Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts

Purification of Natural Pigments Violacein and Deoxyviolacein Produced by Fermentation Using Yarrowia lipolytica

Violacein and deoxyviolacein are bis-indole pigments synthesized by a number of microorganisms. The present study describes the biosynthesis of a mixture of violacein and deoxyviolacein using a genetically modified Y. lipolytica strain as a production chassis, the subsequent extraction of the intracellular pigments, and ultimately their purification using column chromatography. The results show that the optimal separation between the pigments occurs using an ethyl acetate/cyclohexane mixture with different ratios, first 65:35 until both pigments were clearly visible and distinguishable, then 40:60 to create a noticeable separation between them and recover the deoxyviolacein, and finally 80:20, which allows the recovery of the violacein. The purified pigments were then analyzed by thin-layer chromatography and nuclear magnetic resonance.

Natural Pigments Production and Their Application in Food, Health and Other Industries

In addition to fulfilling their function of giving color, many natural pigments are known as interesting bioactive compounds with potential health benefits. These compounds have various applications. In recent times, in the food industry, there has been a spread of natural pigment application in many fields, such as pharmacology and toxicology, in the textile and printing industry and in the dairy and fish industry, with almost all major natural pigment classes being used in at least one sector of the food industry. In this scenario, the cost-effective benefits for the industry will be welcome, but they will be obscured by the benefits for people. Obtaining easily usable, non-toxic, eco-sustainable, cheap and biodegradable pigments represents the future in which researchers should invest.

Functional characterization of a novel violacein biosynthesis operon from Janthinobacterium sp. B9-8

Violacein is a secondary metabolite mainly produced by Gram-negative bacteria that is formed from tryptophan by five enzymes encoded by a single operon. It is a broad-spectrum antibacterial pigment with various important biological activities such as anti-tumor, antiviral, and antioxidative effects. The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8. The key enzyme-encoding genes were cloned to construct the multigene coexpression plasmids pET-vioAB and pRSF-vioCDE. The violacein biosynthesis pathway was heterologously introduced into engineered Escherichia coli VioABCDE and VioABCDE-SD. The factors affecting violacein production, including temperature, pH, inoculum size, carbon and nitrogen source, precursor, and inducers were investigated. The violacein titer of VioABCDE-SD reached 107 mg/L in a two-stage fermentation process, representing a 454.4% increase over the original strain. The violacein operon from B9-8 provides a new microbial gene source for the analysis of the violacein synthesis mechanism, and the constructed engineering E. coli strains lay a foundation for the efficient and rapid synthesis of other natural products.Key points• The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8.• The violacein synthesis pathway was reconstructed in E. coli using two compatible plasmids.• A two-stage fermentation process was optimized for improved violacein accumulation.

Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings

A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives.

Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Recent Advances in Synthetic, Industrial and Biological Applications of Violacein and Its Heterologous Production

Violacein, a purple pigment first isolated from a gram-negative coccobacillus Chromobacterium violaceum, has gained extensive research interest in recent years due to its huge potential in the pharmaceutic area and industry. In this review, we summarize the latest research advances concerning this pigment, which include (1) fundamental studies of its biosynthetic pathway, (2) production of violacein by native producers, apart from C. violaceum, (3) metabolic engineering for improved production in heterologous hosts such as Escherichia coli, Citrobacter freundii, Corynebacterium glutamicum, and Yarrowia lipolytica, (4) biological/pharmaceutical and industrial properties, (5) and applications in synthetic biology. Due to the intrinsic properties of violacein and the intermediates during its biosynthesis, the prospective research has huge potential to move this pigment into real clinical and industrial applications.

Microbial synthesis of violacein pigment and its potential applications

Violacein is a pigment synthesized by Gram-negative bacteria such as Chromobacterium violaceum. It has garnered significant interest owing to its unique physiological and biological activities along with its synergistic effects with various antibiotics. In addition to C. violaceum, several microorganisms, including: Duganella sp., Pseudoalteromonas sp., Iodobacter sp., and Massilia sp., are known to produce violacein. Along with the identification of violacein-producing strains, the genetic regulation, quorum sensing mechanism, and sequence of the vio-operon involved in the biosynthesis of violacein have been elucidated. From an engineering perspective, the heterologous production of violacein using the genetically engineered Escherichia coli or Citrobacter freundii host has also been attempted. Genetic engineering of host cells involves the heterologous expression of genes involved in the vio operon and the optimization of metabolic pathways and gene regulation. Further, the crystallography of VioD and VioE was revealed, and mass production by enzyme engineering has been accelerated. In this review, we highlight the biologically assisted end-use applications of violacein (such as functional fabric development, nanoparticles, functional polymer composites, and sunscreen ingredients) and violacein activation mechanisms, production strains, and the results of mass production with engineered methods. The prospects for violacein research and engineering applications have also been discussed.

