Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria

The development and nutritional quality of Lyophyllum decastes affected by monochromatic or mixed light provided by light-emitting diode

Edible fungi has certain photo-sensitivity during the mushroom emergence stage, but there has been few relevant studies on the responses of Lyophyllum decastes to different light quality. L. decastes were planted in growth chambers with different light qualities that were, respectively, white light (CK), monochromatic red light (R), monochromatic blue light (B), mixed red and blue light (RB), and the mixture of far-red and blue light (FrB). The photo-sensitivity of L. decastes was investigated by analyzing the growth characteristics, nutritional quality, extracellular enzymes as well as the light photoreceptor genes in mushroom exposed to different light treatments. The results showed that R led to mycelium degeneration, fungal skin inactivation and failure of primordial formation in L. decastes. The stipe length, stipe diameter, pileus diameter and the weight of fruiting bodies exposed to RB significantly increased by 8.0, 28.7, 18.3, and 58.2% respectively, compared to the control (p < 0.05). B significantly decreased the stipe length and the weight of fruiting body, with a decrease of 8.5 and 20.2% respectively, compared to the control (p < 0.05). Increased color indicators and deepened simulated color were detected in L. decastes pileus treated with B and FrB in relative to the control. Meanwhile, the expression levels of blue photoreceptor genes such as WC-1, WC-2 and Cry-DASH were significantly up-regulated in mushroom exposed to B and FrB (p < 0.05). Additionally, the contents of crude protein and crude polysaccharide in pileus treated with RB were, respectively, increased by 26.5 and 9.4% compared to the control, while those in stipes increased by 5.3 and 58.8%, respectively. Meanwhile, the activities of extracellular enzyme such as cellulase, hemicellulase, laccase, manganese peroxidase, lignin peroxidase and amylase were significant up-regulated in mushroom subjected to RB (p < 0.05), which may promote the degradation of the culture materials. On the whole, the largest volume and weight as well as the highest contents of nutrients were all detected in L. decastes treated with RB. The study provided a theoretical basis for the regulation of light environment in the industrial production of high quality L. decastes.

Molecular evolution and diversification of phytoene synthase (PSY) gene family

Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.

Purification, Identification, and Properties of a Novel Carotenoid Produced by Arthrobacter sp. QL17 Isolated from Mount Qomolangma

The genus Arthrobacter is a source of many natural products that are critical in the development of new medicines. Here, we isolated a novel carotenoid from Arthrobacter sp. QL17 and characterized its properties. The carotenoid was extracted with methanol, and purified by column chromatography and semi-preparative HPLC. Based on micrOTOF-Q and NMR analyses, the pigment was chemically characterized as 2,2′-((((1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,14,18-tetramethylicosa-1,3,5,7,9,11,13,15,17,19-decaene-1,20-diyl)bis(2,2,4-trimethylcyclohex-3-ene-3,1-diyl)) bis(ethan-2-yl-1-ylidene))bi(propane-1,3-diol), and named arthroxanthin. The biological activities of arthroxanthin were evaluated with DPPH, ABTS and MTT assays. Arthroxanthin exhibited excellent radical scavenging properties, as shown for 2, 20-diphenyl-1-picrylhydrazyl (DPPH) and 2,2-n-(3, 2-ethyl-benzothiazole-6-sulfonic acid) ammonium salt (ABTS), respectively, with IC50s of 69.8 and 21.5 µg/mL. It also showed moderate anticancer activities against HepG2, Hela, MDAB-231, SW480, and MKN-45 with IC50 values of 107.6, 150.4, 143.4, 195.9, and 145.5 μg/mL, respectively. Therefore, arthroxanthin derived from Arthrobacter sp. QL17 may be a potent antioxidant and anticancer agent for food and pharmaceutical use.

