The squalene route to C30 carotenoid biosynthesis and the origins of carotenoid biosynthetic pathways

Substrate utilization and secondary metabolite biosynthesis in the phylum Planctomycetota

The phylum Planctomycetota is changing our understanding of bacterial metabolism, driving critical biogeochemical processes through the transformation of complex polymeric substrates into valuable bioactive compounds. Sophisticated methods for cultivation, genome sequencing and genetic strain engineering developed in the last two decades have stimulated detailed studies on cell propagation, metabolic capabilities and potential applications of phylum members beyond the mere isolation and characterization of novel taxa. This review synthesizes recent advances in understanding the Planctomycetota physiology with a focus on the degradation of phototroph-derived polysaccharides, anaerobic ammonium oxidation (anammox) and biosynthesis of secondary metabolites. New data especially collected over the last 5 years justifies more intensive research of the yet uncharacterized pathways of substrate uptake and utilization, as well as genome mining-assisted bioprospection to exploit the phylum's chemical repertoire. KEY POINTS: • Planctomycetes can degrade high-molecular-weight sugars produced by algae • Anaerobic ammonium oxidation (anammox) is used in technical applications • The first secondary metabolites were discovered in the last 5 years.

Evolution and ecology of C30 carotenoid synthesis in Lactobacillaceae and application of pigmented lactobacilli in pasta production

Pasta is a staple food in many parts of the world. A bright yellow colour of pasta is preferred by consumers. However, the colour is easily degraded during pasta processing. In a sourdough used for pasta production, we identified the pigmented Fructilactobacillus spp. FUA 3913, which represents a novel species that remains to be described ,and carries genes for the carotenoid-producing enzymes CrtM and CrtN in its genome. HPLC and spectral analysis identified the carotenoid as 4,4'-diaponeurosporene which is also produced by other lactobacilli expressing CrtM and CrtN. The topology of the CrtM/N trees does not match the phylogeny of the organisms, indicating that the enzymes were acquired by horizontal gene transfer. Pigmentation is frequent in insect-associated lactobacilli and lactobacilli that are part of the phyllosphere. Pigmented heterofermentative lactobacilli may enhance the yellow colour of durum semolina pasta by two mechanisms, first, by producing carotenoids and second, by preventing lipoxygenase-mediated degradation of durum carotenoids during dough mixing and extrusion. The comparison of the influence of fermentation with the non-pigmented, homofermentative Lactiplantibacillus plantarum, the non-pigmented heterofermentative Fructilactobacillus sanfranciscensis and the pigmented, heterofermentative Fructilactobacillus spp. FUA3913 indicated that inhibition of lipid oxidation is more relevant for the colour of pasta. In summary, our study provides novel insights into the evolution of C30 carotenoid and ecology of lactobacilli, and documents the use of pigmented lactobacilli to enhance the yellow colour of fermented foods.

Novel tools for genomic modification and heterologous gene expression in the phylum Planctomycetota

Members of the phylum Planctomycetota possess a plethora of intriguing and hitherto underexplored features including an enlarged periplasmic space, asymmetric cell division ("budding"), and a mostly undiscovered small molecule portfolio. Due to the large phylogenetic distance to frequently used and easily genetically accessible model bacteria, most of the established genetic tools are not readily applicable for the here-investigated bacterial phylum. However, techniques for targeted gene inactivation and the introduction of heterologous genes are crucial to investigate the cell biology in the phylum in greater detail. In this study, the targeted genomic modification of model planctomycetes was achieved by enforcing two types of homologous recombination events: simultaneous double homologous recombination for the deletion of coding regions and insertion-duplication mutagenesis for the introduction of foreign DNA into the chromosome. Upon testing the expression of commonly used fluorescent protein-encoding genes, many of the tested native promoters could not be harnessed for variation of the expression strength. Since also four commonly used inducible gene expression systems did not work in the tested model strain Planctopirus limnophila, a native rhamnose-dependent transcriptional regulator/promoter pair was established as an inducible expression system. The expanded molecular toolbox will allow the future characterization of genome-encoded features in the understudied phylum. KEY POINTS: • Two recombination methods were used for the genetic modification of planctomycetes • Commonly used fluorescent proteins are functional in model planctomycetes • A rhamnose-dependent regulator was turned into an inducible expression system.

"Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature"

The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.