Biotechnological Activities and Applications of Bacterial Pigments Violacein and Prodigiosin

In this review, we discuss violacein and prodigiosin, two chromogenic bacterial secondary metabolites that have diverse biological activities. Although both compounds were "discovered" more than seven decades ago, interest into their biological applications has grown in the last two decades, particularly driven by their antimicrobial and anticancer properties. These topics will be discussed in the first half of this review. The latter half delves into the current efforts of groups to produce these two compounds. This includes in both their native bacterial hosts and heterogeneously in other bacterial hosts, including discussing some of the caveats related to the yields reported in the literature, and some of the synthetic biology techniques employed in this pursuit.

Direct RBS Engineering of the biosynthetic gene cluster for efficient productivity of violaceins in E. coli

Background

Violaceins have attracted much attention as potential targets used in medicines, food additives, insecticides, cosmetics and textiles, but low productivity was the key factor to limit their large-scale applications. This work put forward a direct RBS engineering strategy to engineer the violacein biosynthetic gene cluster cloned from Chromobacterium violaceum ATCC 12,472 to efficiently improve the fermentation titers.

Results

Through four-rounds of engineering of the native RBSs within the violaceins biosynthetic operon vioABCDE, this work apparently broke through the rate-limiting steps of intermediates conversion, resulting in 2.41-fold improvement of violaceins production compared to the titers of the starting strain Escherichia coli BL21(DE3) (Vio12472). Furthermore, by optimizing the batch-fermentation parameters including temperature, concentration of IPTG inducer and fermentation time, the maximum yield of violaceins from (BCDE)m (tnaA⁻) reached 3269.7 µM at 2 mM tryptophan in the medium. Interestingly, rather than previous reported low temperature (20 ℃), we for the first time found the RBS engineered Escherichia coli strain (BCDE)m worked better at higher temperature (30 ℃ and 37 ℃), leading to a higher-level production of violaceins.

Conclusions

To our knowledge, this is the first time that a direct RBS engineering strategy is used for the biosynthesis of natural products, having the potential for a greater improvement of the product yields within tryptophan hyperproducers and simultaneously avoiding the costly low temperature cultivation for large-scale industrial production of violaciens. This direct RBS engineering strategy could also be easily and helpfully used in engineering the native RBSs of other larger and value-added natural product biosynthetic gene clusters by widely used site-specific mutagenesis methods represented by inverse PCR or CRISPR-Cas9 techniques to increase their fermentation titers in the future.

A Golden-Gate Based Cloning Toolkit to Build Violacein Pathway Libraries in Yarrowia lipolytica

Violacein is a naturally occurring anticancer therapeutic compound with deep purple color. In this work, we harnessed the modular and combinatorial feature of a Golden Gate assembly method to construct a library of violacein producing strains in the oleaginous yeast Yarrowia lipolytica, where each gene in the violacein pathway was controlled by three different promoters with varying transcriptional strength. After optimizing the linker sequence and the Golden Gate reaction, we achieved high transformation efficiency and obtained a panel of representative Y. lipolytica recombinant strains. By evaluating the gene expression profile of 21 yeast strains, we obtained three colorful compounds in the violacein pathway: green (proviolacein), purple (violacein), and pink (deoxyviolacein). Our results indicated that strong expression of VioB, VioC, and VioD favors violacein production with minimal byproduct deoxyvioalcein in Y. lipolytica, and high deoxyviolacein production was found strongly associated with the weak expression of VioD. By further optimizing the carbon to nitrogen ratio and cultivation pH, the maximum violacein reached 70.04 mg/L with 5.28 mg/L of deoxyviolacein in shake flasks. Taken together, the development of Golden Gate cloning protocols to build combinatorial pathway libraries, and the optimization of culture conditions set a new stage for accessing the violacein pathway intermediates and engineering violacein production in Y. lipolytica. This work further expands the toolbox to engineering Y. lipolytica as an industrially relevant host for plant or marine natural product biosynthesis.

Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway

The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.

Consumption of Oleic Acid During Matriphagy in Free-Living Nematodes Alleviates the Toxic Effects of the Bacterial Metabolite Violacein

Maternal behaviors benefit the survival of young, contributing directly to the mother’s reproductive fitness. An extreme form of this is seen in matriphagy, when a mother performs the ultimate sacrifice and offers her body as a meal for her young. Whether matriphagy offers only a single energy-rich meal or another possible benefit to the young is unknown. Here, we characterized the toxicity of a bacterial secondary metabolite, namely, violacein, in Caenorhabditis elegans and found it is not only toxic towards adults, but also arrests growth and development of C. elegans larvae. To counteract this, C. elegans resorted to matriphagy, with the mothers holding their eggs within their bodies and hatching the young larvae internally, which eventually led to the mothers’ death. This violacein-induced matriphagy alleviated some of the toxic effects of violacein, allowing a portion of the internally-hatched young to bypass developmental arrest. Using genetic and pharmacological experiments, we found the consumption of oleate, a monounsaturated fatty acid produced by the mother, during matriphagy is partially responsible. As such, our study provides experimental evidence of why such a drastic and peculiar maternal behavior may have arisen in nematode natural habitats.

