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MetaCyc Pathway: phycocyanobilin biosynthesis
Inferred from experiment

Enzyme View:

Pathway diagram: phycocyanobilin biosynthesis

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisCofactors, Prosthetic Groups, Electron Carriers Biosynthesis

Some taxa known to possess this pathway include : Anabaena variabilis, Gloeobacter violaceus, Nostoc punctiforme, Nostoc sp. PCC 7120, Prochlorococcus marinus pastoris CCMP1986, Synechococcus elongatus PCC 7942, Synechococcus sp. PCC 7002, Synechocystis sp. PCC 6803

Expected Taxonomic Range: Cyanobacteria

General Background

Phytobilins are tetrapyrrole molecules that are synthesized by plants, algae and cyanobacteria. Major classes of phytobilins are:

1. Phycobilins, which are the chromophores of phycobiliproteins [Beale84] and some algal phytochromes [Lagarias95]

2. Phytochromobilins, which are the chromophores of higher plants phytochromes [Cornejo92, Terry95].

Phycobiliproteins are light-harvesting accessory pigments of cyanobacteria, red algae and cryptophytes, and phytochromes are photoreversible light signal-transducing pigments of plants, some algae, and some cyanobacteria.

One of the major class of phycobiliproteins in cyanobacteria is phycocyanins, and its chromophore is called phycocyanobilin. There are two stereoisomers of phycocyanobilin, but apparently only (2R,3Z)-phycocyanobilin is produced initially, with the second isomer potentially produced by a distinct bilin isomerase [Beale91].

About This Pathway

The biosynthetic pathways for the production of the four cyanobacterial phycobilins, as well as the Arabidopsis thaliana pathway for phytochromobilin biosynthesis, have been elucidated. These five chromophores share a common precursor, biliverdin-IX-α, which is the product of heme macrocycle cleavage by EC, heme oxygenase (biliverdin-producing). Biliverdin-IX-α is subsequently reduced by one of several possible ferredoxin-dependent bilin reductases.

(2R,3Z)-phycocyanobilin is biosynthesized from heme in a pathway that begins with the opening of the tetrapyrrole macrocycle of protoheme to form biliverdin-IX-α, in a reaction catalyzed by heme oxygenase 1 [Cornejo98]. In at least some cyanobacteria, such as Synechocystis sp. PCC 6803, biliverdin-IX-α is converted to (2R,3Z)-phycocyanobilin by a single enzyme, phycocyanobilin:ferredoxin oxidoreductase, encoded by the pcyA gene [Frankenberg01]. The same conversion is apparently catalyzed by multiple enzymes in the red algae Cyanidium caldarium [Brown89].

There are two stereoisomers of phycocyanobilin, (2R,3E)-phycocyanobilin and (2R,3Z)-phycocyanobilin. While (2R,3E)-phycocyanobilin is the major pigment that is released from phycobiliproteins by methanolysis [Cornejo92], only (2R,3Z)-phycocyanobilin is produced initially [Frankenberg01], with the second isomer produced either spontaneously or by a distinct bilin isomerase [Beale91].

Created 07-May-2008 by Caspi R, SRI International
Revised 24-Oct-2014 by Caspi R, SRI International


Beale84: Beale SI, Cornejo J (1984). "Enzymic Transformation of Biliverdin to Phycocyanobilin by Extracts of the Unicellular Red Alga Cyanidium caldarium." Plant Physiol 76(1);7-15. PMID: 16663825

Beale91: Beale SI, Cornejo J (1991). "Biosynthesis of phycobilins. 3(Z)-phycoerythrobilin and 3(Z)-phycocyanobilin are intermediates in the formation of 3(E)-phycocyanobilin from biliverdin IX alpha." J Biol Chem 266(33);22333-40. PMID: 1939256

Brown89: Brown SB, Holroyd JA, Vernon DI, Shim YK, Smith KM (1989). "The biosynthesis of the chromophore of phycocyanin. Pathway of reduction of biliverdin to phycocyanobilin." Biochem J 261(1);259-63. PMID: 2505754

Cornejo92: Cornejo J, Beale SI, Terry MJ, Lagarias JC (1992). "Phytochrome assembly. The structure and biological activity of 2(R),3(E)-phytochromobilin derived from phycobiliproteins." J Biol Chem 267(21);14790-8. PMID: 1634523

