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CRT (genetics)

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CRT is the gene cluster responsible for the biosynthesis of carotenoids. Those genes are found in eubacteria,[1] in algae[2] and are cryptic in Streptomyces griseus.[3]

Carotenoid synthesis is probably present in the common ancestor of Bacteria and Archaea; the phytoene synthase gene crtB is universal among carotenoid synthesizers. Among eukaryotes, plants and algae inherited the cyanobacterial pathway via biosynthesis of their plastids, while fungi retain a archaeal-like pathway.[4] Among all these synthesizers, several possible selection and arrangements of biosynthetic genes exist, consisting of one gene cluster cluster, several clusters, or no clustering at all.[5][a]

Role of CRT genes in carotenoid biosynthesis

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The CRT gene cluster consists of twenty-five genes such as crtA, crtB, crtC, crtD, crtE, crtF, crtG, crtH, crtI, crtO, crtP, crtR, crtT, crtU, crtV, and crtY, crtZ. These genes play a role in varying stages of the Astaxanthin biosynthesis and Carotenoid biosynthesis (Table 1).[6]

crtE encodes for an enzyme known as geranylgeranyl diphosphate synthase known to catalyze the condensation reaction of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) into geranylgeranyl diphosphate (GGDP).[7][8] Two GGDP molecules are subsequently converted into a single phytoene molecule by phytoene synthase, an enzyme encoded by crtB, known as PSY in Chlorophyta.[2][7][8] The following desaturation of phytoene into ζ-carotene is catalyzed by the phytoene desaturase encoded by crtI, crtP, and/or PDS.[2][7][8] ζ -carotene can also be obtained through phytoene using the carotene 2,4-desaturase enzyme (crtD).[2][9] Depending on the species, varying carotenoids are accumulated following these steps.[1][10]

Spirilloxanthin

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Spirilloxanthin is obtained from lycopene following a hydration, desaturation, and methylation reaction. These reactions are catalyzed by carotene hydratase (crtC), carotene 3,4- desaturase (crtD), and carotene methyltransferase (crtF), respectively.[8][1]

Canthaxanthin

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Lycopene is cyclized through two enzymes lycopene cyclase and β-C-4-oxygenase/β-carotene ketolase encoded on the crtY (in Chlorophyta) /crtL (in cyanobacteria), and crtW, respectively. crtY cyclizes lycopene into β-carotene, which is subsequently oxygenated by crtW to form canthaxanthin.[8]

Zeaxanthin and lutein

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Zeaxanthin and lutein are obtained through hydroxylation of α- and β-carotene.[1] Hydroxylation of Zeaxanthin occurs by β-carotene hydroxylase an enzyme encoded on the crtR (in cyanobacteria) and crtZ gene (in Chlorophyta).[8]

Other

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Zeaxanthin can be further processed to obtain zeaxanthin-diglucoside by Zeaxanthin glucosyl transferase (crtX).

Echinenone is obtained from β -carotene through the catalyzing enzyme β-C-4-oxygenase/β-carotene ketolase (crtO).[11] CrtO, also known as bkt2 in Chlorophyta, is also involved in the conversion of other carotenoids into Canthaxanthin, 3-Hydroxyechinenone, 3'-Hydroxyechinenone, Adonixanthin, and Astaxanthin.[11][12]CrtZ, similarly to crtO, is also capable of converting carotenoids into β-cryptoxanthin, Zeaxanthin, 3-Hydroxyechinenone, 3'-Hydroxyechinenone, Astaxanthin, Adonixanthin, and  Adonirubin.[11]

crtH catalyzes the isomerization of cis-carotenes into trans-carotenes through carotenoid isomerase.[2]

crtG encodes for carotenoid 2,2'- β-hydroxylase, this enzyme leads to the formation of 2-hydroxylated and 2,2′-dihydroxylated products in E coli.[13]