Diversity and origin of carotenoid biosynthesis: its history of coevolution towards plant photosynthesis

The development of photosynthesis was a highlight in the progression of bacteria. In addition to the photosystems with their structural proteins, the photosynthesis apparatus consists of different cofactors including essential carotenoids. Thus, the evolution of the carotenoid pathways in relation to the functionality of the resulting structures in photosynthesis is the focus of this review. Analysis of carotenoid pathway genes indicates early evolutionary roots in prokaryotes. The pathway complexity leading to a multitude of structures is a result of gene acquisition, including their functional modifications, emergence of novel genes and gene exchange between species. Along with the progression of photosynthesis, carotenoid pathways coevolved with photosynthesis according to their advancing functionality. Cyanobacteria, with their oxygenic photosynthesis, became a landmark for evolutionary events including carotenogenesis. Concurrent with endosymbiosis, the cyanobacterial carotenoid pathways were inherited into algal plastids. In the lineage leading to Chlorophyta and plants, carotenoids evolved to their prominent role in protection and regulation of light energy input as constituents of a highly efficient light-harvesting complex.

Genome analysis of Lactobacillus plantarum subsp. plantarum KCCP11226 reveals a well-conserved C30 carotenoid biosynthetic pathway

Carotenoids are group of colored terpenoids with antioxidant properties and widespread in nature including in microorganisms. Lactobacillus plantarum subsp. plantarum KCCP11226 was previously isolated from kimchi, while exhibiting the production of 4,4'-diaponeurosporene as a C₃₀ carotenoid. In this study, full genome sequencing of the strain KCCP11226 was performed. Genome analysis revealed that the dehydrosqualene synthase (crtM) and dehydrosqualene desaturase (crtN) genes, which are major genes for biosynthesis of 4,4'-diaponeurosporene, were shown to act as an operon in most L. plantarum strains, but they were uncommon in other Lactobacillus species. In vitro experiments revealed that the production of 4,4'-diaponeurosporene was greatly increased by oxidative stress. In this situation, mRNA expressions of crtN and crtM were also significantly increased. In conclusion, genome analysis of L. plantarum subsp. plantarum KCCP11226 suggested the presence of a well-conserved C₃₀ carotenoid biosynthetic pathway that includes the crtM-crtN operon. The genomic information on L. plantarum subsp. plantarum KCCP11226 could further elucidate the functions of genes involved in isoprenoid biosynthetic pathway, especially in C₃₀ carotenoid biosynthesis.

Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

Purpose

The aim of this study is the in silico characterization of the structure and function of the phytoene synthase (PSY) of a red carotenoid producing thermophile Meiothermus taiwanensis strain RP with a comparative approach.

Methods

PSYs from M. taiwanensis strain RP and other groups of thermophilic, mesophilic and psychrophilic bacteria, plants, protozoa, and algae were analyzed by ExPASy ProtParam, NCBI Conserved Domain Search, SOPMA, PSIPRED, Robetta server, ProQ, and QMEAN, with the superposition of 3-D structures in PyMOL.

Results

RP PSY shows the highest (97.5 %) similarity with M. ruber and the lowest with the psychrophile Gelidibacter algens (36.7 %). The amino acid sequence of RP PSY is one of the shortest, with 275 residues. The instability index of RP PSY is much lower compared with plant sequences. Alanine, arginine, glycine, and leucine residues are the highest in Meiothermus sp., and they have a high amount of alpha-helix. Most of the 32 active site residues are conserved in all the sequences. However, some residues are more prone to substitutions in other PSYs except M. ruber. The three-dimensional structures of M. taiwanensis strain RP, Gelidibacter algens, Thermus thermophiles, Meiothermus ruber, and Brassica napus PSYs were homology modeled, validated, and submitted to Protein Model Databank. The superposition of the 3-D structures shows that their active site region structure is identical.

Conclusion

RP PSY is one of the most stable PSYs and knowledge of its individual properties, similarities, and dissimilarities with other PSYs may be useful for genetic engineering and purification of the protein for improved carotenoid production.