Fungi as a Potential Source of Pigments: Harnessing Filamentous Fungi

The growing concern over the harmful effects of synthetic colorants on both the consumer and the environment has raised a strong interest in natural coloring alternatives. As a result the worldwide demand for colorants of natural origin is rapidly increasing in the food, cosmetic and textile sectors. Natural colorants have the capacity to be used for a variety of industrial applications, for instance, as dyes for textile and non-textile substrates such as leather, paper, within paints and coatings, in cosmetics, and in food additives. Currently, pigments and colorants produced through plants and microbes are the primary source exploited by modern industries. Among the other non-conventional sources, filamentous fungi particularly ascomycetous and basidiomycetous fungi (mushrooms), and lichens (symbiotic association of a fungus with a green alga or cyanobacterium) are known to produce an extraordinary range of colors including several chemical classes of pigments such as melanins, azaphilones, flavins, phenazines, and quinines. This review seeks to emphasize the opportunity afforded by pigments naturally found in fungi as a viable green alternative to current sources. This review presents a comprehensive discussion on the capacity of fungal resources such as endophytes, halophytes, and fungi obtained from a range or sources such as soil, sediments, mangroves, and marine environments. A key driver of the interest in fungi as a source of pigments stems from environmental factors and discussion here will extend on the advancement of greener extraction techniques used for the extraction of intracellular and extracellular pigments. The search for compounds of interest requires a multidisciplinary approach and techniques such as metabolomics, metabolic engineering and biotechnological approaches that have potential to deal with various challenges faced by pigment industry.

Exploiting the Feedstock Flexibility of the Emergent Synthetic Biology Chassis Vibrio natriegens for Engineered Natural Product Production

A recent goal of synthetic biology has been to identify new chassis that provide benefits lacking in model organisms. Vibrio natriegens is a marine Gram-negative bacterium which is an emergent synthetic biology chassis with inherent benefits: An extremely fast growth rate, genetic tractability, and the ability to grow on a variety of carbon sources ("feedstock flexibility"). Given these inherent benefits, we sought to determine its potential to heterologously produce natural products, and chose beta-carotene and violacein as test cases. For beta-carotene production, we expressed the beta-carotene biosynthetic pathway from the sister marine bacterium Vibrio campbellii, as well as the mevalonate biosynthetic pathway from the Gram-positive bacterium Lactobacillus acidophilus to improve precursor abundance. Violacein was produced by expressing a biosynthetic gene cluster derived from Chromobacterium violaceum. Not only was V. natriegens able to heterologously produce these compounds in rich media, illustrating its promise as a new chassis for small molecule drug production, but it also did so in minimal media using a variety of feedstocks. The ability for V. natriegens to produce natural products with multiple industrially-relevant feedstocks argues for continued investigations into the production of more complex natural products in this chassis.

Metabolic engineering of microorganisms for production of aromatic compounds

Metabolic engineering has been enabling development of high performance microbial strains for the efficient production of natural and non-natural compounds from renewable non-food biomass. Even though microbial production of various chemicals has successfully been conducted and commercialized, there are still numerous chemicals and materials that await their efficient bio-based production. Aromatic chemicals, which are typically derived from benzene, toluene and xylene in petroleum industry, have been used in large amounts in various industries. Over the last three decades, many metabolically engineered microorganisms have been developed for the bio-based production of aromatic chemicals, many of which are derived from aromatic amino acid pathways. This review highlights the latest metabolic engineering strategies and tools applied to the biosynthesis of aromatic chemicals, many derived from shikimate and aromatic amino acids, including L-phenylalanine, L-tyrosine and L-tryptophan. It is expected that more and more engineered microorganisms capable of efficiently producing aromatic chemicals will be developed toward their industrial-scale production from renewable biomass.

Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli

Strategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Δpgi & ΔpheA were validated using in silico gene deletion analysis. Phenotypic phase plane (PhPP) analysis highlighted sensitivity between tryptophan and NADPH for violacein synthesis at molar growth yields. A synthetic VioABCDE operon (SYNO) sequence was designed to maximize Codon Adaptive Index (CAI: 0.9) and tune translation initiation rates (TIR: 2-50 fold higher) in E. coli. All pSYN E. coli transformants produced higher violacein, with a maximum six-fold increase in yields. The rational design E. coli: ΔpheA SYN: gave the highest violacein titers (33.8 mg/l). Such integrated approaches targeting multiple molecular hierarchies in the cell can be extended further to increase violacein yields.

Enhanced Production of Crude Violacein from Glucose in Escherichia coli by Overexpression of Rate-Limiting Key Enzyme(S) Involved in Violacein Biosynthesis

Crude violacein, consisting of violacein and deoxyviolacein, displays many attractive bio-activities in the field of drug therapy. To produce crude violacein from an industrially economic carbon source, we firstly introduced the violacein pathway into Escherichia coli B8/pTRPH1, which was previously engineered to accumulate tryptophan from glucose. A crude violacein production capacity of 0.25 g L^-1 OD₆₀₀^-1 was obtained using glucose-containing medium. By further overexpressing each of the five genes involved in violacein synthesis pathway, VioE was found as the rate-limiting step for the violacein production. The optimal strain of B8/pTRPH1-pVio-VioE was then used for fed-batch fermentation in a 5-L bioreactor and a crude violacein titer of 4.45 g L^-1, as well as a productivity of 98.7 mg L^-1 h^-1, was obtained. This engineered strain showed the highest violacein titer and productivity reported so far. Our optimal strain of E. coli B8/pTRPH1-pVio-VioE by overexpression of the rate-limiting VioE in violacein synthesis pathway was a potential violacein producer by directly using glucose for industrial application.

