Isolation and characterization of canthaxanthin biosynthesis genes from the photosynthetic bacterium Bradyrhizobium sp. strain ORS278

Bacteria as a source of biopigments and their potential applications

From the prehistoric period, the utilization of pigments as colouring agents was an integral part of human life. Early people may have utilized paint for aesthetic motives, according to archaeologists. The pigments are either naturally derived or synthesized in the laboratory. Different studies reported that certain synthetic colouring compounds were toxic and had adverse health and environmental effects. Therefore, knowing the drawbacks of these synthetic colouring agents now scientists are attracted towards the harmless natural pigments. The main sources of natural pigments are plants, animals or microorganisms. Out of these natural pigments, microorganisms are the most important source for the production and application of bioactive secondary metabolites. Among all kinds of microorganisms, bacteria have specific benefits due to their short life cycle, low sensitivity to seasonal and climatic variations, ease of scaling, and ability to create pigments of various colours. Based on these physical characteristics, bacterial pigments appear to be a promising sector for novel biotechnological applications, ranging from functional food production to the development of new pharmaceuticals and biomedical therapies. This review summarizes the need for bacterial pigments, biosynthetic pathways of carotenoids and different applications of bacterial pigments.

Recent Advances in the Carotenoids Added to Food Packaging Films: A Review

Food spoilage is one of the key concerns in the food industry. One approach is the improvement of the shelf life of the food by introducing active packaging, and another is intelligent packaging. Detecting packed food spoilage in real-time is key to stopping outbreaks caused by food-borne diseases. Using active materials in packaging can improve shelf life, while the nonharmful color indicator can be useful to trace the quality of the food through simple color detection. Recently, bio-derived active and intelligent packaging has gained a lot of interest from researchers and consumers. For this, the biopolymers and the bioactive natural ingredient are used as indicators to fabricate active packaging material and color-changing sensors that can improve the shelf life and detect the freshness of food in real-time, respectively. Among natural bioactive components, carotenoids are known for their good antimicrobial, antioxidant, and pH-responsive color-indicating properties. Carotenoids are rich in fruits and vegetables and fat-soluble pigments. Including carotenoids in the packaging system improves the film's physical and functional performance. The recent progress on carotenoid pigment-based packaging (active and intelligent) is discussed in this review. The sources and biological activity of the carotenoids are briefly discussed, and then the fabrication and application of carotenoid-activated packaging film are reviewed. The carotenoids-based packaging film can enhance packaged food's shelf life and indicate the freshness of meat and vegetables in real-time. Therefore, incorporating carotenoid-based pigment into the polymer matrix could be promising for developing novel packaging materials.

Bacterial Pigments and Their Multifaceted Roles in Contemporary Biotechnology and Pharmacological Applications

Synthetic dyes and colourants have been the mainstay of the pigment industry for decades. Researchers are eager to find a more environment friendly and non-toxic substitute because these synthetic dyes have a negative impact on the environment and people’s health. Microbial pigments might be an alternative to synthetic pigments. Microbial pigments are categorized as secondary metabolites and are mainly produced due to impaired metabolism under stressful conditions. These pigments have vibrant shades and possess nutritional and therapeutic properties compared to synthetic pigment. Microbial pigments are now widely used within the pharmaceuticals, food, paints, and textile industries. The pharmaceutical industries currently use bacterial pigments as a medicine alternative for cancer and many other bacterial infections. Their growing popularity is a result of their low cost, biodegradable, non-carcinogenic, and environmentally beneficial attributes. This audit article has made an effort to take an in-depth look into the existing uses of bacterial pigments in the food and pharmaceutical industries and project their potential future applications.

β-Carotene-production methods, biosynthesis from Phaffia rhodozyma, factors affecting its production during fermentation, pharmacological properties: A review

β-Carotene is the most treasured provitamin A carotenoid molecule exhibiting antioxidant and coloring properties and significant applications in the food, pharmaceutical, and nutraceutical industries. β-Carotene has many biological functions within the human body; however, it is not synthesized within the human body, so its requirements are fulfilled through food and pharmaceuticals. Its manufacturing via chemical synthesis or extraction from plants offers low yields with excessive manufacturing expenses, which attracted the researchers toward microbial production of β-carotene. This alternative provides higher yield and low expenses and thus is more economical. Phaffia rhodozyma is a basidiomycetous yeast that is utilized to prevent cardiovascular diseases and cancer and to enhance immunity and antiaging in people. This paper reviews the methods of production of β-carotene, biosynthesis of β-carotene fromP. rhodozyma, factors affecting β-carotene production during fermentation, and pharmacological properties of β-carotene.

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.

An Overview on Industrial and Medical Applications of Bio-Pigments Synthesized by Marine Bacteria

Marine bacterial species contribute to a significant part of the oceanic population, which substantially produces biologically effectual moieties having various medical and industrial applications. The use of marine-derived bacterial pigments displays a snowballing effect in recent times, being natural, environmentally safe, and health beneficial compounds. Although isolating marine bacteria is a strenuous task, these are still a compelling subject for researchers, due to their promising avenues for numerous applications. Marine-derived bacterial pigments serve as valuable products in the food, pharmaceutical, textile, and cosmetic industries due to their beneficial attributes, including anticancer, antimicrobial, antioxidant, and cytotoxic activities. Biodegradability and higher environmental compatibility further strengthen the use of marine bio-pigments over artificially acquired colored molecules. Besides that, hazardous effects associated with the consumption of synthetic colors further substantiated the use of marine dyes as color additives in industries as well. This review sheds light on marine bacterial sources of pigmented compounds along with their industrial applicability and therapeutic insights based on the data available in the literature. It also encompasses the need for introducing bacterial bio-pigments in global pigment industry, highlighting their future potential, aiming to contribute to the worldwide economy.

Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments

Phytoene desaturases catalyse from two to six desaturation reactions on phytoene, generating a large diversity of molecules that can then be cyclised and produce, depending on the organism, many different carotenoids. We constructed a phylogenetic tree of a subset of phytoene desaturases from the CrtI family for which functional data was available. We expressed in a bacterial system eight codon optimized CrtI enzymes from different clades. Analysis of the phytoene desaturation reactions on crude extracts showed that three CrtI enzymes can catalyse up to six desaturations, forming tetradehydrolycopene. Kinetic data generated using a subset of five purified enzymes demonstrate the existence of characteristic patterns of desaturated molecules associated with various CrtI clades. The kinetic data was also analysed using a classical Michaelis–Menten kinetic model, showing that variations in the reaction rates and binding constants could explain the various carotene patterns observed. Competition between lycopene cyclase and the phytoene desaturases modified the distribution between carotene intermediates when expressed in yeast in the context of the full β-carotene production pathway. Our results demonstrate that the desaturation patterns of carotene molecules in various biological environments cannot be fully inferred from phytoene desaturases classification but is governed both by evolutionary-linked variations in the desaturation rates and competition between desaturation and cyclisation steps.

Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect?

In Tasmania (Australia), during the marine phase, it has been observed that flesh pigmentation significantly drops in summer, possibly due to high water temperatures (> 20 °C). Although this deleterious effect of summer temperatures has been ascertained, there is a lack of knowledge of the actual mechanisms behind the impaired uptake and/or loss of pigments in Atlantic salmon in a challenging environment. Since the microbial community in the fish intestine significantly changes in relation to the variations of water temperature, this study was conducted to assess how the gut microbiota profile also correlates with the flesh color during temperature fluctuation. We sampled 68 fish at three time points covering the end of summer to winter at a marine farm in Tasmania, Australia. Flesh color was examined in two ways: the average color throughout and the evenness of the color between different areas of the fillet. Using 16S rRNA sequencing of the v3-v4 region, we determined that water temperature corresponded to changes in the gut microbiome both with alpha diversity (Kruskal-Wallis tests P = 0.05) and beta diversity indices (PERMANOVA P = 0.001). Also, there was a significant correlation between the microbiota and the color of the fillet (PERMANOVA P = 0.016). There was a high abundance of Pseudoalteromonadaceae, Enterobacteriaceae, Microbacteriaceae, and Vibrionaceae in the pale individuals. Conversely, carotenoid-synthesizing bacteria families (Bacillaceae, Mycoplasmataceae, Pseudomonas, Phyllobacteriaceae, and Comamonadaceae) were found in higher abundance in individuals with darker flesh color.

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.

Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization

Rare actinobacterial species are considered as potential resources of new natural products. Marisediminicola antarctica ZS314^T is the only type strain of the novel actinobacterial genus Marisediminicola isolated from intertidal sediments in East Antarctica. The strain ZS314^T was able to produce reddish orange pigments at low temperatures, showing characteristics of carotenoids. To understand the biosynthetic potential of this strain, the genome was completely sequenced for data mining. The complete genome had 3,352,609 base pairs (bp), much smaller than most genomes of actinomycetes. Five biosynthetic gene clusters (BGCs) were predicted in the genome, including a gene cluster responsible for the biosynthesis of C50 carotenoid, and four additional BGCs of unknown oligosaccharide, salinixanthin, alkylresorcinol derivatives, and NRPS (non-ribosomal peptide synthetase) or amino acid-derived compounds. Further experimental characterization indicated that the strain may produce C.p.450-like carotenoids, supporting the genomic data analysis. A new xanthorhodopsin gene was discovered along with the analysis of the salinixanthin biosynthetic gene cluster. Since little is known about this genus, this work improves our understanding of its biosynthetic potential and provides opportunities for further investigation of natural products and strategies for adaptation to the extreme Antarctic environment.

Structural and functional analysis of the carotenoid biosynthesis genes of a Pseudomonas strain isolated from the excrement of Autumn Darter

There are many reports about carotenoid-producing bacteria and carotenoid biosynthesis genes. In databases for Pseudomonas genome sequences, there are genes homologous to carotenoid biosynthesis genes, but the function of these genes in Pseudomonas has not been elucidated. In this study, we cloned the carotenoid biosynthesis genes from a Pseudomonas sp. strain, named Akiakane, which was isolated from the excrement of the Autumn Darter dragonfly. Using an Escherichia coli functional expression system, we confirmed that the idi, crtE, crtB, crtI, and crtY gene products of the Akiakane strain show predictable catalytic activities. A cluster of six genes was also found, which was comparable to other carotenoid-producing bacteria that belong to the α-Proteobacteria or γ-Proteobacteria class.

