Elucidation of a carotenoid biosynthesis gene cluster encoding a novel enzyme, 2,2'-beta-hydroxylase, from Brevundimonas sp. strain SD212 and combinatorial biosynthesis of new or rare xanthophylls

Identification of a novel monocyclic carotenoid and prediction of its biosynthetic genes in Algoriphagus sp. oki45

Bacteria belonging to the genus Algoriphagus have been isolated from various sources, such as Antarctic sea ice, seawater, and sediment, and some strains are known to produce orange to red pigments. However, the pigment composition and biosynthetic genes have not been fully elucidated. A new red-pigmented Algoriphagus sp. strain, oki45, was isolated from the surface of seaweed collected from Senaga-Jima Island, Okinawa, Japan. Genome comparison revealed oki45's average nucleotide identity of less than 95% to its closely related species, Algoriphagus confluentis NBRC 111222 T and Algoriphagus taiwanensis JCM 19755 T. Comprehensive chemical analyses of oki45's pigments, including 1H and 13C nuclear magnetic resonance and circular dichroism spectroscopy, revealed that the pigments were mixtures of monocyclic carotenoids, (3S)-flexixanthin ((3S)-3,1'-dihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one) and (2R,3S)-2-hydroxyflexixanthin ((2R,3S)-2,3,1'-trihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one); in particular, the latter compound was new and not previously reported. Both monocyclic carotenoids were also found in A. confluentis NBRC 111222 T and A. taiwanensis JCM 19755 T. Further genome comparisons of carotenoid biosynthetic genes revealed the presence of eight genes (crtE, crtB, crtI, cruF, crtD, crtYcd, crtW, and crtZ) for flexixanthin biosynthesis. In addition, a crtG homolog gene encoding 2,2'-β-hydroxylase was found in the genome of the strains oki45, A. confluentis NBRC 111222 T, and A. taiwanensis JCM 19755 T, suggesting that the gene is involved in 2-hydroxyflexixanthin synthesis via 2-hydroxylation of flexixanthin. These findings expand our knowledge of monocyclic carotenoid biosynthesis in Algoriphagus bacteria. KEY POINTS: • Algoriphagus sp. strain oki45 was isolated from seaweed collected in Okinawa, Japan. • A novel monocyclic carotenoid 2-hydroxyflexixanthin was identified from strain oki45. • Nine genes for 2-hydroxyflexixanthin biosynthesis were found in strain oki45 genome.

Astaxanthin: Past, Present, and Future

Astaxanthin (AX), a lipid-soluble pigment belonging to the xanthophyll carotenoids family, has recently garnered significant attention due to its unique physical properties, biochemical attributes, and physiological effects. Originally recognized primarily for its role in imparting the characteristic red-pink color to various organisms, AX is currently experiencing a surge in interest and research. The growing body of literature in this field predominantly focuses on AXs distinctive bioactivities and properties. However, the potential of algae-derived AX as a solution to various global environmental and societal challenges that threaten life on our planet has not received extensive attention. Furthermore, the historical context and the role of AX in nature, as well as its significance in diverse cultures and traditional health practices, have not been comprehensively explored in previous works. This review article embarks on a comprehensive journey through the history leading up to the present, offering insights into the discovery of AX, its chemical and physical attributes, distribution in organisms, and biosynthesis. Additionally, it delves into the intricate realm of health benefits, biofunctional characteristics, and the current market status of AX. By encompassing these multifaceted aspects, this review aims to provide readers with a more profound understanding and a robust foundation for future scientific endeavors directed at addressing societal needs for sustainable nutritional and medicinal solutions. An updated summary of AXs health benefits, its present market status, and potential future applications are also included for a well-rounded perspective.

Proposal to classify Ralstonia solanacearum phylotype I strains as Ralstonia nicotianae sp. nov., and a genomic comparison between members of the genus Ralstonia

A Gram-negative, aerobic, rod-shaped, motile bacterium with multi-flagella, strain RS^T, was isolated from bacterial wilt of tobacco in Yuxi city of Yunnan province, China. The strain contains the major fatty acids of C_16:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The polar lipid profile of strain RS^T consists of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipid. Strain RS^T contains ubiquinones Q-7 and Q-8. 16S rRNA gene sequence (1,407 bp) analysis showed that strain RS^T is closely related to members of the genus Ralstonia and shares the highest sequence identities with R. pseudosolanacearum LMG 9673^T (99.50%), R. syzygii subsp. indonesiensis LMG 27703^T (99.50%), R. solanacearum LMG 2299^T (99.28%), and R. syzygii subsp. celebesensis LMG 27706^T (99.21%). The 16S rRNA gene sequence identities between strain RS^T and other members of the genus Ralstonia were below 98.00%. Genome sequencing yielded a genome size of 5.61 Mbp and a G + C content of 67.1 mol%. The genomic comparison showed average nucleotide identity (ANIb) values between strain RS^T and R. pseudosolanacearum LMG 9673^T, R. solanacearum LMG 2299^T, and R. syzygii subsp. indonesiensis UQRS 627^T of 95.23, 89.43, and 91.41%, respectively, and the corresponding digital DNA-DNA hybridization (dDDH) values (yielded by formula 2) were 66.20, 44.80, and 47.50%, respectively. In addition, strains belonging to R. solanacearum phylotype I shared both ANIb and dDDH with strain RS^T above the species cut-off values of 96 and 70%, respectively. The ANIb and dDDH values between the genome sequences from 12 strains of R. solanacearum phylotype III (Current R. pseudosolanacearum) and those of strain RS^T were below the species cut-off values. Based on these data, we concluded that strains of phylotype I, including RS^T, represent a novel species of the genus Ralstonia, for which the name Ralstonia nicotianae sp. nov. is proposed. The type strain of Ralstonia nicotianae sp. nov. is RS^T (=GDMCC 1.3533^T = JCM 35814^T).