Cornejo98: Cornejo J, Willows RD, Beale SI (1998). "Phytobilin biosynthesis: cloning and expression of a gene encoding soluble ferredoxin-dependent heme oxygenase from Synechocystis sp. PCC 6803." Plant J 15(1);99-107. PMID: 9744099

Frankenberg01: Frankenberg N, Mukougawa K, Kohchi T, Lagarias JC (2001). "Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms." Plant Cell 13(4);965-78. PMID: 11283349

Lagarias95: Lagarias DM, Wu SH, Lagarias JC (1995). "Atypical phytochrome gene structure in the green alga Mesotaenium caldariorum." Plant Mol Biol 29(6);1127-42. PMID: 8616213

Terry95: Terry MJ, McDowell MT, Lagarias JC (1995). "(3Z)- and (3E)-phytochromobilin are intermediates in the biosynthesis of the phytochrome chromophore." J Biol Chem 270(19);11111-8. PMID: 7744741

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Dammeyer08: Dammeyer T, Bagby SC, Sullivan MB, Chisholm SW, Frankenberg-Dinkel N (2008). "Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria." Curr Biol 18(6);442-8. PMID: 18356052

Emborg06: Emborg TJ, Walker JM, Noh B, Vierstra RD (2006). "Multiple heme oxygenase family members contribute to the biosynthesis of the phytochrome chromophore in Arabidopsis." Plant Physiol 140(3);856-68. PMID: 16428602

Frankenberg03: Frankenberg N, Lagarias JC (2003). "Phycocyanobilin:ferredoxin oxidoreductase of Anabaena sp. PCC 7120. Biochemical and spectroscopic." J Biol Chem 278(11);9219-26. PMID: 12514179

Gisk10: Gisk B, Yasui Y, Kohchi T, Frankenberg-Dinkel N (2010). "Characterization of the haem oxygenase protein family in Arabidopsis thaliana reveals a diversity of functions." Biochem J 425(2);425-34. PMID: 19860740

Hagiwara06: Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K (2006). "Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin." Proc Natl Acad Sci U S A 103(1);27-32. PMID: 16380422

Kaneko01: Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A, Iriguchi M, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakazaki N, Shimpo S, Sugimoto M, Takazawa M, Yamada M, Yasuda M, Tabata S (2001). "Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120." DNA Res 8(5);205-13; 227-53. PMID: 11759840

Kaneko95: Kaneko T, Tanaka A, Sato S, Kotani H, Sazuka T, Miyajima N, Sugiura M, Tabata S (1995). "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome." DNA Res 2(4);153-66, 191-8. PMID: 8590279

Kaneko96: Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996). "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions." DNA Res 1996;3(3);109-36. PMID: 8905231

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Nakamura03: Nakamura Y, Kaneko T, Sato S, Mimuro M, Miyashita H, Tsuchiya T, Sasamoto S, Watanabe A, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Nakazaki N, Shimpo S, Takeuchi C, Yamada M, Tabata S (2003). "Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids." DNA Res 10(4);137-45. PMID: 14621292

Palenik03: Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J (2003). "The genome of a motile marine Synechococcus." Nature 424(6952);1037-42. PMID: 12917641

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Schuller99: Schuller DJ, Wilks A, Ortiz de Montellano PR, Poulos TL (1999). "Crystal structure of human heme oxygenase-1." Nat Struct Biol 6(9);860-7. PMID: 10467099

Sugishima04: Sugishima M, Migita CT, Zhang X, Yoshida T, Fukuyama K (2004). "Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme." Eur J Biochem 271(22);4517-25. PMID: 15560792

Willows00: Willows RD, Mayer SM, Foulk MS, DeLong A, Hanson K, Chory J, Beale SI (2000). "Phytobilin biosynthesis: the Synechocystis sp. PCC 6803 heme oxygenase-encoding ho1 gene complements a phytochrome-deficient Arabidopsis thalianna hy1 mutant." Plant Mol Biol 43(1);113-20. PMID: 10949378

Zhao06a: Zhao KH, Su P, Li J, Tu JM, Zhou M, Bubenzer C, Scheer H (2006). "Chromophore attachment to phycobiliprotein beta-subunits: phycocyanobilin:cysteine-beta84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena Sp. PCC7120." J Biol Chem 281(13);8573-81. PMID: 16452471

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Fri Apr 29, 2016, biocyc11.