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.

Feeding strategies for the improved biosynthesis of canthaxanthin from enzymatic hydrolyzed molasses in the fed-batch fermentation of Dietzia natronolimnaea HS-1

The effect of two enzymatic hydrolyzed molasses (EHM)-feeding strategies including constant-(CFR) and exponential-(EFR) feeding rate on canthaxanthin (CTX) biosynthesis by Dietzia natronolimnaea HS-1 fed-batch fermentation was studied. The results showed that the CFR of 7 ml/h with an EHM content of 45 g/l led to the highest values of specific growth rate (0.127 h(-1)), biomass dry weight (17.66 g/l), total carotenoid (16.31 mg/l) and CTX (14.67 mg/l). A significant decrease in the kinetic growth and production parameters by the increasing EHM concentration from 30 to 60 g/l during EFR fed-batch bioprocess was observed (p<0.01). This study concluded that EHM alone can displace glucose-based medium towards improved CTX biosynthesis from D. natronolimnaea HS-1 using a CFR strategy during fed-batch culture.

Biotechnological production of carotenoids by yeasts: an overview

Nowadays, carotenoids are valuable molecules in different industries such as chemical, pharmaceutical, poultry, food and cosmetics. These pigments not only can act as vitamin A precursors, but also they have coloring and antioxidant properties, which have attracted the attention of the industries and researchers. The carotenoid production through chemical synthesis or extraction from plants is limited by low yields that results in high production costs. This leads to research of microbial production of carotenoids, as an alternative that has shown better yields than other aforementioned. In addition, the microbial production of carotenoids could be a better option about costs, looking for alternatives like the use of low-cost substrates as agro-industrials wastes. Yeasts have demonstrated to be carotenoid producer showing an important growing capacity in several agro-industrial wastes producing high levels of carotenoids. Agro-industrial wastes provide carbon and nitrogen source necessary, and others elements to carry out the microbial metabolism diminishing the production costs and avoiding pollution from these agro-industrial wastes to the environmental. Herein, we discuss the general and applied concepts regarding yeasts carotenoid production and the factors influencing carotenogenesis using agro-industrial wastes as low-cost substrates.

Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae

BACKGROUND

Microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. During this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to DNA, proteins, and membranes, thereby decreasing the degradation rate. Carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress.

FINDINGS

Several genes involved in the carotenoid biosynthetic pathway were cloned and characterized from a carbazole-degrading bacterium Sphingobium yanoikuyae XLDN2-5. In addition, a yellow-pigmented carotenoid synthesized by strain XLDN2-5 was identified as zeaxanthin that was synthesized from β-carotene through β-cryptoxanthin. The amounts of zeaxanthin and hydrogen peroxide produced were significantly and simultaneously enhanced during the biodegradation of heterocycles (carbazole < carbazole + benzothiophene < carbazole + dibenzothiophene). These higher production levels were consistent with the transcriptional increase of the gene encoding phytoene desaturase, one of the key enzymes for carotenoid biosynthesis.

CONCLUSIONS/SIGNIFICANCE

Sphingobium yanoikuyae XLDN2-5 can enhance the synthesis of zeaxanthin, one of the carotenoids, which may modulate membrane fluidity and defense against intracellular oxidative stress. To our knowledge, this is the first report on the positive role of carotenoids in the biodegradation of heterocycles, while elucidating the carotenoid biosynthetic pathway in the Sphingobium genus.

Efficient extraction of canthaxanthin from Escherichia coli by a 2-step process with organic solvents

Canthaxanthin has a substantial commercial market in aquaculture, poultry production, and cosmetic and nutraceutical industries. Commercial production is dominated by chemical synthesis; however, changing consumer demands fuel research into the development of biotechnology processes. Highly productive microbial systems to produce carotenoids can be limited by the efficiency of extraction methods. Extraction with hexane, acetone, methanol, 2-propanol, ethanol, 1-butanol, tetrahydrofuran and ethyl acetate was carried out with each solvent separately, and subsequently the most efficient solvents were tested in combination, both as mixtures and sequentially. Sequential application of methanol followed by acetone proved most efficient. Extraction efficiency remained stable over a solvent to biomass range of 100:1 to 55:1, but declined significantly at a ratio of 25:1. Application of this method to a canthaxanthin-producing Escherichia coli production system enabled efficient canthaxanthin extraction of up to 8.5 mg g(-1) dry biomass.

Analysis of canthaxanthin production by Gordonia jacobaea

Commercial interest in the use of natural pigments isolated from microorganisms has increased in recent years; hence, molecules belonging to the polyisoprenoid group (i.e., β-carotene, astaxanthin, and canthaxanthin) have been the focus of much attention. The bacterium Gordonia jacobaea readily synthesizes and accumulates large amounts of canthaxanthin (β-β'-carotene-4,4'-dione), which is widely used in the food and cosmetics industries. In the present work, the integral process of canthaxanthin production by G. jacobaea is analyzed together with its application as natural sources for the industry. A great influence of culture media is observed on canthaxanthin levels. Also, the ability is found of extract the pigments with ethanol from bacteria. The concentration of the samples is a crucial point of the process, being mandatory to discard any process of heating the samples, because this provoked the pigment degradation. Despite this, the described method allows to consider G. jacobaea as a potential canthaxanthin producer for the industry.