Carotenoid Biosynthesis in Fusarium

Many fungi of the genus Fusarium stand out for the complexity of their secondary metabolism. Individual species may differ in their metabolic capacities, but they usually share the ability to synthesize carotenoids, a family of hydrophobic terpenoid pigments widely distributed in nature. Early studies on carotenoid biosynthesis in Fusariumaquaeductuum have been recently extended in Fusarium fujikuroi and Fusarium oxysporum, well-known biotechnological and phytopathogenic models, respectively. The major Fusarium carotenoid is neurosporaxanthin, a carboxylic xanthophyll synthesized from geranylgeranyl pyrophosphate through the activity of four enzymes, encoded by the genes carRA, carB, carT and carD. These fungi produce also minor amounts of β-carotene, which may be cleaved by the CarX oxygenase to produce retinal, the rhodopsin's chromophore. The genes needed to produce retinal are organized in a gene cluster with a rhodopsin gene, while other carotenoid genes are not linked. In the investigated Fusarium species, the synthesis of carotenoids is induced by light through the transcriptional induction of the structural genes. In some species, deep-pigmented mutants with up-regulated expression of these genes are affected in the regulatory gene carS. The molecular mechanisms underlying the control by light and by the CarS protein are currently under investigation.

Isolation and characterization of a muskmelon cDNA encoding Lycopene Beta-cyclase

Lycopene Beta-cyclase (LCY-B) is thought to play a critical role in Beta-carotene synthesis in fruit. A full-length cDNA clone encoding Lycopene Beta-cyclase was isolated from muskmelon (Cucumis melo L.) by RT-PCR and RACE. The clone, designated CmLcyb1, contains 1871 nucleotides, with an open reading frame of 1512 nucleotides. The deduced 504-amino-acid sequence showed high identities with other plant Lycopene Beta-cyclases. Real time quantitative RT-PCR analysis indicated that CmLcyb1 was expressed in all tissues and organs of muskmelon inbred M01-3 with white mesocarp and, 'Homoka', an orange mesocarp cultivar. The expression levels of CmLcyb1 in roots, stems, leaves and flowers in the two genotypes differed little. The expression level was highest in mature fruit of 'Homoka' and was much higher than that in mature fruit of M01-3. Moreover, the mRNA level of CmLcyb1 was very low in fruits before fruit-size fixation and increased dramatically in the size-fixed fruits of these two genotypes. The mRNA levels of CmLcyb1 during fruit development of 'Homoka' were all higher than those of M01-3. Interestingly, Beta-carotene content showed almost the same change trend as mRNA levels during fruit development in these two genotypes, suggesting that Beta-carotene accumulation may be linked to the CmLcyb1 transcript level in muskmelon fruit.

Microbial carotenoids

Carotenoids are among the most widely distributed pigments in nature, and they are exclusively synthesized by plants and microorganisms. These compounds may serve a protective role against many chronic diseases such as cancers, age-related macular degeneration, and cardiovascular diseases and also act as an excellent antioxidant system within cells. Recent advances in the microbial genome sequences and increased understanding about the genes involved in the carotenoid biosynthetic pathways will assist industrial microbiologists in their exploration of novel microbial carotenoid production strategies. Here we present an overview of microbial carotenogenesis from biochemical, proteomic, and biotechnological points of view.

Carotenoids and their cleavage products: biosynthesis and functions

This review focuses on plant carotenoids, but it also includes progress made on microbial and animal carotenoid metabolism to better understand the functions and the evolution of these structurally diverse compounds with a common backbone. Plants have evolved isogenes for specific key steps of carotenoid biosynthesis with differential expression profiles, whose characteristic features will be compared. Perhaps the most exciting progress has been made in studies of carotenoid cleavage products (apocarotenoids) with an ever-expanding variety of novel functions being discovered. This review therefore covers structural, molecular genetic and functional aspects of carotenoids and apocarotenoids alike. Apocarotenoids are specifically tailored from carotenoids by a family of oxidative cleavage enzymes, but whether there are contributions to their generation from chemical oxidation, photooxidation or other mechanisms is largely unknown. Control of carotenoid homeostasis is discussed in the context of biosynthetic and degradative reactions but also in the context of subcellular environments for deposition and sequestration within and outside of plastids. Other aspects of carotenoid research, including metabolic engineering and synthetic biology approaches, will only be covered briefly.

Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics

BACKGROUND

Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data.

METHODOLOGY/PRINCIPAL FINDINGS

Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection.

CONCLUSIONS/SIGNIFICANCE

Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification.

Carotenoid production in Lactobacillus plantarum

Eighteen strains of Lactobacillus plantarum from different origins were screened for carotenoid production, as many of them exhibited a deep yellow pigmentation when cultured as isolated colonies on MRS-agar plates. We found that most of them produced significative amounts of the yellow C(30) carotenoid 4,4'-diaponeurosporene in the range 1.8 to 54 mg/kg of dry cell weight. Although some of the strains produced just trace amounts of this carotenoid, PCR studies showed that all of them harbored the genes crtM and crtN which, inferred from homology, had been predicted in the three L. plantarum complete genome sequences currently available. Our results suggest the full functionality of a C(30) carotenoid biosynthesis pathway in this species, driven by the operon crtNM. DNA sequencing of the entire crtNM operon in the maximum carotenoid-producing strain found in this study, i.e. L. plantarum CECT7531, was accomplished. Genes crtM and crtN were annotated as dehydrosqualene synthase and dehydrosqualene desaturase, respectively, in this strain.

Characterization of canthaxanthin biosynthesis genes from an uncultured marine bacterium

Carotenoids are isoprenoid pigments synthesized in plants, fungi, bacteria and archaea, with roles in light harvesting, protection from stress, and membrane and protein structures. To characterize carotenoid biosynthesis genes from oceanic microbes, a fosmid library derived from microbial samples collected in surface water of the Pacific Ocean was screened in Escherichia coli for pigment-expressing recombinant strains. One DNA fragment enabled production of a bright orange pigment, and was analysed further by sequence analysis and phenotypic characterization. The cloned DNA encoded a five-gene cluster predicted to be involved in the synthesis of canthaxanthin, a ketolated carotenoid. Each of these genes was inactivated by insertion of a transposon, and the biochemical function of each gene product was confirmed. Sequencing of related fosmids generated a 67 kb genomic contig, and comparative analyses suggested that the DNA may originate from a deltaproteobacterium. The carotenoid biosynthesis genes described here are related to well-characterized families of carotenoid biosynthesis genes, but also indicate that the organism harbouring them is only distantly related to any previously characterized bacterial types.

Populus from high altitude has more efficient protective mechanisms under water stress than from low-altitude habitats: a study in greenhouse for cuttings

Cuttings of Populus przewalskii and P. cathayana, which originated from high and low altitudes in southwest China, were used to examine the effect of water stress on the morphological, physiological and biochemical traits of plants in a greenhouse for one growing season. The dry mass accumulation and allocation, gas exchanges, extent of peroxidation damage, osmotic adjustment and antioxidative defenses, and amounts of pigments were measured to characterize the differences in peroxidation damage and protective mechanisms of two poplar species that contrast in drought tolerance. Under water stress, poplars showed a series of biochemical adjustments and morphological changes as follows: a decrease in leaf relative water content, gas exchanges, plant growth and dry mass accumulation; an increase in relative allocation to roots; an increase in the osmolyte contents (e.g. total amino acids). Additionally, water deficit induced an increase in peroxidation damage [as indicated by an increase in electrolyte leakage, malondialdehyde (MDA), carbonyl (C = O ) and hydrogen peroxide (H(2) O(2) ) content], enhanced activities or contents of antioxidants (e.g. ascorbate peroxidase, guaiacol peroxidase, glutathione redutase and ascorbic acid) and reduced amounts of leaf pigments (e.g. chlorophyll and carotenoid). Furthermore, there were significant differences in the extent of morphological and biochemical changes between the two poplar species. Compared with P. cathayana, P. przewalskii responded to water stress by allocating relatively more to root dry mass, possessing a higher net photosynthesis rate, and having more efficient protective mechanisms, such as more osmolyte accumulation, stronger antioxidant activities and lower chlorophyll/carotenoid ratio. Thus, P. przewalskii suffered less damage as deduced from lower levels of electrolyte leakage, MDA, C=O and H(2) O(2) content. Therefore, P. przewalskii originating from high altitude could possess more efficient protective mechanisms than P. cathayana, which is from low-altitude habitats.