Temperature-induced zeaxanthin overproduction in Synechococcus elongatus PCC 7942

The exogenous crtZ gene from Brevundimonas sp. SD212, coding for a 3,3' β-car hydroxylase, was expressed in Synechococcus elongatus PCC 7942 under the control of a temperature-inducible promoter in an attempt to engineer the carotenoid metabolic pathway, to increase the content of zeaxanthin and its further hydroxylated derivatives caloxanthin and nostoxanthin. These molecules are of particular interest due to their renowned antioxidant properties. Cultivation of the engineered strain S7942Z-Ti at 35 °C, a temperature which is well tolerated by the wild-type strain and at which the inducible expression system is activated, led to a significant redistribution of the relative carotenoid content. β-Carotene decreased to about 10% of the pool that is an excess of a threefold decrease with respect to the control, and concomitantly, zeaxanthin became the dominant carotenoid accounting for about half of the pool. As a consequence, zeaxanthin and its derivatives caloxanthin and nostoxanthin collectively accounted for about 90% of the accumulated carotenoids. Yet, upon induction of CrtZ expression at 35 °C the S7942Z-Ti strain displayed a substantial growth impairment accompanied, initially, by a relative loss of carotenoids and successively by the appearance of chlorophyll degradation products which can be interpreted as markers of cellular stress. These observations suggest a limit to the exploitation of Synechococcus elongatus PCC 7942 for biotechnological purposes aimed at increasing the production of hydroxylated carotenoids.

Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids

Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.

Production of High Levels of 3S,3'S-Astaxanthin in Yarrowia lipolytica via Iterative Metabolic Engineering

Astaxanthin is a highly value-added keto-carotenoid compound. The astaxanthin 3S,3'S-isomer is more desirable for food additives, cosmetics, and pharmaceuticals due to health concerns about chemically synthesized counterparts with a mixture of three isomers. Biosynthesis of 3S,3'S-astaxanthin suffers from limited content and productivity. We engineered Yarrowia lipolytica to produce high levels of 3S,3'S-astaxanthin. We first assessed various β-carotene ketolases (CrtW) and β-carotene hydroxylases (CrtZ) from two algae and a plant. HpCrtW and HpCrtZ from Haematococcus pluvialis exhibited the strongest activity in converting β-carotene into astaxanthin in Y. lipolytica. We then fine-tuned the HpCrtW and HpCrtZ transcriptional expression by increasing the rounds of gene integration into the genome and applied a modular enzyme assembly of HpCrtW and HpCrtZ simultaneously. Next, we rescued leucine biosynthesis in the engineered Y. lipolytica, leading to a five-fold increase in biomass. The astaxanthin production achieved from these strategies was 3.3 g/L or 41.3 mg/g dry cell weight under fed-batch conditions, which is the highest level reported in microbial chassis to date. This study provides the potential for industrial production of 3S,3'S-astaxanthin, and this strategy empowers us to build a sustainable biorefinery platform for generating other value-added carotenoids in the future.

Heterologous production of novel and rare C30-carotenoids using Planococcus carotenoid biosynthesis genes

Background

Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C₃₀) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4′-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C₃₀-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes.

Results

A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1–7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4′-diapophytoene synthase (CrtM) and 4,4′-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C₃₀-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4′-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4′-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4′-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C₃₀-carotenoids including the two novel and one rare compounds.

Conclusions

The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C₃₀-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01683-3.

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.

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3^T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11^T (97.0 %), Sphingomonas edaphi DAC4^T (96.8 %), Sphingomonas xanthus AE3^T (96.5 %) and Sphingomonas oryziterrae YC6722^T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3^T grew at 7-50 °C (optimum, 30-35 °C), pH 5.0-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) and C_18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3^T and its reference strains with publicly available genomes were 17.9-18.9 %, 72.0-75.3 % and 63.3-76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas. The type strain is sand1-3^T (=KCTC 82358^T=NBRC 114538^T).