Isolation and light-stimulated expression of canthaxanthin and spirilloxanthin biosynthesis genes from the photosynthetic bacterium Bradyrhizobium sp. strain ORS278

Some aerobic photosynthetic bacteria produce a cocktail of carotenoids, some of them being of a high economic value. A good example is the photosynthetic Bradyrhizobium sp. strain ORS278, which synthesizes, in addition to the photosynthetic carotenoid spirilloxanthin, large amounts of canthaxanthin. Here, we describe the procedures that have been successfully used to isolate the different crt genes involved in the synthesis of both carotenoids in this bacteria. The synthesis of these carotenoids is stimulated under far-red light by a bacteriophytochrome. The procedure we developed to study the effect of the light on carotenoids synthesis is also described. Finally, we describe a procedure to genetically transform photosynthetic Bradyrhizobium strain ORS278 for improvement of canthaxanthin production.

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).

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.

Use of response surface methodology in a fed-batch process for optimization of tricarboxylic acid cycle intermediates to achieve high levels of canthaxanthin from Dietzia natronolimnaea HS-1

In this work, we applied statistical experimental design to a fed-batch process for optimization of tricarboxylic acid cycle (TCA) intermediates in order to achieve high-level production of canthaxanthin from Dietzia natronolimnaea HS-1 cultured in beet molasses. A fractional factorial design (screening test) was first conducted on five TCA cycle intermediates. Out of the five TCA cycle intermediates investigated via screening tests, alfaketoglutarate, oxaloacetate and succinate were selected based on their statistically significant (P<0.05) and positive effects on canthaxanthin production. These significant factors were optimized by means of response surface methodology (RSM) in order to achieve high-level production of canthaxanthin. The experimental results of the RSM were fitted with a second-order polynomial equation by means of a multiple regression technique to identify the relationship between canthaxanthin production and the three TCA cycle intermediates. By means of this statistical design under a fed-batch process, the optimum conditions required to achieve the highest level of canthaxanthin (13172 + or - 25 microg l(-1)) were determined as follows: alfaketoglutarate, 9.69 mM; oxaloacetate, 8.68 mM; succinate, 8.51 mM.

Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis

Horizontal gene transfer and selection are major forces driving microbial evolution. However, interactions between them are rarely studied. Phylogenetic analyses of purple bacterial carotenoid biosynthesis genes suggest two lineages: one producing spheroidenone and the other producing spirilloxanthin. Of the latter lineage, Rubrivivax gelatinosus S1 and Hoeflea phototrophica DFL-43 also or instead produce spheroidenone. Evolution of the spheroidenone pathway from that producing spirilloxanthin theoretically requires changes in the substrate specificity of upstream pathway enzymes and acquisition of a terminal ketolase (CrtA). In R. gelatinosus and likely also in H. phototrophica, CrtA was acquired from the Bacteroidetes, in which it functions as a hydroxylase. Estimation of nonsynonymous and synonymous mutations using several pairwise methods indicated positive selection upon both genes, consistent with their functional changes from hydroxylases to ketolases. Relaxed negative selection upon all other carotenoid biosynthetic genes in these organisms was also apparent, likely facilitating changes in their substrate specificities. Furthermore, all genes responsible for terminal carotenoid biosynthetic pathway steps were under reduced negative selection compared to those known to govern biosynthetic pathway specificity. Horizontal transfer of crtA into R. gelatinosus and H. phototrophica has therefore likely been promoted by (i) the apparent selective advantage of spheroidenone production relative to spirilloxanthin production, (ii) reduced negative selection upon other carotenoid biosynthetic genes, facilitating changes in their substrate specificities, and (iii) preexisting low enzyme substrate specificities due to relaxed negative selection. These results highlight the importance and complexity of selection acting upon both a horizontally transferred gene and the biochemical network into which it is integrating.

Metabolic engineering of ketocarotenoid biosynthesis in higher plants

Ketocarotenoids such as astaxanthin and canthaxanthin have important applications in the nutraceutical, cosmetic, food and feed industries. Astaxanthin is derived from beta-carotene by 3-hydroxylation and 4-ketolation at both ionone end groups. These reactions are catalyzed by beta-carotene hydroxylase and beta-carotene ketolase, respectively. The hydroxylation reaction is widespread in higher plants, but ketolation is restricted to a few bacteria, fungi, and some unicellular green algae. The recent cloning and characterization of beta-carotene ketolase genes in conjunction with the development of effective co-transformation strategies permitting facile co-integration of multiple transgenes in target plants provided essential resources and tools to produce ketocarotenoids in planta by genetic engineering. In this review, we discuss ketocarotenoid biosynthesis in general, and characteristics and functional properties of beta-carotene ketolases in particular. We also describe examples of ketocarotenoid engineering in plants and we conclude by discussing strategies to efficiently convert beta-carotene to astaxanthin in transgenic plants.

Conversion of beta-carotene into astaxanthin: Two separate enzymes or a bifunctional hydroxylase-ketolase protein?

