gene cluster
A gene family is a set of homologous genes within one organism. A gene cluster is a group of two or more genes found within an organism's DNA that encode similar polypeptides, or proteins, which collectively share a generalized function and are o ...
responsible for the
biosynthesis
Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. ...
of
carotenoid
Carotenoids (), also called tetraterpenoids, are yellow, orange, and red organic compound, organic pigments that are produced by plants and algae, as well as several bacteria, and Fungus, fungi. Carotenoids give the characteristic color to pumpki ...
s. Those genes are found in eubacteria,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, in algaeMolecular 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, and are cryptic in ''
Streptomyces griseus
''Streptomyces griseus'' is a species of bacteria in the genus ''Streptomyces'' commonly found in soil. A few strains have been also reported from deep-sea sediments. It is a Gram-positive bacterium with high GC content. Along with most other s ...
''.
Role of ''CRT'' genes in Carotenoid Biosynthesis
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
Astaxanthin is a keto- carotenoid within a group of chemical compounds known as terpenes. Astaxanthin is a metabolite of zeaxanthin and canthaxanthin, containing both hydroxyl and ketone functional groups. It is a lipid-soluble pigment with r ...
biosynthesis and
Carotenoid
Carotenoids (), also called tetraterpenoids, are yellow, orange, and red organic compound, organic pigments that are produced by plants and algae, as well as several bacteria, and Fungus, fungi. Carotenoids give the characteristic color to pumpki ...
biosynthesis (Table 1).
''crtE'' encodes for an enzyme known as geranylgeranyl diphosphate synthase known to catalyze the condensation reaction of
isopentenyl pyrophosphate
Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP) is an isoprenoid precursor. IPP is an intermediate in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway) and in the ''non-mevalonate'' MEP pathway of ...
(IPP) and
dimethylallyl pyrophosphate
Dimethylallyl pyrophosphate (DMAPP; or alternatively, dimethylallyl diphosphate (DMADP); also isoprenyl pyrophosphate) is an isoprenoid precursor. It is a product of both the mevalonate pathway and the MEP pathway of isoprenoid precursor biosynt ...
(DMAPP) into
geranylgeranyl diphosphate
Geranylgeranyl pyrophosphate is an intermediate in the biosynthesis of diterpenes and diterpenoids. It is also the precursor to carotenoids, gibberellins, tocopherols, and chlorophylls.
It is also a precursor to geranylgeranylated proteins, whi ...
(GGDP). Two GGDP molecules are subsequently converted into a single
phytoene
Phytoene () is a 40-carbon intermediate in the biosynthesis of carotenoids. The synthesis of phytoene is the first committed step in the synthesis of carotenoids in plants. Phytoene is produced from two molecules of geranylgeranyl pyrophosphate (G ...
molecule by
phytoene synthase
Phytoene synthase (, ''prephytoene-diphosphate synthase'', ''15-cis-phytoene synthase'', ''PSase'', ''geranylgeranyl-diphosphate geranylgeranyltransferase'') is a transferase enzyme involved in the biosynthesis of carotenoids. It catalyzes the con ...
, an enzyme encoded by ''crtB'', known as ''PSY'' in Chlorophyta. The following desaturation of phytoene into ζ-carotene is catalyzed by the phytoene desaturase encoded by ''crtI, crtP,'' and/or ''PDS.'' ζ -carotene can also be obtained through phytoene using the carotene 2,4-desaturase enzyme (''crtD''). Depending on the species, varying carotenoids are accumulated following these steps.
Spirilloxanthin
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.
Canthaxanthin
Canthaxanthin is a keto-carotenoid pigment widely distributed in nature. Carotenoids belong to a larger class of phytochemicals known as terpenoids. The chemical formula of canthaxanthin is C40H52O2. It was first isolated in edible mushrooms. It ...
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.
Zeaxanthin
Zeaxanthin is one of the most common carotenoids in nature, and is used in the xanthophyll cycle. Synthesized in plants and some micro-organisms, it is the pigment that gives paprika (made from bell peppers), corn, saffron, goji ( wolfberries), ...
Hydroxylation of Zeaxanthin occurs by β-carotene hydroxylase an enzyme encoded on the ''crtR'' (in cyanobacteria) and ''crtZ'' gene (in Chlorophyta).
Other
Zeaxanthin can be further processed to obtain zeaxanthin-diglucoside by Zeaxanthin glucosyl transferase (''crtX'').
Echinenone
Echinenone is a xanthophyll, with formula C40H54O. It is found in some cyanobacteria. It is synthesized from β-carotene by the enzyme beta-carotene ketolase (or CrtW). It has also been isolated from sea urchins
Sea urchins () are spiny, g ...
is obtained from β -carotene through the catalyzing enzyme β-C-4-oxygenase/β-carotene ketolase (''crtO''). ''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.''CrtZ'', similarly to ''crtO'', is also capable of converting carotenoids into β-cryptoxanthin, Zeaxanthin, 3-Hydroxyechinenone, 3'-Hydroxyechinenone, Astaxanthin, Adonixanthin, and Adonirubin.
''crtH'' catalyzes the isomerization of cis-carotenes into trans-carotenes through carotenoid isomerase.
''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
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...
''.
Phylogeny
Previous studies have indicated through phylogenetic analysis that evolutionary patterns of ''crt'' genes are characterized by
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
and
gene duplication
Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
events.
Horizontal gene transfer has been hypothesized to have occurred between
cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...
and
Chlorophyta
Chlorophyta or Prasinophyta is a taxon of green algae informally called chlorophytes. The name is used in two very different senses, so care is needed to determine the use by a particular author. In older classification systems, it refers to ...
, as similarities in these genes have been found across taxa. 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. 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.
Gene duplications are suspected to have occurred due to the presence of multiple copies of ctr clusters or genes within a single species. An example of this can be seen in the ''
Bradyrhizobium
''Bradyrhizobium'' is a genus of Gram-negative soil bacteria, many of which fix nitrogen. Nitrogen fixation is an important part of the nitrogen cycle. Plants cannot use atmospheric nitrogen (N2); they must use nitrogen compounds such as nitrat ...
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
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...