Carotenoid Nostoxanthin Production by Sphingomonas sp. SG73 Isolated from Deep Sea Sediment

Carotenoids are used commercially for dietary supplements, cosmetics, and pharmaceuticals because of their antioxidant activity. In this study, colored microorganisms were isolated from deep sea sediment that had been collected from Suruga Bay, Shizuoka, Japan. One strain was found to be a pure yellow carotenoid producer, and the strain was identified as Sphingomonas sp. (Proteobacteria) by 16S rRNA gene sequence analysis; members of this genus are commonly isolated from air, the human body, and marine environments. The carotenoid was identified as nostoxanthin ((2,3,2',3')-β,β-carotene-2,3,2',3'-tetrol) by mass spectrometry (MS), MS/MS, and ultraviolet-visible absorption spectroscopy (UV-Vis). Nostoxanthin is a poly-hydroxy yellow carotenoid isolated from some photosynthetic bacteria, including some species of Cyanobacteria. The strain Sphingomonas sp. SG73 produced highly pure nostoxanthin of approximately 97% (area%) of the total carotenoid production, and the strain was halophilic and tolerant to 1.5-fold higher salt concentration as compared with seawater. When grown in 1.8% artificial sea salt, nostoxanthin production increased by 2.5-fold as compared with production without artificial sea salt. These results indicate that Sphingomonas sp. SG73 is an efficient producer of nostoxanthin, and the strain is ideal for carotenoid production using marine water because of its compatibility with sea salt.

Carotenoid Production in Oleaginous Yeasts

Oleaginous yeasts, Yarrowia lipolytica and Lipomyces starkeyi, can synthesize more than 20% of lipids per dry cell weight from a wide variety of substrates. This feature is attractive for cost-efficient production of industrial biodiesel fuel. These yeasts are also very promising hosts for the efficient production of more value-added lipophilic compound carotenoids, e.g., lycopene and astaxanthin, although they cannot naturally biosynthesize carotenoids. Here, we review recent progress in researches on carotenoid production by oleaginous yeasts, which include red yeasts that naturally produce carotenoids, e.g., Rhodotorula glutinis and Xanthophyllomyces dendrorhous. Our new results on pathway engineering of L. starkeyi for lycopene production are also revealed in the present review.

When Carotenoid Biosynthesis Genes Met Escherichia coli : The Early Days and These Days

Nowadays, carotenoid biosynthetic pathways are sufficiently elucidated at gene levels in bacteria, fungi, and higher plants. Also, in pathway engineering for isoprenoid (terpene) production, carotenoids have been one of the most studied targets. However, in 1988 when the author started carotenoid research, almost no carotenoid biosynthesis genes were identified. It was because carotenogenic enzymes are easily inactivated when extracted from their organism sources, indicating that their purification and the subsequent cloning of the corresponding genes were infeasible or difficult. On the other hand, natural product chemistry of carotenoids had advanced a great deal. Thus, those days, carotenoid biosynthetic pathways had been proposed based mainly on the chemical structures of carotenoids without findings on relevant enzymes and genes. This chapter shows what happened on carotenoid research, when carotenoid biosynthesis genes met non-carotenogenic Escherichia coli around 1990, followed by subsequent developments.

Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments

Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.

Carotenoids produced by the deep-sea bacterium Erythrobacter citreus LAMA 915: detection and proposal of their biosynthetic pathway

Technologies based on synthetic biology to produce bacterial natural carotenoids depend on information regarding their biosynthesis. Although the biosynthetic pathway of common carotenoids is known, there are carotenoids whose pathways are not completely described. This work aimed to mine the genome of the deep-sea bacterium Erythrobacter citreus LAMA 915, an uncommon bacterium that forms yellow colonies under cultivation. This work further explores the potential application of the carotenoids found and low-cost substrates for bacterial growth. A combined approach of genome mining and untargeted metabolomics analysis was applied. The carotenoid erythroxanthin sulfate was detected in E. citreus LAMA 915 cell extract. A proposal for carotenoid biosynthesis by this bacterium is provided, involving the genes crtBIYZWG. These are responsible for the biosynthesis of carotenoids from the zeaxanthin pathway and their 2,2'-hydroxylated derivatives. E. citreus LAMA 915 extracts showed antioxidant and sun protection effects. Based on the high content of proteases and lipases, it was possible to rationally select substrates for bacterial growth, with residual oil from fish processing the best low-cost substrate selected. This work advances in the understanding of carotenoid biosynthesis and provides a genetic basis that can be further explored as a biotechnological route for carotenoid production.

Integrative analyses of transcriptomics and metabolomics in Raphidocelis subcapitata treated with clarithromycin

As a macrolide antibiotic, clarithromycin (CLA) has a high detection rate in surface water and sewage treatment plant effluents worldwide, posing a considerably high ecological risk to aquatic ecosystem. However, algal transcriptome and metabolome in response to CLA remains largely unknown. In this study, a model alga Raphidocelis subcapitata (R. subcapitata), was exposed to CLA at the concentrations of 0, 3, 10, and 15 μg L^-1. Transcriptomic analysis was performed for all the treatment groups, whereas metabolomics was merely applied to 0, 3, and 10 μg L^-1 groups because of the limited amount of algal biomass. After 7 d cultivation, the growth of R. subcapitata was significantly hindered at the concentrations above 10 μg L^-1. A total of 115, 1833, 2911 genes were differentially expressed in 3, 10, and 15 μg L^-1 groups, respectively; meanwhile, 134 and 84 differentially accumulated metabolites (DAMs) were found in the 3 and 10 μg L^-1 groups. Specifically, expression levels of DEGs and DAMs related to xenobiotic metabolism, electron transport and energy synthesis were dysregulated, leading to the produced reactive oxygen species (ROS). To confront the CLA-induced injury, the biosynthesis of unsaturated fatty acids and carotenoids of R. subcapitata in 3 μg L^-1 were up-regulated; although the photosynthesis was up-regulated in both 10 μg L^-1 and 15 μg L^-1 groups, the energy synthesis and the ability to resist ROS in these two groups were down-regulated. Overall, this study shed light on the mechanism underlying the inhibitory effects of macrolide antibiotics in algae.