Astaxanthin is a xanthophyll of great interest in animal nutrition and human health. The market prospect in the nutraceutics industries for this health-protective molecule is very promising. Astaxanthin is synthesized by several bacteria, algae and plants from β-carotene by the sequential action of two enzymes: a β-carotene, 3,3'-hydroxylase that introduces an hydroxyl group at the 3 (and 3') positions of each of the two β-ionone rings of β-carotene, and a β-carotene ketolase that introduces keto groups at carbons 4 and 4' of the β-ionone rings. Astaxanthin is also produced by the yeast-like basidiomycete Xanthophyllomyces dendrorhous. A gene crtS involved in the conversion of β-carotene to astaxanthin has been cloned simultaneously by two research groups. Complementation studies of X. dendrorhous mutants and expression analysis in Mucor circinelloides reveals that the CrtS enzyme is a β-carotene hydroxylase of the P-450 monooxygenase family that converts β-carotene to the hydroxylated derivatives β-cryptoxanthin and zeaxanthin, but it does not form astaxanthin or the ketolated intermediates in this fungus. A bifunctional β-carotene hydroxylase-ketolase activity has been proposed for the CrtS protein. The evidence for and against this hypothesis is analyzed in detail in this review.

Improvement of a CrtO-type of β-carotene ketolase for canthaxanthin production in Methylomonas sp

Two types of non-homologous beta-carotene ketolases (CrtW and CrtO) were previously described. We report improvement of a CrtO-type of beta-carotene ketolase for canthaxanthin production in a methylotrophic bacterium, Methylomonas sp. 16a, which could use the C1 substrate (methane or methanol) as sole carbon and energy source. The crtO gene from Rhodococcus erythropolis was improved for canthaxanthin production in an E. coli strain engineered to produce high titer carotenoids by error-prone PCR mutagenesis followed by in vitro recombination. The best mutants from protein engineering could produce approximately 90% of total carotenoids as canthaxanthin in the high titer E. coli strain compared to approximately 20% canthaxanthin produced by the starting gene. Canthaxanthin production in Methylomonas was also significantly improved to approximately 50% of total carotenoids by the mutant genes. Further improvement of canthaxanthin production to approximately 93% in Methylomonas was achieved by increased expression of the best mutant gene. Some mutations were found in many of the improved genes, suggesting that these sites, and possibly the regions around these sites, were important for improving the crtO's activity for canthaxanthin production.

Functional expression of the astaxanthin biosynthesis genes from a marine bacterium, Paracoccus haeundaensis

The astaxanthin biosynthesis gene cluster in Paracoccus haeundaensis consists of six genes: crtW, crtZ, crtY, crtI, crtB, and crtE contain 726, 486, 1158, 1503, 912, and 879 base pairs, respectively. Individual carotenoid biosynthesis genes of P. haeundaensis have now been expressed in E. coli and each gene product has been purified to homogeneity. Their molecular characteristics, including enzymatic activities, are reported here.

Bradyrhizobia isolated from root nodules of Parasponia (Ulmaceae) do not constitute a separate coherent lineage

Rhizobial bacteria almost exclusively nodulate members of the families Fabaceae, Mimosaceae and Caesalpiniaceae, but are found on a single non-legume taxon, Parasponia (Ulmaceae). Based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from Parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. This hypothesis was investigated by focusing on four isolates that are representative of the morphological and cultural types of Parasponia-nodulating bradyrhizobia. Their evolutionary relationships with other rhizobia were analysed using 16S rRNA gene sequences and their nodulation properties were explored using the nodA gene as a proxy for host-range specificity. Phylogenetic analyses of the 16S rRNA and nodA gene sequences revealed that bacterial isolates from Parasponia species are embedded among other bradyrhizobia. They did not cluster together in topologies based on the 16S rRNA or nodA gene sequences, but were scattered among other bradyrhizobia belonging to either the Bradyrhizobium japonicum or the Bradyrhizobium elkanii lineages. These data suggest that the ability of some bradyrhizobia to nodulate species of the genus Parasponia does not represent a historical relationship that predates the relationship between rhizobia and legumes, but is probably a more recent host switch for some rhizobia.

A carotenoid synthesis gene cluster from Algoriphagus sp. KK10202C with a novel fusion-type lycopene β-cyclase gene

A carotenoid synthesis gene cluster was isolated from a marine bacterium Algoriphagus sp. strain KK10202C that synthesized flexixanthin. Seven genes were transcribed in the same direction, among which five of them were involved in carotenoid synthesis. This cluster had a unique gene organization, with an isoprenoid gene, ispH (previously named lytB), being present among the carotenoid synthesis genes. The lycopene beta-cyclase encoded by the crtY ( cd ) gene appeared to be a fusion of bacterial heterodimeric lycopene cyclase CrtY(c) and CrtY(d). This was the first time that a fusion-type of lycopene beta-cyclase was reported in eubacteria. Heterologous expression of the Algoriphagus crtY ( cd ) gene in lycopene-accumulating Escherichia coli produced bicyclic beta-carotene. A biosynthesis pathway for monocyclic flexixanthin was proposed in Algoriphagus sp. strain KK10202C, though several of the carotenoid synthesis genes not linked with the cluster have not yet been cloned.