A novel carotenoid 1,2-hydratase (CruF) from two species of the non-photosynthetic bacterium Deinococcus

A novel carotenoid 1,2-hydratase (CruF) responsible for the C-1',2' hydration of gamma-carotene was identified in the non-photosynthetic bacteria Deinococcus radiodurans R1 and Deinococcus geothermalis DSM 11300. Gene expression and disruption experiments demonstrated that dr0091 and dgeo2309 encode CruF in D. radiodurans and D. geothermalis, respectively. Their homologues were also found in the genomes of cyanobacteria, and exhibited little homology to the hydroxyneurosporene synthase (CrtC) proteins found mainly in photosynthetic bacteria. Phylogenetic analysis showed that CruF homologues form a separate family, which is evolutionarily distant from the known CrtC family.

Molecular Phylogenies and Evolution ofcrtGenes in Algae

The carotenoids constitute the most widespread class of pigments in nature. Most previous work has concentrated on the identification and characterization of their chemical physical properties and bioavailability. In recent years, significant amounts of research have been conducted in an attempt to analyze the genes and the molecular regulation of the genes involved in the biosynthesis of carotenoids. However, it is important not to lose sight of the early evolution of carotenoid biosynthesis. One of the major obstacles in understanding the evolution of the respective enzymes and their patterns of selection is a lack of a well-supported phylogenic analysis. In the present research, a major long-term objective was to provide a clearer picture of the evolutionary history of genes, together with an evaluation of the patterns of selection in algae. These phylogenies will be important in studies characterizing the evolution of algae. The gene sequences of the enzymes involved in the major steps of the carotenoid biosynthetic pathway in algae (cyanobacteria, rhofophyta, chlorophyta) have been analyzed. Phylogenetic relationships among protein-coding DNA sequences were reconstructed by neighbor-joining (NJ) analysis for the respective carotenoid biosynthetic pathway genes (crt) in algae. The analysis also contains an estimation of the rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)), synonymous nucleotide substitution per synonymous site (d(S)), and the ratio of nonsynonmous (d(N)/d(S)) for the test of selection patterns. The phylogenetic trees show that the taxa of some genera have a closer evolutionary relationship with other genera in some gene sequences, which suggests a common ancient origin and that lateral gene transfer has occurred among unrelated genera. The d(N) values of crt genes in the early pathway are relatively low, while those of the following steps are slightly higher, while the d(N) values of crt genes in chlorophyta are higher than those in cyanobacteria. Most of the d(N)/d(S) values exceed 1. The phylogenetic analysis revealed that lateral gene transfer may have taken place across algal genomes and the d(N) values suggest that most of the early crt genes are well conserved compared to the later crt genes. Furthermore, d(N) values also revealed that the crt genes of chlorophyta are more evolutionary than cyanobacteria. The amino acids' changes are mostly adaptive evolution under the influence of positive diversity selection.