Diversity and Evolution of Carotenoid Biosynthesis from Prokaryotes to Plants

Carotenoids exist in pro- and eukaryotic organisms, but not in animals (with one exception). Their biosynthesis evolved from a common ancestor of Archaea and Bacteria and via the latter by endosymbiosis to algae and plants. The formation of carotenoids in fungi can be regarded as a lineage from the archaea. This review highlights the distribution and evolution of carotenogenic pathways in taxonomic groups of prokaryotes and eukaryotes with a special emphasis on the evolutionary aspects of prominent carotenogenic genes in relation to the assigned function of their corresponding enzymes. The latter aspect includes a focus on paralogs of gene families evolving novel functions and unrelated genes encoding enzymes with the same function.

Reprogramming microorganisms for the biosynthesis of astaxanthin via metabolic engineering

There is an increasing demand for astaxanthin in food, feed, cosmetics and pharmaceutical applications because of its superior anti-oxidative and coloring properties. However, naturally produced astaxanthin is expensive, mainly due to low productivity and limited sources. Reprogramming of microorganisms for astaxanthin production via metabolic engineering is a promising strategy. We primarily focus on the application of synthetic biology, enzyme engineering and metabolic engineering in enhancing the synthesis and accumulation of astaxanthin in microorganisms in this review. We also discuss the biosynthetic pathways of astaxanthin within natural producers, and summarize the achievements and challenges in reprogramming microorganisms for enhancing astaxanthin production. This review illuminates recent biotechnological advances in microbial production of astaxanthin. Future perspectives on utilization of new technologies for boosting microbial astaxanthin production are also discussed.

A novel carotenoids-producing marine bacterium from noble scallop Chlamys nobilis and antioxidant activities of its carotenoid compositions

Marine bacteria produce many bioactive compounds, including carotenoids. However, the quality of bacterium carotenoids is relatively unknown. Therefore, in this study, a novel carotenoids-producing bacterium Brevundimonas scallop Zheng & Liu was isolated from Chlamys nobilis. The genome of the isolate was analyzed, carotenoid compounds were screened using HPLC-MS and the carotenoid production in B. scallop was monitored. The results revealed that the genome of B. scallop contained a carotenoid synthesis gene cluster, which involved in astaxanthin and hydroxy-astaxanthin biosynthesis. The 2,2'-dihydroxy-astaxanthin was the major carotenoid produced by B. scallop. The optimum culture condition for the highest carotenoids production (1303.62 ± 61.06 µg/g dry cells) for B. scallop was at temperature and salinity of 20 °C and 3% salt, respectively, in 10 g/L glucose as carbon source. The results showed the B. scallop is a new carotenoids resource in marine bivalve, which has an excellent antioxidative activity and potential industrial use.

Comparison of Gut Microbiota Between Golden and Brown Noble Scallop Chlamys nobilis and Its Association With Carotenoids

Many marine bivalves are regarded as healthy foods due to their high carotenoid content. Only plants and microorganisms have natural carotenoids biosynthesis ability, hence, animals such as bivalves must obtain carotenoids from their diets. Due to the filter-feeding behavior of bivalves, they have high diversity of gut microbes. However, the relationship between gut microbes and carotenoids has not been explored in mollusks. In the present study, the interaction between gut microbes and carotenoids in two polymorphic noble scallop Chlamys nobilis, golden scallops (designated GG) and brown scallops (designated BW), were studied. The gut of GG and BW showed statistically different bacteria communities. Results from 16S rRNA gene sequencing and qPCR analysis revealed that the gut of GG had significantly higher relative abundance of carotenoids-producing bacteria Brevundimonas, compared with BW. Moreover, HPLC-MS analysis showed that isolate Brevundimonas could produce astaxanthin. The current findings are very useful as they could form the basis for future studies in determining the relationship between gut microbiota and carotenoids absorption in bivalves.

Combinatorial expression of different β-carotene hydroxylases and ketolases in Escherichia coli for increased astaxanthin production

In natural produced bacteria, β-carotene hydroxylase (CrtZ) and β-carotene ketolase (CrtW) convert β-carotene into astaxanthin. To increase astaxanthin production in heterologous strain, simple and effective strategies based on the co-expression of CrtZ and CrtW were applied in E. coli. First, nine artificial operons containing crtZ and crtW genes from different sources were constructed and, respectively, introduced into E. coli ZF237T, a β-carotene producing host. Among the nine resulting strains, five accumulated detectable amounts of astaxanthin ranging from 0.49 to 8.07 mg/L. Subsequently, the protein fusion CrtZ to CrtW using optimized peptide linkers further increased the astaxanthin production. Strains expressing fusion proteins with CrtZ rather than CrtW attached to the N-terminus accumulated much more astaxanthin. The astaxanthin production of the best strain ZF237T/CrtZ_As-(GS)₁-W_Bs was 127.6% and 40.2% higher than that of strains ZF237T/crtZ_AsW_Bs and ZF237T/crtZ_BsW_Ps, respectively. The strategies depicted here also will be useful for the heterologous production of other natural products.