Structural diversity and functional novelty of new carotenoid biosynthesis genes

Many new carotenoid synthesis genes have recently been identified through genomic sequencing or functional cloning. Some of them exhibit novel structures and/or novel functions. This review describes such examples in the families of lycopene beta-cyclases, putative homologues of phytoene dehydrogenases and new carotenoid hydroxylases. Both the functionally novel lycopene beta-monocyclases and structurally novel fusion-type of lycopene beta-cyclases were described. Another newly discovered sequence of lycopene beta-cyclase described might represent a new class of lycopene beta-cyclases previously not identified in several cyanobacteria. Three examples of putative homologues of phytoene dehydrogenases were described, however, they were confirmed to encode different and/or new functions such as beta-carotene ketolase, 4,4'-diapolycopene oxygenase or prolycopene isomerase. Two new carotenoid hydroxylase genes were described that encoded the new function of 2,2'-beta-ionone ring hydroxylase or 3,3'-isorenieratene hydroxylase. Phylogenetic analysis of these genes shed light on their possible evolutionary origins. These new genes also provide tools for synthesis of novel and desirable carotenoids by genetic engineering.

Cloning and characterization of the astaxanthin biosynthesis gene cluster from the marine bacterium Paracoccus haeundaensis

Carotenoids are important natural pigments produced by many microorganisms and plants. In a previous study, we isolated and characterized a marine bacterium, Paracoccus haeundaensis, which produces carotenoids, mainly astaxanthin. In the present study, a carotenoid biosynthesis gene cluster involved in the production of astaxanthin was isolated and characterized from this marine bacterium. The cluster contained six carotenogenic genes, five of which, with the same orientation, were designated crtW, crtZ, crtY, crtI, and crtB, and one of which, with the opposite orientation, was designated crtE. The crtW, crtZ, crtY, crtI, crtB, and crtE genes contained 726, 486, 1158, 1503, 912, and 879 base pairs, respectively, and encoded polypeptides of 242, 162, 386, 501, 304, and 293 amino acid residues, respectively. The stop codon of each crt gene, except crtE, overlapped the start codon of the following crt gene. Comparisons of the structures and nucleotide sequences of the crt genes showed that the signature domains of the carotenoid biosynthesis genes are highly conserved. The molecular phylogenetic tree analysis showed the evolutionary relationships among the carotenoid biosynthesis genes of various organisms. An expression vector (pCR-XR-TOPO-Crt-full vector) containing the astaxanthin biosynthesis genes was constructed and transformed into Escherichia coli BL21(DE3) Codon Plus cells. The E. coli transformants produced 400 microg astaxanthin per gram of dry cell weight.

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

A carotenoid biosynthesis gene cluster mediating the production of 2-hydroxyastaxanthin was isolated from the marine bacterium Brevundimonas sp. strain SD212 by using a common crtI sequence as the probe DNA. A sequence analysis revealed this cluster to contain 12 open reading frames (ORFs), including the 7 known genes, crtW, crtY, crtI, crtB, crtE, idi, and crtZ. The individual ORFs were functionally analyzed by complementation studies using Escherichia coli that accumulated various carotenoid precursors due to the presence of other bacterial crt genes. In addition to functionally identifying the known crt genes, we found that one (ORF11, named crtG) coded for a novel enzyme, carotenoid 2,2'-beta-hydroxylase, which showed intriguingly partial homology with animal sterol-C5-desaturase. When this crtG gene was introduced into E. coli accumulating zeaxanthin and canthaxanthin, the resulting transformants produced their 2-hydroxylated and 2,2'-dihydroxylated products which were structurally novel or rare xanthophylls, as determined by their nuclear magnetic resonance and high-performance liquid chromatography/photodiode array detector/atmospheric pressure chemical ionization mass spectrometry spectral data. The new carotenoid produced was suggested to have a strong inhibitory effect on lipid peroxidation.

Characterization of beta-carotene ketolases, CrtW, from marine bacteria by complementation analysis in Escherichia coli

A complementation analysis was performed in Escherichia coli to evaluate the efficiency of beta-carotene ketolases (CrtW) from the marine bacteria Brevundimonas sp. SD212, Paracoccus sp. PC1 (Alcaligenes PC-1), and Paracoccus sp. N81106 (Agrobacterium aurantiacum), for astaxanthin production. Each crtW gene was expressed in Escherichia coli synthesizing zeaxanthin due to the presence of plasmid pACCAR25DeltacrtX. Carotenoids that accumulated in the resulting E. coli transformants were examined by chromatographic and spectroscopic analyses. The transformant carrying the Paracoccus sp. PC1 or N81106 crtW gene accumulated high levels of adonixanthin, which is the final astaxanthin precursor for CrtW, and astaxanthin, while the E. coli transformant with crtW from Brevundimonas sp. SD212 did not accumulate any adonixanthin and produced a high level of astaxanthin. These results show efficient conversion by CrtW of Brevundimonas sp. SD212 from adonixanthin to astaxanthin, which is a new-found characteristic of a bacterial CrtW enzyme. The phylogenetic positions between CrtW of the two genera, Brevundimonas and Paracoccus, are distant, although they fall into alpha-Proteobacteria.