Antiplasmodial and trypanocidal activity of violacein and deoxyviolacein produced from synthetic operons

BACKGROUND

Violacein is a deep violet compound that is produced by a number of bacterial species. It is synthesized from tryptophan by a pathway that involves the sequential action of 5 different enzymes (encoded by genes vioA to vioE). Violacein has antibacterial, antiparasitic, and antiviral activities, and also has the potential of inducing apoptosis in certain cancer cells.

RESULTS

Here, we describe the construction of a series of plasmids harboring the complete or partial violacein biosynthesis operon and their use to enable production of violacein and deoxyviolacein in E.coli. We performed in vitro assays to determine the biological activity of these compounds against Plasmodium, Trypanosoma, and mammalian cells. We found that, while deoxyviolacein has a lower activity against parasites than violacein, its toxicity to mammalian cells is insignificant compared to that of violacein.

CONCLUSIONS

We constructed E. coli strains capable of producing biologically active violacein and related compounds, and propose that deoxyviolacein might be a useful starting compound for the development of antiparasite drugs.

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.

Novel Tools for the Functional Expression of Metagenomic DNA

Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus. Different broad-host-range shuttle vectors are described that allow activity-based screening of metagenomic DNA in these bacteria. Furthermore, we describe the newly developed transfer-and-expression system TREX which comprises genetic elements essential to allow for expression of large clusters of functionally coupled genes in different microbial species.

Citrobacter freundii as a test platform for recombinant cellulose degradation systems

Cellulosic biomass represents a huge reservoir of renewable carbon, but converting it into useful products is challenging. Attempts to transfer cellulose degradation capability to industrially useful micro-organisms have met with limited success, possibly due to poorly understood synergy between multiple cellulases. This is best studied by co-expression of many combinations of cellulases and associated proteins. Here, we describe the development of a test platform based on Citrobacter freundii, a cellobiose-assimilating organism closely related to Escherichia coli. Standard E. coli cloning vectors worked well in Cit. freundii. Expression of cellulases CenA and Cex of Cellulomonas fimi in Cit. freundii gave recombinant strains which were able to grow at the expense of cellulosic filter paper or microcrystalline cellulose (Avicel) in a mineral medium supplemented with a small amount of yeast extract. Periodic physical agitation of the cultures was highly beneficial for growth at the expense of filter paper. This provides a test platform for the expression of combinations of genes encoding biomass-degrading enzymes to develop effective genetic cassettes for degradation of different biomass streams.

SIGNIFICANCE AND IMPACT OF THE STUDY

Biofuels have been shown to be the best sustainable and alternative source of fuel to replace fossil fuels. Of the different types of feedstocks used for producing biofuels, lignocellulosic biomass is the most abundant. Converting this biomass to useful products has met with little success. Different approaches are being used and microbial platforms are the most promising and sustainable method. This study shows that Citrobacter freundii is a better test platform than Escherichia coli for testing various combinations of cellulases for the development of microbial systems for biomass conversion.

Engineering Corynebacterium glutamicum for violacein hyper production

BACKGROUND

Corynebacterium glutamicum was used as a metabolic engineering chassis for production of crude violacein (mixture of violacein and deoxyviolacein) due to Corynebacterium's GRAS status and advantages in tryptophan fermentation. The violacein is a commercially potential compound with various applications derived from L-tryptophan.

RESULTS

Corynebacterium glutamicum ATCC 21850 that could produce 162.98 mg L(-1) tryptophan was employed as a novel host for metabolic engineering chassis. Heterologous vio operon from Chromobacterium violaceum was over-expressed in ATCC 21850 strain with constitutive promoter to have obtained 532 mg L(-1) violacein. Considering toxicity of violacein, vio operon was expressed with inducible promoter and 629 mg L(-1) violacein was obtained in batch culture. Due to the economical coding nature of vio operon, the compressed RBS of vio genes were replaced with complete strong C. glutamicum ones. And extended expression units were assembled to form a synthetic operon. With this strategy, 1116 mg L(-1) violacein in batch culture was achieved. Fermentation process was then optimized by studying induction time, induction concentration, culture composition and fermentation temperature. as a result, a titer of 5436 mg L(-1) and a productivity of 47 mg L(-1) h(-1) were achieved in 3 L bioreactor.

CONCLUSIONS

With metabolic engineering and fermentation optimization practice, C. glutamicum 21850 (pEC-C-vio1) was able to produce violacein with both titer and productivity at the highest level ever reported. Due to advantages of mature C. glutamicum fermentation industry, this work has built basis for commercial production of violacein.