Sulfur-Containing Carotenoids from A Marine Coral Symbiont Erythrobacter flavus Strain KJ5

Erythrobacter flavus strain KJ5 (formerly called Erythrobacter sp. strain KJ5) is a yellowish marine bacterium that was isolated from a hard coral Acropora nasuta in the Karimunjawa Islands, Indonesia. The complete genome sequence of the bacterium has been reported recently. In this study, we examined the carotenoid composition of this bacterium using high-performance liquid chromatography coupled with ESI-MS/MS. We found that the bacterium produced sulfur-containing carotenoids, i.e., caloxanthin sulfate and nostoxanthin sulfate, as the most abundant carotenoids. A new carotenoid zeaxanthin sulfate was detected based on its ESI-MS/MS spectrum. The unique presence of sulfated carotenoids found among the currently known species of the Erythrobacter genus were discussed.

Nonnatural biosynthetic pathway for 2-hydroxylated xanthophylls with C50-carotenoid backbone

Carotenoids are structurally diverse pigments with various important biological functions. There has been a large interest in the search for novel carotenoid structures, since only a slight structural changes can result in a drastic difference in their biological functions. Carotenoid-modifying enzymes show remarkable substrate promiscuity, allowing rapid access to a vast set of novel carotenoids by combinatorial biosynthesis. We previously constructed a nonnatural carotenoid biosynthetic pathway in Escherichia coli that can produce C₅₀ carotenoids having a longer chain than their natural C₄₀ counterparts. In this study, a carotenoid 2,2'-hydroxylase (crtG) from Brevundimonas sp. SD212 was coexpressed together with our laboratory-engineered C₅₀-zeaxanthin and C₅₀-astaxanthin biosynthetic pathways. We identified six novel nonnatural C₅₀-xanthophylls, namely, C₅₀-nostoxanthin, C₅₀-caloxanthin, C₅₀-adonixanthin, C₅₀-4-ketonostoxanthin, C₅₀-2-hydroxyastaxanthin, and C₅₀-2,2'-dihydroxyastaxanthin.

In Vivo Platforms for Terpenoid Overproduction and the Generation of Chemical Diversity

Terpenoids represent a highly diverse group of natural products with wide applications. Engineering approaches have been used to increase titers of many value-added terpenoids, such as farnesene, taxadiene, lycopene, and astaxanthin. In this chapter, we review the in vitro reconstitution-based targeted engineering of terpenoids, as well as approaches for the mining of terpene cyclases and for increasing the chemical diversity. Information gained from in vitro reconstitution extends our understanding of the mechanisms underlying terpenoid biosynthesis, the contributions of enzymes and cofactors, and key enzymes and rate-limiting steps for the development of an ideal biosynthetic production system. The in vitro reconstitution-based targeted engineering strategy provides a rational and accurate engineering approach for terpenoid overproduction with high efficiency. Furthermore, an efficient terpenoid overproduction platform can accelerate the entire process for the mining of terpene cyclases and the discovery of novel terpenoids and can substantially increase the chemical diversity of these kinds of terpenoids.

Selected Methods of Extracting Carotenoids, Characterization, and Health Concerns: A Review

Carotenoids are the most powerful nutrients (medicine) on earth due to their potent antioxidant properties. The ability of these tetraterpenoids in obviating human chronic ailments like cancer, cardiovascular disease, osteoporosis, and diabetes has drawn public attention toward these novel compounds. Conventionally, carotenoids have been extracted from plant materials and agro-industrial byproduct using different solvents, but these procedures result in contaminating the target compound (carotenoids) with extraction solvents. Furthermore, some utilized solvents are not safe and hence are harmful to the environment. This has attracted criticism from consumers, ecologists, environmentalists, and public health workers. However, there is clear consumer preference for carotenoids from natural origin without traces of extracting solvent. Therefore, this review seeks to discuss methods for higher recovery of pure carotenoids without contamination from a solvent. Methods such as enzyme-based extraction, supercritical fluid extraction, microwave-assisted extraction, Soxhlet extraction, ultrasonic extraction, and postextraction treatment (saponification) are discussed. Merits and demerits of these methods along with health concerns during intake of carotenoids were also considered.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C₄₀ carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.

Optimizing the localization of astaxanthin enzymes for improved productivity

BACKGROUND

One important metabolic engineering strategy is to localize the enzymes close to their substrates for improved catalytic efficiency. However, localization configurations become more complex the greater the number of enzymes and substrates is involved. Indeed, optimizing synthetic pathways by localizing multiple enzymes remains a challenge. Terpenes are one of the most valuable and abundant natural product groups. Phytoene, lycopene and β-carotene serve as common intermediates for the synthesis of many carotenoids and derivative compounds, which are hydrophobic long-chain terpenoids, insoluble in water and usually accumulate in membrane compartments.