Table 1: role of CRT genes in carotenoid biosynthesis [2]
Gene Enzyme Catalyzed reaction
crtE GGDP synthase IPP and DMAPP conversion to GGDP
crtB (PSY*) Phytoene Synthase (universal) GGDP conversion to phytoene
crtP (PDS*) Phytoene desaturase (Chlorobi, Cyanobacteria, plant, algae)[5] Conversion of phytoene into ζ- carotene
crtI Phytoeine desaturase (Archaea, fungi, most Bacteria) Conversion of phytoene into ζ- carotene
crtQ ζ- carotene desaturase (Qa: 'evolved from CrtI; Qb: evolved from CrtP)[5] Desaturation of ζ- carotene to lycopene
crtH Carotenoid isomerase Isomeration of cis to trans carotones
crtY Lycopene cyclase (Bacteria except Firmicutes, Chlorobi, Cyanobacteria, Actinobacteria)[4] Cyclization of lycopene
crtL Lycopene cyclase (two in Cyanobacteria: crtL-b became plant lcy-B, crtL-e became plant lcy-E)[5] Cyclization of lycopene
crtD Carotene 3,4-desaturase Conversion of phytoene to ζ-carotene
crtA Spheroidene monooxygenase Conversion of spheroidene to spheroidenone
crtR+ β-carotene hydroxylase (various Cyanobacteria) Hydroxylation of β-carotene to zeaxanthin
crtZ* β-carotene hydroxylase (various Chlorophyta) Hydroxylation of β-carotene to zeaxanthin
crtX Zeaxanthin glucosyl transferase Conversion of zeaxanthin to zeaxanthin-diglucoside
crtW (bkt2*) β-C-4-oxygenase/β-carotene ketolase Conversion of β-carotene to canthaxanthin
crtO β-C-4-oxygenase/β-carotene ketolase Conversion of β-carotene to echinenone
crtC Carotene hydratase Conversion of neurosporene to demethylspheroidene and lycopene to hydroxy derivatives
crtG Carotenoid 2,2′-β-hydroxylase Conversion of myxol to 2-hydroxymyxol and zeaxanthin to nostoxanthin
crtK Carotenoid regulation -
* In Chlorophyta, + In cyanobacteria

Phylogeny

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Previous studies have indicated through phylogenetic analysis that evolutionary patterns of crt genes are characterized by horizontal gene transfer and gene duplication events.[14]

Horizontal gene transfer has been hypothesized to have occurred between cyanobacteria and Chlorophyta, as similarities in these genes have been found across taxa.[14] Note, however, that some cyanobacteria retained their nature. Horizontal gene transfer among species occurred with a high probability in genes involved in the initial steps of the carotenoid biosynthesis pathway such as crtE, crtB, crtY, crtL, PSY, and crtQ. These genes are often well conserved while others involved in the later stages of Carotenoid biosynthesis such as crtW and crtO are less conserved.[1] The less conserved nature of these genes allowed for the expansion of the carotenoid biosynthesis pathway and its end products. Amino acid variations within crt genes have evolved due to purifying and adaptive selection.[2]

Gene duplications are suspected to have occurred due to the presence of multiple copies of ctr clusters or genes within a single species.[2] An example of this can be seen in the Bradyrhizobium ORS278 strain, where initial crt genes can be found (excluding crtC, crtD, and crtF genes) as well as a second crt gene cluster. This second gene cluster has been shown to also be involved in carotenoid biosynthesis using its crt paralogs.[8][15]