Advances in Chromobacterium violaceum and properties of violacein-Its main secondary metabolite: A review

Chromobacterium violaceum is important in the production of violacein, like other bacteria, such as Alteromonas, Janthinobacterium, Pseudoalteromonas, Duganella, Collimonas and Escherichia. Violacein is a versatile pigment, where it exhibits several biological activities, and every year, it shows increasing commercially interesting uses, especially for industrial applications in cosmetics, medicines and fabrics. This review on violacein focuses mainly on the last five years of research regarding this target compound and describes production and importance of quorum sensing in C. violaceum, mechanistic aspects of its biosynthesis, monitoring processes, genetic perspectives, pathogenic effects, antiparasitic and antimicrobial activities, immunomodulatory potential and uses, antitumor potential and industrial applications.

High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus

A violacein-producing bacterial strain was isolated and identified as a relative of Duganella violaceinigra YIM 31327 based upon phylogenetic analyses using the 16S rRNA, gyrB and vioA gene sequences and a fatty acid methyl ester (FAME) analysis. This new strain was designated D. violaceinigra str. NI28. Although these two strains appear related based upon these analyses, the new isolate was phenotypically different from the type strain as it grew 25% faster on nutrient media and produced 45-fold more violacein. When compared with several other violacein producing strains, including Janthinobacterium lividum, D. violaceinigra str. NI28 was the best violacein producer. For instance, the crude violacein yield with D. violaceinigra str. NI28 was 6.0 mg/OD at 24 hours, a value that was more than two-fold higher than all the other strains. Finally, the antibacterial activity of D. violaceinigra str. NI28 crude violacein was assayed using several multidrug resistant Staphylococcus aureus. Addition of 30 μM crude violacein led to a 96% loss in the initial S. aureus population while the minimum inhibitory concentration was 1.8 μM. Consequently, this novel isolate represents a phenotypic variant of D. violaceinigra capable of producing much greater quantities of crude violacein, an antibiotic effective against multidrug resistant S. aureus.

Violacein: Properties and Production of a Versatile Bacterial Pigment

Violacein-producing bacteria, with their striking purple hues, have undoubtedly piqued the curiosity of scientists since their first discovery. The bisindole violacein is formed by the condensation of two tryptophan molecules through the action of five proteins. The genes required for its production, vioABCDE, and the regulatory mechanisms employed have been studied within a small number of violacein-producing strains. As a compound, violacein is known to have diverse biological activities, including being an anticancer agent and being an antibiotic against Staphylococcus aureus and other Gram-positive pathogens. Identifying the biological roles of this pigmented molecule is of particular interest, and understanding violacein's function and mechanism of action has relevance to those unmasking any of its commercial or therapeutic benefits. Unfortunately, the production of violacein and its related derivatives is not easy and so various groups are also seeking to improve the fermentative yields of violacein through genetic engineering and synthetic biology. This review discusses the recent trends in the research and production of violacein by both natural and genetically modified bacterial strains.

Variation in the Presence of Anti-Batrachochytrium dendrobatidis Bacteria of Amphibians Across Life Stages and Elevations in Ecuador

Amphibian populations are decreasing worldwide due to a variety of factors. In South America, the chytrid fungus Batrachochytrium dendrobatidis (Bd) is linked to many population declines. The pathogenic effect of Bd on amphibians can be inhibited by specific bacteria present on host skin. This symbiotic association allows some amphibians to resist the development of the disease chytridiomycosis. Here, we aimed (1) to determine for the first time if specific anti-Bd bacteria are present on amphibians in the Andes of Ecuador, (2) to monitor anti-Bd bacteria across developmental stages in a focal amphibian, the Andean marsupial tree frog, Gastrotheca riobambae, that deposits larvae in aquatic habitats, and (3) to compare the Bd presence associated with host assemblages including 10 species at sites ranging in biogeography from Amazonian rainforest (450 masl) to Andes montane rainforest (3200 masl). We sampled and identified skin-associated bacteria of frogs in the field using swabs and a novel methodology of aerobic counting plates, and a combination of morphological, biochemical, and molecular identification techniques. The following anti-Bd bacteria were identified and found to be shared among several hosts at high-elevation sites where Bd was present at a prevalence of 32.5%: Janthinobacterium lividum, Pseudomonas fluorescens, and Serratia sp. Bd were detected in Gastrotheca spp. and not detected in the lowlands (sites below 1000 masl). In G. riobambae, recognized Bd-resistant bacteria start to be present at the metamorphic stage. Overall bacterial abundance was significantly higher post-metamorphosis and on species sampled at lower elevations. Further metagenomic studies are needed to evaluate the roles of host identity, life-history stage, and biogeography of the microbiota and their function in disease resistance.

Expression, crystallization and preliminary crystallographic data analysis of VioD, a hydroxylase in the violacein-biosynthesis pathway

Violacein, a natural purple secondary metabolite, is sequentially biosynthesized by five enzymes in the following pathway: VioA-VioB-VioE-VioD-VioC. VioD, a flavin-dependent oxygenase, catalyzes the hydroxylation of the intermediate product prodeoxyviolaceinic acid (PVA) at the 5-position of one indole ring to yield proviolacein. In vitro biochemical data have revealed this process, but the catalytic mechanism still remains largely unclear. Here, the cloning, expression, purification, crystallization and diffraction of VioD are reported. Crystals of VioD diffracted to 1.7 Å resolution and belonged to space group P31, with unit-cell parameters a = b = 90.0, c = 94.5 Å, α = β = 90, γ = 120°. Solvent-content calculation and molecular-replacement results suggest the presence of two molecules of VioD in the asymmetric unit.