RESULTS

While β-ionone synthesis by β-carotene cleavage dioxygenase PhCCD1 and astaxanthin synthesis by β-carotene ketolase (CrtW) and β-carotene hydroxylase (CrtZ) differ in complexity (single and multiple step pathways), the productivity of both pathways benefited from controlling enzyme localization to the E. coli cell membrane via a GlpF protein fusion. Especially, the astaxanthin synthesis pathway comprises both CrtW and CrtZ, which perform four interchangeable reactions initiated from β-carotene. Up to four localization strategies of CrtW and CrtZ were exhaustively discussed in this work, and the optimal positioning strategy was achieved. CrtW and CrtZ were linked using a flexible linker and localized to the membrane via a GlpF protein fusion. Enzymes in the optimal localization configuration allowed a 215.4% astaxanthin production increase.

CONCLUSIONS

This work exploits a localization situation involving membrane-bound substrates, intermediates and multiple enzymes for the first time, and provides a workable positioning strategy to solve problems in similar circumstances.

Carotenoids biosynthesis and cleavage related genes from bacteria to plants

Carotenoids are essential for photosynthesis and photoprotection in photosynthetic organisms and beneficial for human health. Apocarotenoids derived from carotenoid degradation can serve critical functions including hormones, volatiles, and signals. They have been used commercially as food colorants, animal feed supplements, and nutraceuticals for cosmetic and pharmaceutical purposes. This review focuses on the molecular evolution of carotenogenic enzymes and carotenoid cleavage oxygenases (CCOs) from bacteria, fungi, cyanobacteria, algae, and plants. The diversity of carotenoids and apocarotenoids as well as their complicated biosynthetic pathway in different species can shed light on the history of early molecular evolution. Some carotenogenic genes (such as phytoene synthases) have high protein sequence similarity from bacteria to land plants, but some (such as phytoene desaturases, lycopene cyclases, carotenoid hydroxylases, and CCOs) have low similarity. The broad diversity of apocarotenoid volatile compounds can be attributed to large numbers of carotenoid precursors and the various cleavage sites catalyzed by CCOs enzymes. A variety of carotenogenic enzymes and CCOs indicate the functional diversification of carotenoids and apocrotenoids in different species. New carotenoids, new apocarotenoids, new carotenogenic enzymes, new CCOs, and new pathways still need to be explored.

Combinatorial Biosynthesis of Novel Multi-Hydroxy Carotenoids in the Red Yeast Xanthophyllomyces dendrorhous

The red yeast Xanthophyllomyces dendrorhous is an established platform for the synthesis of carotenoids. It was used for the generation of novel multi oxygenated carotenoid structures. This was achieved by a combinatorial approach starting with the selection of a β-carotene accumulating mutant, stepwise pathway engineering by integration of three microbial genes into the genome and finally the chemical reduction of the resulting 4,4'-diketo-nostoxanthin (2,3,2',3'-tetrahydroxy-4,4'-diketo-β-carotene) and 4-keto-nostoxanthin (2,3,2',3'-tetrahydroxy-4-monoketo-β-carotene). Both keto carotenoids and the resulting 4,4'-dihydroxy-nostoxanthin (2,3,4,2',3',4'-hexahydroxy-β-carotene) and 4-hydroxy-nostoxanthin (2,3,4,2'3'-pentahydroxy-β-carotene) were separated by high-performance liquid chromatography (HPLC) and analyzed by mass spectrometry. Their molecular masses and fragmentation patterns allowed the unequivocal identification of all four carotenoids.

ProCarDB: a database of bacterial carotenoids

Background

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids.

Results

Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli

As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the α-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future.

Optimising ketocarotenoid production in potato tubers: effect of genetic background, transgene combinations and environment

Astaxanthin is a high value carotenoid produced by some bacteria, a few green algae, several fungi but only a limited number of plants from the genus Adonis. Astaxanthin has been industrially exploited as a feed supplement in poultry farming and aquaculture. Consumption of ketocarotenoids, most notably astaxanthin, is also increasingly associated with a wide range of health benefits, as demonstrated in numerous clinical studies. Currently astaxanthin is produced commercially by chemical synthesis or from algal production systems. Several studies have used a metabolic engineering approach to produce astaxanthin in transgenic plants. Previous attempts to produce transgenic potato tubers biofortified with astaxanthin have met with limited success. In this study we have investigated approaches to optimising tuber astaxanthin content. It is demonstrated that the selection of appropriate parental genotype for transgenic approaches and stacking carotenoid biosynthetic pathway genes with the cauliflower Or gene result in enhanced astaxanthin content, to give six-fold higher tuber astaxanthin content than has been achieved previously. Additionally we demonstrate the effects of growth environment on tuber carotenoid content in both wild type and astaxanthin-producing transgenic lines and describe the associated transcriptome and metabolome restructuring.

