Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis

Melanin: Nature's 4th bioorganic polymer

The pigments known as the melanins are widely recognized for their responsibility in the coloration of human skin, eyes, hair, and minimising the harmful effects of solar ultraviolet radiation. But specialists are aware that the melanins are present in all living kingdoms, barring viruses, and have functionality that extends beyond neutralizing ionising radiation. The ubiquitous presence of melanin in almost all human organs, recognized in recent years, as well as the presence of melanin in organisms that are evolutionarily distant from each other, indicate the fundamental importance of this class of material for all life forms. In this review, we argue for the need to accept melanins as the fourth primordial class of biological polymers, along with nucleic acids, proteins and polysaccharides. We consistently compare the properties of these canonical biological polymers with the properties of melanin and highlight key features that fundamentally distinguish melanins, their function and its mysteries.

Effect of Melanization on Thallus Microstructure in the Lichen Lobaria pulmonaria

Lichens often grow in microhabitats where they experience severe abiotic stresses. Some species respond to high UV radiation by synthesizing dark brown melanic pigments in the upper cortex. However, unlike the melanized structures of non-lichenized fungi, the morphology of the melanic layer in lichens remains unstudied. Here, we analyzed the morphology, ultrastructure, and elemental composition of the melanized layer in UV-exposed thalli of the lichen Lobaria pulmonaria (L.) Hoffm. Using light microscopy, we detected a pigmented layer sensitive to staining with 3,4-L-dihydroxyphenylalanine, a precursor of eumelanin, in the upper cortex of melanized thalli. Analysis of cross-sections of melanized thalli using scanning electron microscopy revealed that melanin-like granules are deposited into the hyphal lumens. Melanized thalli also possessed thicker hyphal cell walls compared to pale thalli. Energy-dispersive X-ray spectroscopy analysis of the elemental composition of the hyphal walls and extracted melanin indicated that the type of melanin synthesized by L. pulmonaria is eumelanin. Transmission electron microscopy was used to show that during melanization melanosome-like dark vesicles are transported to the cell surface and secreted into the cell walls of the fungal hyphae. Results from this study provide new insights into the effects of melanin synthesis on the microstructure of lichen thalli.

Production and characterization of crude laccase from Irpex sp. JS7 that decolorizes synthetic and natural melanin

The JS7 strain, isolated from an old forest tree, produces extracellular enzymes that decolorize synthetic and natural melanin from human hair. Phylogenetic analysis based on the internal transcribed spacer (ITS) sequence indicated that JS7 belongs to the genus Irpex. The JS7 strain has laccase activity while it lacks manganese and lignin peroxidase activity, which suggests that the JS7 strain melanin decolorization activity originated from laccase. Laccase production from the Irpex sp. JS7 improved three-fold in the presence of veratryl alcohol, compared to without an inducer. The optimum pH and temperature for melanin decolorization were 7.5 and 40 °C, respectively. The crude enzyme half-life at 25 °C was about 100 days, and it had high storage stability. The melanin decolorization reaction rate by the crude enzyme conformed to typical enzyme kinetic principles. In the presence of syringaldehyde as a redox mediator, the melanin decolorization rate was 75% within 5 days, similar to the decolorization percentage obtained using the enzyme alone. Based on these results, the Irpex sp. JS7 enzyme is suitable for use in melanin decolorization by whitening agents in the cosmetics industry.

