 3dB populations in the field (Grébert et al. 2018).
• MpeY family The mpeY gene is present in the "PEII subregion" of the "phycobilisome rod gene region" of all PEII-containing marine Synechococcus strains belonging to pigment types 3a and 3dA (Sanfilippo et al. 2019; Grébert et al. 2021); it is found at the same position as mpeQ in the phycobilisome gene region of pigment types 3c and 3dB (Grébert et al. 2021, 2022). MpeW was biochemically characterized as a PEB:Cys-83 alpha-PEII lyase in the pigment 3dA Synechococcus strain RS9916 (Sanfilippo et al. 2019). In Synechococcus pigment type 3a strains, this position therefore constitutively binds a PEB, whereas in pigment type 3dA strains, this position binds a PUB in blue light and a PEB in green light, as the result of a competition between MpeY and the PEB lyase-isomerase MpeZ, which is specifically and strongly activated in blue light but repressed in green light (Shukla et al. 2012; Humily et al. 2013).
• MpeZ family MpeZ is specific of marine Synechococcus belonging to pigment type 3dA, one of two kinds of type IV chromatic acclimaters. The mpeZ gene is located in the CA4-A genomic island, which also comprises the transcriptional regulators fciA-B-C and the yet uncharacterized gene unk10 (Humily et al. 2013; Sanfilippo et al. 2016, 2019). The CA4-A island is generally localized outside the main phycobilisome rod region, with rare exceptions (Grébert et al. 2022). MpeW has been biochemically characterized as a PEB:Cys-83 alpha-PEII lyase-isomerase in Synechococcus strain RS9916 (Shukla et al. 2012). In this and other pigment type 3dA strains, this site binds a PUB in blue light and a PEB in green light, as the result of a competition between the constitutively expressed PEB lyase gene mpeY and the PEB lyase-isomerase gene mpeZ, which is strongly activated in blue light but repressed in green light (Humily et al. 2013; Sanfilippo et al. 2019).
• E/F subclan 2 - Proteins related to lyases or lyase chaperones Members of this group usually have PBS lyase HEAT repeats domains or at least Armadillo-type folds. Most of them are uncharacterized yet and there is no evidence that they are bona fide phycobilin lyases, though they are clearly related to the latter. Among them, CpeZ is not a lyase per se but it was found to significantly enhance the activity of the PEB lyase CpeY (Biswas et al., 2011).
• CpeZ family CpeZ enhances the activity of CpeY. CpeYZ is involved in the attachment of PEB at Cys-82 alpha-PE (CpeA). CpeY alone, but not CpeZ can ligate PEB to CpeA, but with a reduced yield than CpeY and CpeZ together (Biswas et al., 2011). More recently Kronfel et al. (2019) showed that CpeZ acts as a chaperone-like protein, assisting in the folding/stability of PE subunits, allowing bilin lyases such as CpeY and CpeS to attach PEB to their PE subunit.
• IaiH family Forms a complex with IscA which is involved in iron-sulfur cluster formation in cyanobacteria (Morimoto et al. 2003)
• L8106_11777 homologs family Homologs of the L8106_11777 protein in CCY9616. Some similarity with CpeF and MpeU.
• L8106_16949 homologs family Homologs of the L8106_16949 protein in CCY9616.
  Some similarity with MpeU and CpeF.
• L8106_22089 homologs family Homologs of the L8106_22089 protein in CCY9616.
  Some similarity with CpeZ and iaiH.
• MC7420_3535 homologs family Maybe a fusion protein. Its C-terminus shows similarity with MpeU
• MC7420_4701 homologs family All members of this family possess several PBS lyase HEAT-like repeat domains and a C-term dual specificity phosphatase, catalytic domain.
• NblB/CotB superfamily This group gathers enzymes that either have been biochemically characterized and have another function than phycobilin lyases or are still uncharacterized. All share structural motifs with (and possibly have a similar enzymatic activity as) phycobilin lyases.
• CotB family Described in Balabas et al. (2003) as being involved in the activation of green light-induced genes during complementary chromatic adaptation, but given its presence in strains with a variety of pigmentation, it most likely has another yet-to-be determined function.
• CotB homologs 1 family Members of this family contain an Armadillo-like helical fold. This family is found in all marine Synechococcus as well as some freshwater species.
• CotB homologs 2 family Unknown function. Sequence containing 6 PBS lyase HEAT-like repeats domains.
• NblB family NblB has a role in PBS degradation (together with NblA and NblC). A Synechococcus sp. PCC7942 nblB-less mutant was shown to lack the ability to degrade its phycobilisomes during either sulfur or nitrogen limitation and exhibited an increased ratio of phycocyanin to chlorophyll during nutrient-replete growth (Dolganov and Grossman, 1999). NblB is absent from marine picocyanobacteria. Recently Hu et al. (2019) showed that together with NblA, NblB can 1) interfere with chromophorylation as well as chromophore-detachment of phycobiliprotein; 2) promote dissociation of whole phycobilisomes, cores and, in particular, allophycocyanin trimers. 3) While NblA and NblB do not interact with each other, both interact with lyases, apo- and holo-biliproteins; 4) They promote synergistically the lyase-catalyzed chromophorylation of the β-subunit of the major rod component, C-phycocyanin. 5) They modulate lyase-catalyzed and lyase-independent chromophore transfers among biliproteins, with the core protein, ApcF, the rod protein, CpcA, and sensory biliproteins (phytochromes, cyanobacteriochromes) acting as potential traps. Altogether NblA/B can cooperate with the lyases in remodeling the phycobilisomes.
• Unknown PEB lyase or lyase-isomerase In marine PE-containing Synechococcus strains, PEB are found at Cys-139 of alpha-PEI and PUB at Cys-140 and Cys-75 of alpha-PEII (Ong & Glazer 1991), as well as on PEII-associated linker polypeptides (Wilbanks & Glazer 1993b; Six et al. 2005), with no obvious candidate lyase-isomerase identified for these functions so far (Grébert et al. 2022). So these sites, which interestingly are absent from the PE-III of most Prochlorococcus strains, might either be auto-catalytically chromophorylated or the chromophore linkage catalyzed by a yet-to-be characterized lyase or lyase-isomerase.