Biosynthetic routes of hydroxylated carotenoids (xanthophylls) in Marchantia polymorpha, and production of novel and rare xanthophylls through pathway engineering in Escherichia coli

MpBHY codes for a carotene β-ring 3(,3')-hydroxylase responsible for both zeaxanthin and lutein biosynthesis in liverwort. MpCYP97C functions as an ε-ring hydroxylase (zeinoxanthin 3'-hydroxylase) to produce lutein in liverwort. Xanthophylls are oxygenated or hydroxylated carotenes that are most abundant in the light-harvesting complexes of plants. The plant-type xanthophylls consist of α-xanthophyll (lutein) and β-xanthophylls (zeaxanthin, antheraxanthin, violaxanthin and neoxanthin). The α-xanthophyll and β-xanthophylls are derived from α-carotene and β-carotene by carotene hydroxylase activities, respectively. β-Ring 3,3'-hydroxylase that mediates the route of zeaxanthin from β-carotene via β-cryptoxanthin is present in higher plants and is encoded by the BHY (BCH) gene. On the other hand, CYP97A (or BHY) and CYP97C genes are responsible for β-ring 3-hydroxylation and ε-ring 3'-hydroxylation, respectively, in routes from α-carotene to lutein. To elucidate the evolution of the biosynthetic routes of such hydroxylated carotenoids from carotenes in land plants, we identified and functionally analyzed carotenoid hydroxylase genes of liverwort Marchantia polymorpha L. Three genes homologous to higher plants, BHY, CYP97A, and CYP97C, were isolated and named MpBHY, MpCYP97A, and MpCYP97C, respectively. MpBHY was found to code for β-ring hydroxylase, which is responsible for both routes starting from β-carotene and α-carotene. MpCYP97C functioned as an ε-ring hydroxylase not for α-carotene but for zeinoxanthin, while MpCYP97A showed no hydroxylation activity for β-carotene or α-carotene. These findings suggest the original functions of the hydroxylation enzymes of carotenes in land plants, which are thought to diversify in higher plants. In addition, we generated recombinant Escherichia coli cells, which produced rare and novel carotenoids such as α-echinenone and 4-ketozeinoxanthin, through pathway engineering using bacterial carotenogenic genes that include crtW, in addition to the liverwort MpLCYb, MpLCYe and MpBHY genes.

Construction of transplastomic lettuce (Lactuca sativa) dominantly producing astaxanthin fatty acid esters and detailed chemical analysis of generated carotenoids

The plastid genome of lettuce (Lactuca sativa L.) cv. Berkeley was site-specifically modified with the addition of three transgenes, which encoded β,β-carotenoid 3,3'-hydroxylase (CrtZ) and β,β-carotenoid 4,4'-ketolase (4,4'-oxygenase; CrtW) from a marine bacterium Brevundimonas sp. strain SD212, and isopentenyl diphosphate isomerase from a marine bacterium Paracoccus sp. strain N81106. Constructed transplastomic lettuce plants were able to grow on soil at a growth rate similar to that of non-transformed lettuce cv. Berkeley and generate flowers and seeds. The germination ratio of the lettuce transformants (T0) (98.8%) was higher than that of non-transformed lettuce (93.1 %). The transplastomic lettuce (T1) leaves produced the astaxanthin fatty acid (myristate or palmitate) diester (49.2% of total carotenoids), astaxanthin monoester (18.2%), and the free forms of astaxanthin (10.0%) and the other ketocarotenoids (17.5%), which indicated that artificial ketocarotenoids corresponded to 94.9% of total carotenoids (230 μg/g fresh weight). Native carotenoids were there lactucaxanthin (3.8%) and lutein (1.3 %) only. This is the first report to structurally identify the astaxanthin esters biosynthesized in transgenic or transplastomic plants producing astaxanthin. The singlet oxygen-quenching activity of the total carotenoids extracted from the transplastomic leaves was similar to that of astaxanthin (mostly esterified) from the green algae Haematococcus pluvialis.

New and rare carotenoids isolated from marine bacteria and their antioxidant activities

Marine bacteria have not been examined as extensively as land bacteria. We screened carotenoids from orange or red pigments-producing marine bacteria belonging to rare or novel species. The new acyclic carotenoids with a C₃₀ aglycone, diapolycopenedioc acid xylosylesters A-C and methyl 5-glucosyl-5,6-dihydro-apo-4,4'-lycopenoate, were isolated from the novel Gram-negative bacterium Rubritalea squalenifaciens, which belongs to phylum Verrucomicrobia, as well as the low-GC Gram-positive bacterium Planococcus maritimus strain iso-3 belonging to the class Bacilli, phylum Firmicutes, respectively. The rare monocyclic C₄₀ carotenoids, (3R)-saproxanthin and (3R,2'S)-myxol, were isolated from novel species of Gram-negative bacteria belonging to the family Flavobacteriaceae, phylum Bacteroidetes. In this review, we report the structures and antioxidant activities of these carotenoids, and consider relationships between bacterial phyla and carotenoid structures.

A novel carotenoid, 4-keto-α-carotene, as an unexpected by-product during genetic engineering of carotenogenesis in rice callus

Rice endosperm is devoid of carotenoids because the initial biosynthetic steps are absent. The early carotenogenesis reactions were constituted through co-transformation of endosperm-derived rice callus with phytoene synthase and phytoene desaturase transgenes. Subsequent steps in the pathway such as cyclization and hydroxylation reactions were catalyzed by endogenous rice enzymes in the endosperm. The carotenoid pathway was extended further by including a bacterial ketolase gene able to form astaxanthin, a high value carotenoid which is not a typical plant carotenoid. In addition to astaxanthin and precursors, a carotenoid accumulated in the transgenic callus which did not fit into the pathway to astaxanthin. This was subsequently identified as 4-keto-α-carotene by HPLC co-chromatography, chemical modification, mass spectrometry and the reconstruction of its biosynthesis pathway in Escherichia coli. We postulate that this keto carotenoid is formed from α-carotene which accumulates by combined reactions of the heterologous gene products and endogenous rice endosperm cyclization reactions.