Advances in laccase-triggered anabolism for biotechnology applications

This is the first comprehensive overview of laccase-triggered anabolism from fundamental theory to biotechnology applications. Laccase is a typical biological oxidordeuctase that induces the one-electronic transfer of diverse substrates for engendering four phenoxy radicals with concomitant reduction of O₂ into 2H₂O. In vivo, laccase can participate in anabolic processes to create multifarious functional biopolymers such as fungal pigments, plant lignins, and insect cuticles, using mono/polyphenols and their derivatives as enzymatic substrates, and is thus conducive to biological tissue morphogenesis and global carbon storage. Exhilaratingly, fungal laccase has high redox potential (E° = 500-800 mV) and thermodynamic efficiency, making it a remarkable candidate for utilization as a versatile catalyst in the green and circular economy. This review elaborates the anabolic mechanisms of laccase in initiating the polymerization of natural phenolic compounds and their derivatives in vivo via radical-based self/cross-coupling. Information is also presented on laccase immobilization engineering that expands the practical application ranges of laccase in biotechnology by improving the enzymatic catalytic activity, stability, and reuse rate. Particularly, advances in biotechnology applications in vitro through fungal laccase-triggered macromolecular biosynthesis may provide a key research direction beneficial to the rational design of green chemistry.

Influence of secondary metabolites on surface chemistry and metal adsorption of a devitalized lichen biomonitor

Despite the broad use of lichens as biomonitors of airborne trace elements, the surface chemistry and metal adsorption parameters of these organisms are still poorly known. The current investigation is aimed at (i) quantifying the acid-base surface properties and the first-order physical-chemical parameters of Cu2+ and Zn2+ adsorption of devitalized Pseudevernia furfuracea, a lichen commonly used in biomonitoring of airborne trace elements, and (ii) comparing the results with those available for moss biomonitors. Equilibrium constants and metal-binding site concentrations were calculated with a thermodynamic model by taking into account the presence/absence of ancillary extracellular cell wall compounds, namely melanin and acetone-soluble lichen substances. An acid-base titration experiment performed in the pH range of 3-10 showed that melanised and non-melanised P. furfuracea samples have lower pHPZC (3.53-3.99) and higher metal-binding site concentrations (0.96-1.20 mmol g-1) compared to that of the mosses investigated so far at the same experimental conditions. Melanin biosynthesis increased the content of carboxyl and phosphoryl groups and reduces that of amine/polyphenols. Cu2+ and Zn2+ adsorption was unaffected by the degree of melanisation while the removal of extracellular lichen substances slightly decreased Zn2+ adsorption. Although Cu2+ and Zn2+ adsorption parameters related to P. furfuracea surfaces were 3 times lower than in the mosses, lichen samples adsorbed the same amount of Cu2+ and 30% more Zn2+. The present study contributes in understanding the role of ancillary cell wall compounds in Cu2+ and Zn2+ adsorption in a model lichen. It also provides a first comparison between the surface physico-chemical characteristics of lichens and mosses frequently used as biomonitors of trace elements.

Computation-Driven Analysis of Model Polyextremo-tolerant Fungus Exophiala dermatitidis: Defensive Pigment Metabolic Costs and Human Applications

The polyextremotolerant black yeast Exophiala dermatitidis is a tractable model system for investigation of adaptations that support growth under extreme conditions. Foremost among these adaptations are melanogenesis and carotenogenesis. A particularly important question is their metabolic production cost. However, investigation of this issue has been hindered by a relatively poor systems-level understanding of E. dermatitidis metabolism. To address this challenge, a genome-scale model (iEde2091) was developed. Using iEde2091, carotenoids were found to be more expensive to produce than melanins. Given their overlapping protective functions, this suggests that carotenoids have an underexplored yet important role in photo-protection. Furthermore, multiple defensive pigments with overlapping functions might allow E. dermatitidis to minimize cost. Because iEde2091 revealed that E. dermatitidis synthesizes the same melanins as humans and the active sites of the key tyrosinase enzyme are highly conserved this model may enable a broader understanding of melanin production across kingdoms.

Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses

Laccases belong to ligninolytic enzymes and play important roles in various biological processes of filamentous fungi, including fruiting-body formation and lignin degradation. The process of fruiting-body development in Lentinula edodes is complex and is greatly affected by environmental conditions. In this paper, 14 multicopper oxidase-encoding (laccase) genes were analyzed in the draft genome sequence of L. edodes strain W1-26, followed by a search of multiple stress-related Cis-elements in the promoter region of these laccase genes, and then a transcription profile analysis of 14 laccase genes (Lelcc) under the conditions of different carbon sources, temperatures, and photoperiods. All laccase genes were significantly regulated by varying carbon source materials. The expression of only two laccase genes (Lelcc5 and Lelcc6) was induced by sodium-lignosulphonate and the expression of most laccase genes was specifically upregulated in glucose medium. Under different temperature conditions, the expression levels of most laccase genes decreased at 39 °C and transcription was significantly increased for Lelcc1, Lelcc4, Lelcc5, Lelcc9, Lelcc12, Lelcc13, and Lelcc14 after induction for 24 h at 10 °C, indicating their involvement in primordium differentiation. Tyrosinase, which is involved in melanin synthesis, was clustered with the same group as Lelcc4 and Lelcc7 in all the different photoperiod treatments. Meanwhile, five laccase genes (Lelcc8, Lelcc9, Lelcc12, Lelcc13, and Lelcc14) showed similar expression profiles to that of two blue light receptor genes (LephrA and LephrB) in the 12 h light/12 h dark treatment, suggesting the involvement of laccase genes in the adaptation process of L. edodes to the changing environment and fruiting-body formation. This study contributes to our understanding of the function of the different Lelcc genes and facilitates the screening of key genes from the laccase gene family for further functional research.

Melanin biosynthesis in bacteria, regulation and production perspectives

The production of black pigments in bacteria was discovered more than a century ago and related to tyrosine metabolism. However, their diverse biological roles and the control of melanin synthesis in different bacteria have only recently been investigated. The broad distribution of these pigments suggests that they have an important role in a variety of organisms. Melanins protect microorganisms from many environmental stress conditions, ranging from ultraviolet radiation and toxic heavy metals to oxidative stress. Melanins can also affect bacterial interactions with other organisms and are important in pathogenesis and survival in many environments. Bacteria produce several types of melanin through dedicated pathways or as a result of enzymatic imbalances in altered metabolic routes. The control of the melanin synthesis in bacteria involves metabolic and transcriptional regulation, but many aspects remain still largely unknown. The diverse properties of melanins have spurred a large number of applications, and recent efforts have been done to produce the pigment at biotechnologically relevant scales.

An Evolutionary Perspective of Dopachrome Tautomerase Enzymes in Metazoans

Melanin plays a pivotal role in the cellular processes of several metazoans. The final step of the enzymically-regulated melanin biogenesis is the conversion of dopachrome into dihydroxyindoles, a reaction catalyzed by a class of enzymes called dopachrome tautomerases. We traced dopachrome tautomerase (DCT) and dopachrome converting enzyme (DCE) genes throughout metazoans and we could show that only one class is present in most of the phyla. While DCTs are typically found in deuterostomes, DCEs are present in several protostome phyla, including arthropods and mollusks. The respective DCEs belong to the yellow gene family, previously reported to be taxonomically restricted to insects, bacteria and fungi. Mining genomic and transcriptomic data of metazoans, we updated the distribution of DCE/yellow genes, demonstrating their presence and active expression in most of the lophotrochozoan phyla as well as in copepods (Crustacea). We have traced one intronless DCE/yellow gene through most of the analyzed lophotrochozoan genomes and we could show that it was subjected to genomic diversification in some species, while it is conserved in other species. DCE/yellow was expressed in most phyla, although it showed tissue specific expression patterns. In the parasitic copepod Mytilicola intestinalis DCE/yellow even belonged to the 100 most expressed genes. Both tissue specificity and high expression suggests that diverse functions of this gene family also evolved in other phyla apart from insects.