High crude violacein production from glucose by Escherichia coli engineered with interactive control of tryptophan pathway and violacein biosynthetic pathway

Background

As bacteria-originated crude violacein, a natural indolocarbazole product, consists of violacein and deoxyviolacein, and can potentially be a new type of natural antibiotics, the reconstruction of an effective metabolic pathway for crude violacein (violacein and deoxyviolacein mixture) synthesis directly from glucose in Escherichia coli was of importance for developing industrial production process.

Results

Strains with a multivariate module for varied tryptophan productivities were firstly generated by combinatorial knockout of trpR/tnaA/pheA genes and overexpression of two key genes trpE^fbr/trpD from the upstream tryptophan metabolic pathway. Then, the gene cluster of violacein biosynthetic pathway was introduced downstream of the generated tryptophan pathway. After combination of these two pathways, maximum crude violacein production directly from glucose by E. coli B2/pED + pVio was realized with a titer of 0.6 ± 0.01 g L⁻¹ in flask culture, which was four fold higher than that of the control without the tryptophan pathway up-regulation. In a 5-L bioreactor batch fermentation with glucose as the carbon source, the recombinant E. coli B2/pED + pVio exhibited a crude violacein titer of 1.75 g L⁻¹ and a productivity of 36 mg L⁻¹ h⁻¹, which was the highest titer and productivity reported so far under the similar culture conditions without tryptophan addition.

Conclusion

Metabolic pathway analysis using ¹³C labeling illustrated that the up-regulated tryptophan supply enhanced tryptophan metabolism from glucose, whereas the introduction of violacein pathway drew more carbon flux from glucose to tryptophan, thereby contributing to the effective production of crude violacein in the engineered E. coli cell factory.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0192-x) contains supplementary material, which is available to authorized users.

Alternative hosts for functional (meta)genome analysis

Microorganisms are ubiquitous on earth, often forming complex microbial communities in numerous different habitats. Most of these organisms cannot be readily cultivated in the laboratory using standard media and growth conditions. However, it is possible to gain access to the vast genetic, enzymatic, and metabolic diversity present in these microbial communities using cultivation-independent approaches such as sequence- or function-based metagenomics. Function-based analysis is dependent on heterologous expression of metagenomic libraries in a genetically amenable cloning and expression host. To date, Escherichia coli is used in most cases; however, this has the drawback that many genes from heterologous genomes and complex metagenomes are expressed in E. coli either at very low levels or not at all. This review emphasizes the importance of establishing alternative microbial expression systems consisting of different genera and species as well as customized strains and vectors optimized for heterologous expression of membrane proteins, multigene clusters encoding protein complexes or entire metabolic pathways. The use of alternative host-vector systems will complement current metagenomic screening efforts and expand the yield of novel biocatalysts, metabolic pathways, and useful metabolites to be identified from environmental samples.

Systems metabolic engineering of Escherichia coli for production of the antitumor drugs violacein and deoxyviolacein

Violacein and deoxyviolacein are interesting therapeutics against pathogenic bacteria and viruses as well as tumor cells. In the present work, systems-wide metabolic engineering was applied to target Escherichia coli, a widely accepted recombinant host in pharmaceutical biotechnology, for production of these high-value products. The basic producer, E. coli dVio-1, that expressed the vioABCE cluster from Chromobacterium violaceum under control of the inducible araC system, accumulated 180 mg L(-1) of deoxyviolacein. Targeted intracellular metabolite analysis then identified bottlenecks in tryptophan supporting pathways, the major product building block. This was used for comprehensive engineering of serine, chorismate and tryptophan biosynthesis and the non-oxidative pentose-phosphate pathway. The final strain, E. coli dVio-6, accumulated 320 mg L(-1) deoxyviolacein in shake flask cultures. The created chassis of a high-flux tryptophan pathway was complemented by genomic integration of the vioD gene of Janthinobacterium lividum, which enabled exclusive production of violacein. In a fed-batch process, the resulting producer E. coli Vio-4 accumulated 710 mg L(-1) of the desired product. With straightforward broth extraction and subsequent crystallization, violacein could be obtained with 99.8% purity. This demonstrates the potential of E. coli as a platform for production of tryptophan based therapeutics.

Exploring in vivo violacein biosynthesis by application of multivariate curve resolution on fused UV-VIS absorption, fluorescence, and liquid chromatography-mass spectrometry data

In this work, the application of multivariate curve resolution-alternating least squares (MCR-ALS) is proposed for extracting information from multitechnique fused multivariate data (UV-VIS absorption, fluorescence, and liquid chromatography-mass spectrometry) gathered during the biosynthesis of violacein pigment. Experimental data sets were pretreated and arranged in a row-wise augmented data matrix before their chemometric investigation. Five different chemical components were resolved. Kinetic and spectral information about these components were obtained and their relationship with violacein biosynthesis was established. Three new chemical compounds with molar masses of 453, 465, and 479 u, until now not reported in the literature, were identified and proposed as intermediates in the biosynthesis of other indolocarbazoles. The precursor (tryptophan), one intermediate (deoxyviolacein), and the final product (violacein) of violacein biosynthesis were identified and characterized using the proposed approach. The chemometric procedure based on the MCR-ALS method has proved to be a powerful tool to investigate violacein biosynthesis and its application can be easily extended to the study of other bioprocesses.