Distribution of C30 carotenoid biosynthesis genes suggests habitat adaptation function in insect-adapted and nomadic Lactobacillaceae

Carotenoids are membrane-bound pigments that are essential for photosynthesizing plants and algae, widely applied in food, feed and cosmetics due to their antioxidant and anti-inflammatory properties. The production of carotenoids, particularly C30 forms, has been documented in some non-photosynthetic prokaryotes. However, their function, distribution and ecology beyond photosynthesizing organisms remains understudied. In this study, we performed an eco-evolutionary analysis of terpenoid biosynthetic gene clusters in the Lactobacillaceae family, screening 4203 dereplicated genomes for terpenoid biosynthesis genes, and detected crtMN genes in 28/361 (7.7%) species across 14/34 (41.2%) genera. These genes encode key enzymes for producing the C30 carotenoid 4,4'-diaponeurosporene. crtMN genes appeared to be convergently gained within Fructilactobacillus and horizontally transferred across species and genera, including Lactiplantibacillus to Levilactobacillus. The phenotype was confirmed in 87% of the predicted crtMN gene carriers (27/31). Nomadic and insect-adapted species, particularly those isolated from vegetable fermentations, e.g., Lactiplantibacillus, and floral habitats, e.g., Fructilactobacillus, contained crtMN genes, while vertebrate-associated species, including vaginal associated species, lacked this trait. This habitat association aligned with the observations that C30 carotenoid-producing strains were more resistant to UV-stress. In summary, C30 carotenoid biosynthesis plays a role in habitat adaptation and is scattered across Lactobacillaceae in line with this habitat adaptation.

Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface

On the deep and dark seafloor, a cryptic and yet untapped microbial diversity flourishes around hydrothermal vent systems. This remote environment of difficult accessibility exhibits extreme conditions, including high pressure, steep temperature- and redox gradients, limited availability of oxygen and complete darkness. In this study, we analysed the genomes of three aerobic strains belonging to the phylum Planctomycetota that were isolated from two deep-sea iron- rich hydroxide deposits with low temperature diffusive vents. The vents are located in the Arctic and Pacific Ocean at a depth of 600 and 1,734 m below sea level, respectively. The isolated strains Pr1dT, K2D and TBK1r were analyzed with a focus on genome-encoded features that allow phenotypical adaptations to the low temperature iron-rich deep-sea environment. The comparison with genomes of closely related surface-inhabiting counterparts indicates that the deep-sea isolates do not differ significantly from members of the phylum Planctomycetota inhabiting other habitats, such as macroalgae biofilms and the ocean surface waters. Despite inhabiting extreme environments, our "deep and dark"-strains revealed a mostly non-extreme genome biology.

Sustainable production of C50 carotenoid bacterioruberin from methane using soil-enriched microbial consortia

Bacterioruberin is widely used in medicine, food, and cosmetics owing to its prominent characteristics of antioxidants and bioactivities. Bioconversion of methane into bacterioruberin is a promising way to address biomanufacturing substrate costs and greenhouse gas emissions but has not been achieved yet. Herein, this study aimed to upcycle methane to bacterioruberin by microbial consortia. The microbial consortia consist of Methylomonas and Methylophilus capable of synthesizing carotenoids from methane was firstly enriched from paddy soil. Through this microbial community, methane was successfully converted into C50 bacterioruberin for the first time. The bioconversion process was then optimized by the response surface methodology. Finally, the methane-derived bacterioruberin reached a record yield of 280.88 ± 2.94 μg/g dry cell weight. This study presents a cost-effective and eco-friendly approach for producing long-chain carotenoids from methane, offering a significant advancement in the direct conversion of greenhouse gases into value-added products.

Biosynthesis of carotenoids in Azospirillum brasilense Cd is mediated via squalene (C30) route

Azospirillum brasilense is a non-photosynthetic α-Proteobacteria, belongs to the family of Rhodospirillaceae and produces carotenoids to protect itself from photooxidative stress. In this study, we have used Resonance Raman Spectra to show similarity of bacterioruberins of Halobacterium salinarum to that of A. brasilense Cd. To navigate the role of genes involved in carotenoid biosynthesis, we used mutational analysis to inactivate putative genes predicted to be involved in carotenoid biosynthesis in A. brasilense Cd. We have shown that HpnCED enzymes are involved in the biosynthesis of squalene (C30), which is required for the synthesis of carotenoids in A. brasilense Cd. We also found that CrtI and CrtP desaturases were involved in the transformation of colorless squalene into the pink-pigmented carotenoids. This study elucidates role of some genes which constitute very pivotal role in biosynthetic pathway of carotenoid in A. brasilense Cd.

Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes

The human intestinal microbiota that comprise over 1,000 species thrive in dark and anaerobic environments. They are recognized for the production of diverse low-molecular-weight metabolites crucial to human health and diseases. Carotenoids, low-molecular-weight pigments known for their antioxidative activity, are delivered to humans through oral intake. However, it remains unclear whether human intestinal bacteria biosynthesize carotenoids as part of the in-situ microbiota. In this study, we investigated carotenoid synthesis genes in various human gut and probiotic bacteria. As a result, novel candidates, the crtM and crtN genes, were identified in the carbon monoxide-utilizing gut anaerobe Eubacterium limosum and the lactic acid bacterium Leuconostoc mesenteroides subsp. mesenteroides. These gene candidates were isolated, introduced into Escherichia coli, which synthesized a carotenoid substrate, and cultured aerobically. Structural analysis of the resulting carotenoids revealed that the crtM and crtN gene candidates of E. limosum and L. mesenteroides mediate the production of 4,4'-diaponeurosporene through 15-cis-4,4'-diapophytoene. Evaluation of the crtE-homologous genes in these bacteria indicated their non-functionality for C40-carotenoid production. E. limosum and L. mesenteroides, along with the known carotenogenic lactic acid bacterium Lactiplantibacillus plantarum, were observed to produce no carotenoids under strictly anaerobic conditions. The two lactic acid bacteria synthesized detectable levels of 4,4'-diaponeurosporene under semi-aerobic conditions. The findings highlight that the obligate anaerobe E. limosum retains aerobically functional C30-carotenoid biosynthesis genes, potentially with no immediate self-utility, suggesting an evolutionary direction in carotenoid biosynthesis. (229 words).

Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany

In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6%. Optimal growth of strain SH412T occurs at pH 7.0-7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division ("budding") and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.

A type III polyketide synthase cluster in the phylum Planctomycetota is involved in alkylresorcinol biosynthesis

Members of the bacterial phylum Planctomycetota have recently emerged as promising and for the most part untapped sources of novel bioactive compounds. The characterization of more than 100 novel species in the last decade stimulated recent bioprospection studies that start to unveil the chemical repertoire of the phylum. In this study, we performed systematic bioinformatic analyses based on the genomes of all 131 described members of the current phylum focusing on the identification of type III polyketide synthase (PKS) genes. Type III PKSs are versatile enzymes involved in the biosynthesis of a wide array of structurally diverse natural products with potent biological activities. We identified 96 putative type III PKS genes of which 58 are encoded in an operon with genes encoding a putative oxidoreductase and a methyltransferase. Sequence similarities on protein level and the genetic organization of the operon point towards a functional link to the structurally related hierridins recently discovered in picocyanobacteria. The heterologous expression of planctomycetal type III PKS genes from strains belonging to different families in an engineered Corynebacterium glutamicum strain led to the biosynthesis of pentadecyl- and heptadecylresorcinols. Phenotypic assays performed with the heterologous producer strains and a constructed type III PKS gene deletion mutant suggest that the natural function of the identified compounds differs from that confirmed in other bacterial alkylresorcinol producers. KEY POINTS: • Planctomycetal type III polyketide synthases synthesize long-chain alkylresorcinols. • Phylogenetic analyses suggest an ecological link to picocyanobacterial hierridins. • Engineered C. glutamicum is suitable for an expression of planctomycete-derived genes.

Mining natural products for advanced biofuels and sustainable bioproducts

Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.

All Kinds of Sunny Colors Synthesized from Methane: Genome-Encoded Carotenoid Production by Methylomonas Species

Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display fast growth on methane or natural gas, are of particular interest as potential producers of a feed protein enriched with carotenoids. Until recently, Methylomonas strain 16a and Methylomonas sp. ZR1 remained the only representatives of the genus for which detailed carotenoid profile was determined. In this study, we analyzed the genome sequences of five strains of Methylomonas species whose pigmentation varied from white and yellow to orange and red, and identified carotenoids produced by these bacteria. Carotenoids synthesized using four pigmented strains included C30 fraction, primarily composed of 4,4'-diaplycopene-4,4'-dioic acid and 4,4'-diaplycopenoic acid, as well as C40 fraction with the major compound represented by 1,1'-dihydroxy-3,4-didehydrolycopene. The genomes of studied Methylomonas strains varied in size between 4.59 and 5.45 Mb and contained 4201-4735 protein-coding genes. These genomes and 35 reference Methylomonas genomes available in the GenBank were examined for the presence of genes encoding carotenoid biosynthesis. Genomes of all pigmented Methylomonas strains harbored genes necessary for the synthesis of 4,4'-diaplycopene-4,4'-dioic acid. Non-pigmented "Methylomonas montana" MW1T lacked the crtN gene required for carotenoid production. Nearly all strains possessed phytoene desaturases, which explained their ability to naturally synthesize lycopene. Thus, members of the genus Methylomonas can potentially be considered as producers of C30 and C40 carotenoids from methane.