Melanosomes: Biogenesis, Properties, and Evolution of an Ancient Organelle

Melanosomes are organelles that produce and store melanin, a widespread biological pigment with a unique suite of properties including high refractive index, semiconducting capabilities, material stiffness, and high fossilization potential. They are involved in numerous critical biological functions in organisms across the tree of life. Individual components such as melanin chemistry and melanosome development have recently been addressed, but a broad synthesis is needed. Here, we review the hierarchical structure, development, functions, and evolution of melanosomes. We highlight variation in melanin chemistry and melanosome morphology and how these may relate to function. For example, we review what is known of the chemical differences between different melanin types (eumelanin, pheomelanin, allomelanin) and whether/how melanosome morphology relates to chemistry and color. We integrate the distribution of melanin across living organisms with what is known from the fossil record and produce hypotheses on its evolution. We suggest that melanin was present in life forms early in evolutionary history and that melanosomes evolved at the origin of organelles. Throughout, we discuss the (sometimes gaping) holes in our knowledge and suggest areas that need particular attention as we move forward in our understanding of these still-mysterious organelles and the materials that they contain.

Morphological and biological characterization of a light-colored mutant in the multicolored Asian lady beetle, Harmonia axyridis

Insect cuticle color formed with melanin pigments has numerous types of mutants which usually cause pleiotropic effects. Melanism has been widely studied, but mutants with light-colored phenotype as well as the consequent fitness changes have rarely been reported.Here, in the laboratory strain of Harmonia axyridis, we found a novel mutant gr and confirmed that the mutation was inherited in a simple Mendelian autosomal recessive manner. This mutant (HAM) continuously displayed a light-colored pigmentation versus dark blackish in the wild phenotype (HAW). L-DOPA and dopamine are melanin precursors, and less L-DOPA was present in the cuticle of larval and adult HAM mutants compared to HAW wild type, but more dopamine was detected in the larval cuticle of HAM (p ≤ 0.0235). For the orange background of elytra, the composition as well as total concentration of carotenoids was different between HAM and HAW, which resulted in significantly lower saturation value but significantly higher hue value in HAM than in HAW (p < 0.0001).Extensive fitness changes were detected in HAM. (a) HAM larvae had similar predation capacity and preimaginal development time as HAW, but the newly emerged adults were much smaller (p < 0.0001). (b) Both fecundity and egg hatch rate in cross ♀(HAM) × ♂(HAM) were significantly lower than those in ♀(HAW) × ♂(HAW) (p ≤ 0.0087), but were not different with those in ♀(HAW) × ♂(HAM).

A population of wheat multiple synthetic derivatives: an effective platform to explore, harness and utilize genetic diversity of Aegilops tauschii for wheat improvement

The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding. Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding.

Toward Understanding the Repeated Occurrence of Associations between Melanin-Based Coloration and Multiple Phenotypes

Melanin is the most widespread pigment in organisms. Melanin-based coloration has been repeatedly observed to be associated with the same traits and in the same direction in different vertebrate and insect species. However, whether any factors that are common to different taxa account for the repeated evolution of melanin-phenotype associations remains unclear. We propose to approach this question from the perspective of convergent and parallel evolution to clarify to what extent different species have evolved the same associations owing to a shared genetic basis and being subjected to similar selective pressures. Our current understanding of the genetic basis of melanin-phenotype associations allows for both convergent and parallel evolution, but this understanding is still limited. Further research is needed to clarify the generality and interdependencies of the different proposed mechanisms (supergenes, pleiotropy based on hormones, or neural crest cells). The general ecological scenarios whereby melanin-based coloration is under selection-protection from ultraviolet radiation, thermoregulation in cold environments, or as a signal of social status-offer a good opportunity to study how melanin-phenotype associations evolve. Reviewing these scenarios shows that some traits associated with melanin-based coloration might be selected together with coloration by also favoring adaptation but that other associated traits might impede adaptation, which may be indicative of genetic constraints. We therefore encourage further research on the relative roles that selection and genetic constraints play in shaping multiple melanin-phenotype associations. Placed into a phylogenetic context, this will help clarify to what extent these associations result from convergent or parallel evolutionary processes and why melanin-phenotype associations are so common across the tree of life.