References

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  1. ^ For concrete examples of the diversity of gene organization, compare the clusters presented in [6] figure 1 (6 genomes), PMID 37887056 figure 1 (4 genomes), PMID 22963379 figure 1 (10 genomes), and PMID 32155882 figure 3 (11 genomes).
  1. ^ a b c d e Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria. Phadwal K, Gene, 17 January 2005, volume 345, issue 1, pages 35-43, PMID 15716108
  2. ^ a b c d e f g h Molecular phylogenies and evolution of crt genes in algae. Chen Q, Jiang JG and Wang F, Crit Rev Biotechnol., Apr-Jun 2007;, volume 27, issue 2, pages 77-91, PMID 17578704
  3. ^ Activation and analysis of cryptic crt genes for carotenoid biosynthesis from Streptomyces griseus. Schumann G1, Nürnberger H, Sandmann G and Krügel H, Mol Gen Genet., 28 October 1996, volume 252, issue 6, pages 658-666, PMID 8917308
  4. ^ a b Sandmann, G (2021). "Diversity and Evolution of Carotenoid Biosynthesis from Prokaryotes to Plants.". Carotenoids: Biosynthetic and Biofunctional Approaches. Advances in experimental medicine and biology. Vol. 1261. pp. 79–94. doi:10.1007/978-981-15-7360-6_7. PMID 33783732.
  5. ^ a b c d Sandmann, Gerhard (October 2021). "Diversity and origin of carotenoid biosynthesis: its history of coevolution towards plant photosynthesis". New Phytologist. 232 (2): 479–493. doi:10.1111/nph.17655.
  6. ^ a b Nishida, Yasuhiro; Adachi, Kyoko; Kasai, Hiroaki; Shizuri, Yoshikazu; Shindo, Kazutoshi; Sawabe, Akiyoshi; Komemushi, Sadao; Miki, Wataru; Misawa, Norihiko (August 2005). "Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2′-β-Hydroxylase, from Brevundimonas sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls". Applied and Environmental Microbiology. 71 (8): 4286–4296. Bibcode:2005ApEnM..71.4286N. doi:10.1128/AEM.71.8.4286-4296.2005. ISSN 0099-2240. PMC 1183362. PMID 16085816.
  7. ^ a b c Sandmann, Gerhard; Misawa, Norihiko (January 1992). "New functional assignment of the carotenogenic genescrtBandcrtEwith constructs of these genes fromErwiniaspecies". FEMS Microbiology Letters. 90 (3): 253–258. doi:10.1111/j.1574-6968.1992.tb05162.x. ISSN 0378-1097.
  8. ^ a b c d e f g Giraud, Eric; Hannibal, Laure; Fardoux, Joël; Jaubert, Marianne; Jourand, Philippe; Dreyfus, Bernard; Sturgis, James N.; Verméglio, Andre (April 2004). "Two Distinct crt Gene Clusters for Two Different Functional Classes of Carotenoid in Bradyrhizobium". Journal of Biological Chemistry. 279 (15): 15076–15083. doi:10.1074/jbc.m312113200. ISSN 0021-9258. PMID 14734565.
  9. ^ Yang, Ying; Yatsunami, Rie; Ando, Ai; Miyoko, Nobuhiro; Fukui, Toshiaki; Takaichi, Shinichi; Nakamura, Satoshi (2015-02-23). "Complete Biosynthetic Pathway of the C50Carotenoid Bacterioruberin from Lycopene in the Extremely Halophilic Archaeon Haloarcula japonica". Journal of Bacteriology. 197 (9): 1614–1623. doi:10.1128/jb.02523-14. ISSN 0021-9193. PMC 4403650. PMID 25712483.
  10. ^ Maoka, Takashi (2019-10-01). "Carotenoids as natural functional pigments". Journal of Natural Medicines. 74 (1): 1–16. doi:10.1007/s11418-019-01364-x. ISSN 1340-3443. PMC 6949322. PMID 31588965.
  11. ^ a b c Harker, Mark; Hirschberg, Joseph (1997-03-10). "Biosynthesis of ketocarotenoids in transgenic cyanobacteria expressing the algal gene for β-C-4-oxygenase, crtO". FEBS Letters. 404 (2–3): 129–134. doi:10.1016/s0014-5793(97)00110-5. ISSN 0014-5793. PMID 9119049. S2CID 9125542.
  12. ^ Fernández-González, Blanca; Sandmann, Gerhard; Vioque, Agustín (April 1997). "A New Type of Asymmetrically Acting β-Carotene Ketolase Is Required for the Synthesis of Echinenone in the Cyanobacterium Synechocystis sp. PCC 6803". Journal of Biological Chemistry. 272 (15): 9728–9733. doi:10.1074/jbc.272.15.9728. ISSN 0021-9258. PMID 9092504.
  13. ^ Nishida, Yasuhiro; Adachi, Kyoko; Kasai, Hiroaki; Shizuri, Yoshikazu; Shindo, Kazutoshi; Sawabe, Akiyoshi; Komemushi, Sadao; Miki, Wataru; Misawa, Norihiko (August 2005). "Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2′-β-Hydroxylase, from Brevundimonas sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls". Applied and Environmental Microbiology. 71 (8): 4286–4296. Bibcode:2005ApEnM..71.4286N. doi:10.1128/aem.71.8.4286-4296.2005. ISSN 0099-2240. PMC 1183362. PMID 16085816.
  14. ^ a b Phadwal, Kanchan (January 2005). "Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria". Gene. 345 (1): 35–43. doi:10.1016/j.gene.2004.11.038. ISSN 0378-1119. PMID 15716108.
  15. ^ Tran, Duc; Haven, James; Qiu, Wei-Gang; Polle, Juergen E. W. (2008-12-09). "An update on carotenoid biosynthesis in algae: phylogenetic evidence for the existence of two classes of phytoene synthase". Planta. 229 (3): 723–729. doi:10.1007/s00425-008-0866-2. ISSN 0032-0935. PMC 6008256. PMID 19066941.
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