A study in scarlet: enzymes of ketocarotenoid biosynthesis in the flowers of Adonis aestivalis

The red ketocarotenoid astaxanthin (3,3'-dihydroxy-4,4'-diketo-beta,beta-carotene) is widely used as an additive in feed for the pigmentation of fish and crustaceans and is frequently included in human nutritional supplements as well. There is considerable interest in developing a plant-based biological production process for this valuable carotenoid. Adonis aestivalis (Ranunculaceae) is unusual among plants in synthesizing and accumulating large amounts of astaxanthin and other ketocarotenoids. The formation of astaxanthin requires only the addition of a carbonyl at the number 4 carbon of each beta-ring of zeaxanthin (3,3'-dihydroxy-beta,beta-carotene), a carotenoid typically present in the green tissues of higher plants. We screened an A. aestivalis flower library to identify cDNAs that might encode the enzyme that catalyzes the addition of the carbonyls. Two closely related cDNAs selected in this screen were found to specify polypeptides similar in sequence to plant beta-carotene 3-hydroxylases, enzymes that convert beta-carotene (beta,beta-carotene) into zeaxanthin. The Adonis enzymes, however, exhibited neither 4-ketolase nor 3-hydroxylase activity when presented with beta-carotene as the substrate in Escherichia coli. Instead, the products of the Adonis cDNAs were found to modify beta-rings in two distinctly different ways: desaturation at the 3,4 position and hydroxylation of the number 4 carbon. The 4-hydroxylated carotenoids formed in E. coli were slowly metabolized to yield compounds with ketocarotenoid-like absorption spectra. It is proposed that a 3,4-desaturation subsequent to 4-hydroxylation of the beta-ring leads to the formation of a 4-keto-beta-ring via an indirect and unexpected route: a keto-enol tautomerization.

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

Phylogenetic analysis of carotenoid biosynthetic pathway genes and their evolutionary rate variations were studied among eubacterial taxa. The gene sequences for the enzymes involved in this pathway were obtained for major phylogenetic groups of eubacteria (green sulfur bacteria, green nonsulphur bacteria, Gram-positive bacteria, proteobacteria, flavobacteria, cyanobacteria) and archeabacteria. These gene datasets were distributed under five major steps of carotenoid biosynthesis in eubacteria; isoprenoid precursor biosynthesis, phytoene synthesis, dehydrogenation of phytoene, lycopene cyclization, formation of acyclic xanthophylls, formation of cyclic xanthophylls and carotenoid biosynthesis regulation. The NJ algorithm was used on protein coding DNA sequences to deduce the evolutionary relationship for the respective crt genes among different eubacterial lineages. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and synonymous nucleotide substitutions per synonymous site (d(S)) were calculated for different clades of the respective phylogenetic tree for specific crt genes. The phylogenetic analysis suggests that evolutionary pattern of crt genes in eubacteria is characterized by lateral gene transfer and gene duplication events. The d(N) values indicate that carotenoid biosynthetic genes are more conserved in proteobacteria than in any other eubacterial phyla. Furthermore, of the genes involved in carotenoid biosynthesis pathway, structural genes evolve slowly than the regulatory genes in eubacteria.

Novel beta-carotene ketolases from non-photosynthetic bacteria for canthaxanthin synthesis

We reported previously that the Rhodococcus erythropolis strain AN12 synthesizes the monocyclic carotenoids 4-keto gamma-carotene and gamma-carotene. We also identified a novel lycopene beta-monocyclase in this strain. Here we report the identification of the rest of the carotenoid synthesis genes in AN12. Two of these showed apparent homology to putative phytoene dehydrogenases. Analysis of Rhodococcus knockout mutants suggested that one of them ( crtI) encodes a phytoene dehydrogenase, whereas the other ( crtO) encodes a beta-carotene ketolase. Expression of the beta-carotene ketolase gene in an Escherichia coli strain which accumulates beta-carotene resulted in the production of canthaxanthin. In vitro assays using a crude extract of the E. coli strain expressing the crtO gene confirmed its ketolase activity. A crtO homologue (DR0093) from Deinococcus radiodurans R1 was also shown to encode a beta-carotene ketolase, despite its sequence homology to phytoene dehydrogenases. The Rhodococcus and Deinococcus CrtO ketolases both catalyze the symmetric addition of two keto groups to beta-carotene to produce canthaxanthin. Even though this activity is similar to the CrtW-type of ketolase activity, the CrtO ketolases show no significant sequence homology to CrtW-type ketolases. The presence of six conserved regions may be a signature for the CrtO-type of beta-carotene ketolases.

Two Distinct crt Gene Clusters for Two Different Functional Classes of Carotenoid in Bradyrhizobium

Aerobic photosynthetic bacteria possess the unusual characteristic of producing different classes of carotenoids. In this study, we demonstrate the presence of two distinct crt gene clusters involved in the synthesis of spirilloxanthin and canthaxanthin in a Bradyrhizobium strain. Each cluster contains the genes crtE, crtB, and crtI leading to the common precursor lycopene. We show that spirilloxanthin is associated with the photosynthetic complexes, while canthaxanthin protects the bacteria from oxidative stress. Only the spirilloxanthin crt genes are regulated by light via the control of a bacteriophytochrome. Despite this difference in regulation, the biosyntheses of both carotenoids are strongly interconnected at the level of the common precursors. Phylogenetic analysis suggests that the canthaxanthin crt gene cluster has been acquired by a lateral gene transfer. This acquisition may constitute a major selective advantage for this class of bacteria, which photosynthesize only under conditions where harmful reactive oxygen species are generated.