Characterization and identification of productivity-associated rhizobacteria in wheat

The rhizosphere is populated by a numerous and diverse array of rhizobacteria, and many impact productivity in largely unknown ways. Here we characterize the rhizobacterial community in a wheat variety categorized according to shoot biomass using 16S rRNA pyrosequencing abundance data. Plants were grown in homogenized field soil under greenhouse conditions, and DNA was extracted and pyrosequenced, resulting in 29,007 quality sequences. Operational taxonomic units (OTUs) that were significantly associated with biomass productivity were identified using an exact test adjusted for the false-discovery rate. The productivity deviation expressed as a percentage of the total mean square for regression (PMSR) was determined for each OTU. Out of 719 OTUs, 42 showed significant positive associations and 39 showed significant negative associations (q value, ≤0.05). OTUs with the greatest net positive associations, by genus, were as follows: Duganella, OTU 43 and OTU 3; Janthinobacterium, OTU 278; Pseudomonas, OTU 588; and Cellvibrio, OTU 1847. Those with negative associations were as follows: Bacteria, OTU 273; Chryseobacterium, OTU 508; Proteobacteria, OTU 249; and Enterobacter, OTU 357. Shoot biomass productivity was strongly correlated with the balance between the overall abundances of positive- and negative-productivity-associated OTUs. High-productivity rhizospheres contained 9.2 significant positives for every negatively associated rhizobacterium, while low-productivity rhizospheres showed 2.3 significant negatives for every positively associated rhizobacterium. Overall rhizobacterial community diversity as measured by the Chao1, Shannon, and Simpson indexes was nonlinearly related to productivity, closely fitting a wavelike cubic equation. We conclude that shoot biomass productivity is strongly related to the ratio of positive- to negative-productivity-associated rhizobacteria in the rhizosphere. This study identifies significant OTUs composing the productive and unproductive rhizobacterial communities.

Pathway redesign for deoxyviolacein biosynthesis in Citrobacter freundii and characterization of this pigment

Violacein (Vio) is an important purple pigment with many potential bioactivities. Deoxyviolacein, a structural analog of Vio, is always synthesized in low concentrations with Vio in wild-type bacteria. Due to deoxyviolacein's low production and difficulties in isolation and purification, little has been learned regarding its function and potential applications. This study was the first effort in developing a stable and efficient biosynthetic system for producing pure deoxyviolacein. A recombinant plasmid with vioabce genes was constructed by splicing using an overlapping extension-polymerase chain reaction, based on the Vio-synthesizing gene cluster of vioabcde, originating from Duganella sp. B2, and was introduced into Citrobacter freundii. With the viod gene disrupted in the Vio synthetic pathway, Vio production was completely abolished and the recombinant C. freundii synthesized only deoxyviolacein. Interestingly, vioe gene expression was strongly stimulated in the viod-deleted recombinant strain, indicating that viod disruptions could potentially induce polar effects upon the downstream vioe gene within this small operon. Deoxyviolacein production by this strain reached 1.9 g/L in shaker flasks. The product exhibited significant acid/alkali and UV resistance as well as significant inhibition of hepatocellular carcinoma cell proliferation at low concentrations of 0.1-1 μM. These physical characteristics and antitumor activities of deoxyviolacein contribute to illuminating its potential applications.

Microbial production of the drugs violacein and deoxyviolacein: analytical development and strain comparison

Violacein and deoxyviolacein display a broad range of interesting biological properties but their production is rarely distinguished due to the lack of suitable analytical methods. An HPLC method has been developed for the separation and quantification of violacein and deoxyviolacein and can determine the content of both molecules in microbial cultures. A comparison of different production microorganisms, including recombinant Escherichia coli and the natural producer Janthinobacterium lividum, revealed that the formation of violacein and deoxyviolacein is strain-specific but showed significant variation during growth although the ratio between the two compounds remained constant.

Bioactive pigments from marine bacteria: applications and physiological roles

Research into natural products from the marine environment, including microorganisms, has rapidly increased over the past two decades. Despite the enormous difficulty in isolating and harvesting marine bacteria, microbial metabolites are increasingly attractive to science because of their broad-ranging pharmacological activities, especially those with unique color pigments. This current review paper gives an overview of the pigmented natural compounds isolated from bacteria of marine origin, based on accumulated data in the literature. We review the biological activities of marine compounds, including recent advances in the study of pharmacological effects and other commercial applications, in addition to the biosynthesis and physiological roles of associated pigments. Chemical structures of the bioactive compounds discussed are also presented.