Identification of a fourth family of lycopene cyclases in photosynthetic bacteria

A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechococcus sp. PCC 7002 has two homologs of CruA, denoted CruA and CruP, and both were shown to have lycopene cyclase activity. Although all characterized lycopene cyclases in plants are CrtL-type proteins, genes orthologous to cruP also occur in plant genomes. The CruA- and CruP-type carotenoid cyclases are members of the FixC dehydrogenase superfamily and are distantly related to CrtL- and CrtY-type lycopene cyclases. Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria.

Sequence variation of chalcone synthase gene in a spontaneous white-flower mutant of Chinese cabbage-pak-choi

A spontaneous white-flower mutant of Chinese cabbage-pak-choi (Brassica campestris ssp. chinenesis, syn. B. rapa ssp. chinenesis) was found in our test fields, and all the plant characters except flower color were identical with wild type ones. We hypothesized that a mutational event had occurred in the gene coding for chalcone synthase (CHS), the key enzyme of flavonoid biosynthesis pathway. Two genes, later designated BcCHS and BcCHS-wf, were isolated from wild type and mutant Chinese cabbage-pak-choi, respectively, using gene-specific primer pairs. Comparison of the genomic sequences revealed two mutations in BcCHS-wf, both with A to G transitions, one at position +37 bp and the other at +970 bp. Both nucleotide substitutions occurred in AGA codes for arginine into GGA for glycin at residue +13 and into AGC coding for serine at residue +229, respectively. Homologous genes of BcCHS were isolated from another four cruciferous plants, though there were some differences among the genomic and deduced amino acid sequences, the mutation locus of the mutant, as we called it, were identical to the wild type Chinese cabbage-pak-choi.

Two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium Chlorobium tepidum

The green sulfur bacterium Chlorobium tepidum produces chlorobactene as its primary carotenoid. Small amounts of chlorobactene are hydroxylated by the enzyme CrtC and then glucosylated and acylated to produce chlorobactene glucoside laurate. The genes encoding the enzymes responsible for these modifications of chlorobactene, CT1987, and CT0967, have been identified by comparative genomics, and these genes were insertionally inactivated in C. tepidum to verify their predicted function. The gene encoding chlorobactene glucosyltransferase (CT1987) has been named cruC, and the gene encoding chlorobactene lauroyltransferase (CT0967) has been named cruD. Homologs of these genes are found in the genomes of all sequenced green sulfur bacteria and filamentous anoxygenic phototrophs as well as in the genomes of several nonphotosynthetic bacteria that produce similarly modified carotenoids. The other bacteria in which these genes are found are not closely related to green sulfur bacteria or to one another. This suggests that the ability to synthesize modified carotenoids has been a frequently transferred trait.

Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics

Carotenoids are widely distributed pigments in nature and their biosynthetic pathway has been extensively studied in various organisms. The recent access to the overwhelming amount genomic data of cyanobacteria has given birth to a novel approach called comparative genomics. The putative enzymes involved in the carotenoid biosynthesis among the cyanobacteria were determined by similarity-based tools. The reconstruction of biosynthetic pathway was based on the related enzymes. It is interesting to find that nearly all the cyanobacteria share quite similar pathway to synthesize β-carotene except for Gloeobacter violaceus PCC 7421. The enzymes, crtE-B-P-Qb-L, involved in the upstream pathway are more conserved than the subsequent ones (crtW-R). In addition, many carotenoid synthesis enzymes exhibit diversity in structure and function. Such examples in the families of ζ –carotene desaturase, lycopene cylases and carotene ketolases were described in this article. When we mapped these crt genes to the cyanobacterial genomes, the crt genes showed great structural variation among species. All of them are dispersed on the whole chromosome in contrast to the linear adjacent distribution of the crt gene cluster in other eubacteria. Moreover, in unicellular cyanobacteria, each step of the carotenogenic pathway is usually catalyzed by one gene product, whereas multiple ketolase genes are found in filamentous cyanobacteria. Such increased numbers of crt genes and their correlation to the ecological adaptation were carefully discussed.