Cloning and characterization of genes involved in nostoxanthin biosynthesis of Sphingomonas elodea ATCC 31461

Most Sphingomonas species synthesize the yellow carotenoid nostoxanthin. However, the carotenoid biosynthetic pathway of these species remains unclear. In this study, we cloned and characterized a carotenoid biosynthesis gene cluster containing four carotenogenic genes (crtG, crtY, crtI and crtB) and a β-carotene hydroxylase gene (crtZ) located outside the cluster, from the gellan-gum producing bacterium Sphingomonas elodea ATCC 31461. Each of these genes was inactivated, and the biochemical function of each gene was confirmed based on chromatographic and spectroscopic analysis of the intermediates accumulated in the knockout mutants. Moreover, the crtG gene encoding the 2,2′-β-hydroxylase and the crtZ gene encoding the β-carotene hydroxylase, both responsible for hydroxylation of β-carotene, were confirmed by complementation studies using Escherichia coli producing different carotenoids. Expression of crtG in zeaxanthin and β-carotene accumulating E. coli cells resulted in the formation of nostoxanthin and 2,2′-dihydroxy-β-carotene, respectively. Based on these results, a biochemical pathway for synthesis of nostoxanthin in S. elodea ATCC 31461 is proposed.

Novel approach in the biosynthesis of functional carotenoids in Escherichia coli

Many carotenoid pigments are present in a small quantity in nature or low yielding from their natural sources, despite these vivid colorations. Thus, the synthesis of useful carotenoids with metabolic pathway-engineered microorganisms should offer an alternative and promising approach for their efficient production. Here, we describe a novel method for an efficient production of such carotenoids, using E. coli cells that carry heterologous mevalonate pathway-based genes. This method also enables relevant researchers to efficiently identify the function of an isolated carotenogenic gene candidate. For example, the recombinant E. coli cells, which harbor a lycopene-producing plasmid, can synthesize 12.5 mg/g dry cell weight of lycopene with the addition of lithium acetoacetate to the medium. This level corresponded to an 11.8-fold increase of that of E. coli cells carrying only the lycopene-producing plasmid.

Production of caloxanthin 3'-β-D-glucoside, zeaxanthin 3,3'-β-D-diglucoside, and nostoxanthin in a recombinant Escherichia coli expressing system harboring seven carotenoid biosynthesis genes, including crtX and crtG

The aim of this study was to produce rare β-carotene-modified carotenoids possessing 2-O (-H or -glu) and/or 3-O (-H or -glu) functionalities in their β-ionone ring(s) using a recombinant Escherichia coli approach. This involved expressing seven carotenoid biosynthesis genes (crtE, crtB, crtI, crtY, crtZ, crtX and crtG). From the cells of the recombinant E. coli, caloxanthin (β,β-carotene-2,3,2',3'-tetrol)-3'-β-D-glucose, zeaxanthin (β,β-carotene-3,3'-diol) 3,3'-β-D-diglucoside, and nostoxanthin (β,β-carotene-2,3,3'-triol) (rare carotenoids) were isolated and identified. Caloxanthin 3'-β-D-glucose displayed potent (1)O(2) quenching activity (IC(50) 19 μM).

Carotenoid β-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls

Marine bacteria belonging to genera Paracoccus and Brevundimonas of the α-Proteobacteria class can produce C₄₀-type dicyclic carotenoids containing two β-end groups (β rings) that are modified with keto and hydroxyl groups. These bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid β-ring 4(4′)-ketolase (4(4′)-oxygenase; CrtW) and hydroxylated by carotenoid β-ring 3(3′)-hydroxylase (CrtZ). In addition, the genus Brevundimonas possesses a gene for carotenoid β-ring 2(2′)-hydroxylase (CrtG). This review focuses on these carotenoid β-ring-modifying enzymes that are promiscuous for carotenoid substrates, and pathway engineering for the production of xanthophylls (oxygen-containing carotenoids) in Escherichia coli, using these enzyme genes. Such pathway engineering researches are performed towards efficient production not only of commercially important xanthophylls such as astaxanthin, but also of xanthophylls minor in nature (e.g., β-ring(s)-2(2′)-hydroxylated carotenoids).

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.

Novel approaches and achievements in biosynthesis of functional isoprenoids in Escherichia coli

Isoprenoids, also referred to as terpenes, are the most diverse class of natural products appearing in a variety of natural sources, specifically in higher plants, and have a wide range of biological functions. This review describes novel or recent approaches and achievements in pathway engineering of Escherichia coli towards efficient biosynthesis of functional isoprenoids, specifically carotenoids and sesquiterpene, following description of "regularity and simplicity" in the biosynthesis of isoprenoid basic structures. The introduction of heterologous mevalonate pathway-based genes into E. coli has been shown to improve the productivity of carotenoids or sesquiterpenes that are synthesized from farnesyl diphosphate. This achievement also enables relevant researchers to efficiently analyze an isolated gene candidate for a terpene synthase (terpene cyclase).