Asymmetrically acting lycopene beta-cyclases (CrtLm) from non-photosynthetic bacteria

Carotenoids have important functions in photosynthesis, nutrition, and protection against oxidative damage. Some natural carotenoids are asymmetrical molecules that are difficult to produce chemically. Biological production of carotenoids using specific enzymes is a potential alternative to extraction from natural sources. Here we report the isolation of lycopene beta-cyclases that selectively cyclize only one end of lycopene or neurosporene. The crtLm genes encoding the asymmetrically acting lycopene beta-cyclases were isolated from non-photosynthetic bacteria that produced monocyclic carotenoids. Co-expression of these crtLm genes with the crtEIB genes from Pantoea stewartii (responsible for lycopene synthesis) resulted in the production of monocyclic gamma-carotene in Escherichia coli. The asymmetric cyclization activity of CrtLm could be inhibited by the lycopene beta-cyclase inhibitor 2-(4-chlorophenylthio)-triethylamine (CPTA). Phylogenetic analysis suggested that bacterial CrtL-type lycopene beta-cyclases might represent an evolutionary link between the common bacterial CrtY-type of lycopene beta-cyclases and plant lycopene beta- and epsilon-cyclases. These lycopene beta-cyclases may be used for efficient production of high-value asymmetrically cyclized carotenoids.

Nitrogen-fixing symbiosis between photosynthetic bacteria and legumes

Rhizobia having photosynthetic systems form nitrogen-fixing nodules on the stem and/or root of some species of the legumes Aeschynomene and Lotononis. This review is focused on the recent knowledge about the physiology, genetics and role of the photosystem in these bacteria. Photosynthetic electron transport seems to involve reaction centers, soluble cytochrome c2 and cytochrome bc1. Anaerobically, the electron transport system becomes over-reduced. The photosynthesis genes have been partially characterized; their organization is classical but their regulation is unusual as it is activated by far-red light via a bacteriophytochrome. This original mechanism of regulation seems well adapted to promote photosynthesis during stem symbiosis. Photosynthesis plays a major role in the efficiency of stem nodulation. It is also observed that infrared light stimulates nitrogen fixation in nodules containing photosynthetic bacteroids, suggesting that photosynthesis may additionally provides energy for nitrogen fixation, allowing for more efficient plant growth. Other aspects of these bacteria are discussed, in particular their taxonomic position and nodulation ability, the role of carotenoids and the potential for application of photosynthetic rhizobia in rice culture.

Phytoene desaturase, CrtI, of the purple photosynthetic bacterium, Rubrivivax gelatinosus, produces both neurosporene and lycopene

Biosynthetic pathways for carotenoids in the purple photosynthetic bacterium, Rubrivivax gelatinosus, which synthesizes spirilloxanthin in addition to spheroidene and OH-spheroidene, were investigated by means of genetic manipulation. A phytoene desaturase gene (crtI) found in the photosynthesis gene cluster of this bacterium was expressed in an Escherichia coli strain that can produce phytoene. Both neurosporene and lycopene were synthesized in the recombinant, probably by three- and four-step desaturation reactions of CrtI. A mutant of RVI: gelatinosus lacking the crtI gene produced only phytoene, indicating that this organism had no other phytoene desaturases. When the crtI deletion mutant was complemented by the three-step phytoene desaturase of Rhodobacter capsulatus, spirilloxanthin and its precursors were not synthesized, although spheroidene and OH-spheroidene were accumulated. It was concluded that neurosporene and lycopene are produced by a single phytoene desaturase in RVI: gelatinosus resulting in the synthesis of spheroidene and spirilloxanthin, and that there are no pathways for spirilloxanthin synthesis via spheroidene.

Characterization of the common nodulation genes of the photosynthetic Bradyrhizobium sp. ORS285 reveals the presence of a new insertion sequence upstream of nodA

We isolated and characterized nodA genes from photosynthetic and non-photosynthetic rhizobia nodulating the legume genus Aeschynomene, and found that the nodA sequence from photosynthetic stem-nodulating bacteria was phylogenetically distant from the other already described nodA genes. Characterization of the photosynthetic strain ORS285 common nod gene cluster (nodABC) showed, upstream of nodA, the presence of a new insertion sequence element belonging to the IS3 family and specific to a group of photosynthetic strains from Aeschynomene.

Effect of Bradyrhizobium photosynthesis on stem nodulation of Aeschynomene sensitiva

Some leguminous species of the genus Aeschynomene are specifically stem-nodulated by photosynthetic bradyrhizobia. To study the effect of bacterial photosynthesis during symbiosis, we generated a photosynthesis-negative mutant of the Bradyrhizobium sp. strain ORS278 symbiont of Aeschynomene sensitiva. The presence of a functional photosynthetic unit in bacteroids and the high expression of the photosynthetic genes observed in stem nodules demonstrate that the bacteria are photosynthetically active during stem symbiosis. Stem inoculation by the photosynthetic mutant gave a 50% decrease in stem-nodule number, which reduced nitrogen fixation activity and plant growth in the same proportion. These results indicate an important role of bacterial photosynthesis in the efficiency of stem nodulation.