Stratiformator vulcanicus gen. nov., sp. nov., a marine member of the family Planctomycetaceae isolated from a red biofilm in the Tyrrhenian Sea close to the volcanic island Panarea

A novel planctomycetal strain, designated Pan189T, was isolated from biofilm material sampled close to Panarea Island in the Tyrrhenian Sea. Cells of strain Pan189T are round grain rice-shaped, form pink colonies and display typical planctomycetal characteristics including asymmetric cell division through polar budding and presence of crateriform structures. Cells bear a stalk opposite to the division pole and fimbriae cover the cell surface. Strain Pan189T has a mesophilic (optimum at 24 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. Under laboratory-scale cultivation conditions, it reached a generation time of 102 h (µmax = 0.0068 h-1), which places the strain among the slowest growing members of the phylum Planctomycetota characterized so far. The genome size of the strain is with 5.23 Mb at the lower limit among the family Planctomycetaceae (5.1-8.9 Mb). Phylogenetically, the strain represents a novel genus and species in the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. We propose the name Stratiformator vulcanicus gen. nov., sp. nov. for the novel taxon, that is represented by the type strain Pan189T (= DSM 101711 T = CECT 30699 T).

Characterization of C30 carotenoid and identification of its biosynthetic gene cluster in Methylobacterium extorquens AM1

Methylobacterium species, the representative bacteria distributed in phyllosphere region of plants, often synthesize carotenoids to resist harmful UV radiations. Methylobacterium extorquens is known to produce a carotenoid pigment and recent research revealed that this carotenoid has a C30 backbone. However, its exact structure remains unknown. In the present study, the carotenoid produced by M. extorquens AM1 was isolated and its structure was determined as 4-[2-O-11Z-octadecenoyl-β-glucopyranosyl]-4,4'-diapolycopenedioc acid (1), a glycosylated C30 carotenoid. Furthermore, the genes related to the C30 carotenoid synthesis were investigated. Squalene, the precursor of the C30 carotenoid, is synthesized by the co-occurrence of META1p1815, META1p1816 and META1p1817. Further overexpression of the genes related to squalene synthesis improved the titer of carotenoid 1. By using gene deletion and gene complementation experiments, the glycosyltransferase META1p3663 and acyltransferase META1p3664 were firstly confirmed to catalyze the tailoring steps from 4,4'-diapolycopene-4,4'-dioic acid to carotenoid 1. In conclusion, the structure and biosynthetic genes of carotenoid 1 produced by M. extorquens AM1 were firstly characterized in this work, which shed lights on engineering M. extorquens AM1 for producing carotenoid 1 in high yield.

Anti-Inflammatory and Antioxidant Properties of Squalene in Copper Sulfate-Induced Inflammation in Zebrafish (Danio rerio)

Long-term or excessive oxidative stress can cause serious damage to fish. Squalene can be added to feed as an antioxidant to improve the body constitution of fish. In this study, the antioxidant activity was detected by 2,2-diphenyl-1-acrylhydrazyl (DPPH) test and fluorescent probe (dichloro-dihydro-fluorescein diacetate). Transgenic Tg (lyz: DsRed2) zebrafish were used to evaluate the effect of squalene on CuSO₄-induced inflammatory response. Quantitative real-time reverse transcription polymerase chain reaction was used to examine the expression of immune-related genes. The DPPH assay demonstrated that the highest free radical scavenging exerted by squalene was 32%. The fluorescence intensity of reactive oxygen species (ROS) decreased significantly after 0.7% or 1% squalene treatment, and squalene could exert an antioxidative effect in vivo. The number of migratory neutrophils in vivo was significantly reduced after treatment with different doses of squalene. Moreover, compared with CuSO₄ treatment alone, treatment with 1% squalene upregulated the expression of sod by 2.5-foldand gpx4b by 1.3-fold to protect zebrafish larvae against CuSO₄-induced oxidative damage. Moreover, treatment with 1% squalene significantly downregulated the expression of tnfa and cox2. This study showed that squalene has potential as an aquafeed additive to provide both anti-inflammatory and antioxidative properties.