Purple-pigmented violacein-producing Duganella spp. inhabit the rhizosphere of wild and cultivated olives in southern Spain

Bacteria have evolved mechanisms that allow them to grow and survive in highly competitive environments like soil and the rhizosphere. Using classical microbiological, physiological, and genetic analyses, we isolated and identified for the first time Duganella spp. associated with the rhizosphere of woody plants in Mediterranean environments that are able to produce violacein, a blue-purple secondary metabolite of considerable biotechnological interest. Based on physiological and biochemical characterization and phylogenetic analysis of different genes including 16S rRNA, gyrB, and vioA (implicated in the synthesis of violacein), the seven Duganella spp. strains isolated and studied were differentiated according to their host of origin (wild versus cultivated olives) and potentially might belong to new species. All the Duganella spp. strains produced violacein in vitro, with natural production levels significantly higher than that previously reported for other violacein-producing bacteria without optimizing growing conditions. The important biological, medical, and industrial applications of violacein make these bacteria good candidates for their biotechnological exploitation because low violacein yields are considered as one of the main limitations of using wild-type strains for extensive exploitation and pigment production. Independent of violacein production, purple-pigmented strains from olives showed proteolytic and lipolytic activities and a weak siderophore production. No in vitro inhibitory activity was demonstrated for bacteria or crude violacein filtrates against plant-pathogenic Gram-negative bacteria and fungi, but they did inhibit Gram-positive bacteria.

Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core

Violacein is a natural violet pigment produced by several gram-negative bacteria, including Chromobacterium violaceum, Janthinobacterium lividum, and Pseudoalteromonas tunicata D2, among others. This pigment has potential medical applications as antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs. The structure of violacein consists of three units: a 5-hydroxyindole, an oxindole, and a 2-pyrrolidone. The biosynthetic origins of hydrogen, nitrogen, and carbon in the pyrrolidone nucleus were established by feeding experiments using various stable isotopically labeled tryptophans (Trps). Pro-S hydrogen of CH(2) at the 3-position of Trp is retained during biosynthesis. The nitrogen atom is exclusively from the α-amino group, and the skeletal carbon atoms originate from the side chains of the two Trp molecules. All three oxygen atoms in the violacein core are derived from molecular oxygen. The most interesting biosynthetic mechanism is the 1,2-shift of the indole nucleus on the left side of the violacein scaffold. The alternative Trp molecule is directly incorporated into the right side of the violacein core. This indole shift has been observed only in violacein biosynthesis, despite the large number of natural products having been isolated. There were remarkable advances in biosynthetic studies in 2006-2008. During the 3 years, most of the intermediates and the complete pathway were established. Two independent processes are involved: the enzymatic process catalyzed by the five proteins VioABCDE or the alternative nonenzymatic oxidative decarboxylation reactions. The X-ray crystallographic structure of VioE that mediates the indole rearrangement reaction was recently identified, and the mechanism of the indole shift is discussed here.

Characterization of a gene cluster and its putative promoter region for violacein biosynthesis in Pseudoalteromonas sp. 520P1

Violacein, a purple pigment produced by some Gram-negative bacteria, has various physiological properties, such as antitrypanosomal and antitumoral activities. A gene cluster that encodes five enzymes, VioA-VioE, is responsible for synthesizing violacein. The expression of these enzymes is known to be regulated by a quorum sensing mechanism in Chromobacterium violaceum and Pseudoalteromonas sp. 520P1. To clarify the molecular mechanism of regulation of violacein synthesis, we cloned and characterized the gene cluster from Pseudoalteromonas sp. 520P1. A fosmid library of strain 520P1 was constructed and clones containing the gene cluster were isolated. The gene cluster was 7383 bp in length and encoded five enzyme genes, vioA-vioE. A putative promoter sequence was predicted in the upstream region of the cluster. In the promoter region, two contiguous palindromic sequences, a possible quorum sensing regulatory site, were found. However, the isolated Escherichia coli clones harboring the gene cluster and its upstream region were unable to produce violacein probably due to the lack of quorum sensing machinery for expression. To further examine the ability of vioA-vioE genes to synthesize violacein in vivo, the upstream promoter region was removed from the cluster and heterologous expression of the treated cluster was performed in E. coli using a recombinant pET vector with T7 promoter. Purple pigment was expressed, and the pigment was identified to be violacein using ultraviolet and visible light and HPLC analysis. These results will contribute to further studies regarding violacein biosynthesis and its mass production.

Violacein-producing Collimonas sp. from the sea surface microlayer of costal waters in Trøndelag, Norway

A new strain belonging to the genus Collimonas was isolated from the sea surface microlayer off the coast of Trøndelag, Norway. The bacterium, designated Collimonas CT, produced an antibacterial compound active against Micrococcus luteus. Subsequent studies using LC-MS identified this antibacterial compound as violacein, known to be produced by several marine-derived bacteria. Fragments of the violacein biosynthesis genes vioA and vioB were amplified by PCR from the Collimonas CT genome and sequenced. Phylogenetic analysis of these sequences demonstrated close relatedness of the Collimonas CT violacein biosynthetic gene cluster to those in Janthinobacterium lividum and Duganella sp., suggesting relatively recent horizontal gene transfer. Considering diverse biological activities of violacein, Collimonas CT shall be further studied as a potential producer of this compound.