Loss of bcbrn1 and bcpks13 in Botrytis cinerea Not Only Blocks Melanization But Also Increases Vegetative Growth and Virulence

Botrytis cinerea is a necrotrophic pathogen that causes gray mold disease in a broad range of plants. Dihydroxynaphthalene (DHN) melanin is a major component of the extracellular matrix of B. cinerea, but knowledge of the exact role of melanin biosynthesis in this pathogen is unclear. In this study, we characterize two genes in B. cinerea, bcpks13 and bcbrn1, encoding polyketide synthase and tetrahydroxynaphthalene (THN) reductases, respectively, and both have predicted roles in DHN melanin biosynthesis. The ∆bcpks13 and ∆bcbrn1 mutants show white and orange pigmentation, respectively, and the mutants are also deficient in conidiation in vitro but show enhanced growth rates and virulence on hosts. Moreover, the mutants display elevated acidification of the complete medium (CM), probably due to oxalic acid secretion and secretion of cell wall-degrading enzymes, and preferably utilize plant cell-wall components as carbon sources for mycelium growth in vitro. In contrast, overexpression of bcbrn1 (OE::bcbrn1 strain) results in attenuated hydrolytic enzyme secretion, acidification ability, and virulence. Taken together, these results indicate that bcpks13 and bcbrn1 participate in diverse cellular and developmental processes, such as melanization and conidiation in B. cinerea in vitro, but they negatively regulate the virulence of this pathogen.

Melanin-Like Pigment Synthesis by Soil Bacillus weihenstephanensis Isolates from Northeastern Poland

Although melanin is known for protecting living organisms from harmful physical and chemical factors, its synthesis is rarely observed among endospore-forming Bacillus cereus sensu lato. Here, for the first time, we reported that psychrotolerant Bacillus weihenstephanensis from Northeastern Poland can produce melanin-like pigment. We assessed physicochemical properties of the pigment and the mechanism of its synthesis in relation to B. weihenstephanensis genotypic and phenotypic characteristics. Electron paramagnetic resonance (EPR) spectroscopy displayed a stable free radical signal of the pigment from environmental isolates which are consistent with the commercial melanin. Fourier transform infrared spectroscopy (FT-IR) and physicochemical tests indicated the phenolic character of the pigment. Several biochemical tests showed that melanin-like pigment synthesis by B. weihenstephanensis was associated with laccase activity. The presence of the gene encoding laccase was confirmed by the next generation whole genome sequencing of one B. weihenstephanensis strain. Biochemical (API 20E and 50CHB tests) and genetic (Multi-locus Sequence Typing, 16S rRNA sequencing, and Pulsed-Field Gel Electrophoresis) characterization of the isolates revealed their close relation to the psychrotrophic B. weihenstephanensis DSMZ 11821 reference strain. The ability to synthesize melanin-like pigment by soil B. weihenstephanensis isolates and their psychrotrophic character seemed to be a local adaptation to a specific niche. Detailed genetic and biochemical analyses of melanin-positive environmental B. weihenstephanensis strains shed some light on the evolution and ecological adaptation of these bacteria. Moreover, our study raised new biotechnological possibilities for the use of water-soluble melanin-like pigment naturally produced by B. weihenstephanensis as an alternative to commercial non-soluble pigment.

Insect prophenoloxidase: the view beyond immunity

Insect prophenoloxidase (PPO) is an important innate immunity protein due to its involvement in cellular and humoral defense. It belongs to a group of type-3 copper-containing proteins that occurs in almost all organisms. Insect PPO has been studied for over a century, and the PPO activation cascade is becoming clearer. The insect PPO activation pathway incorporates several important proteins, including pattern-recognition receptors (PGRP, β GRP, and C-type lectins), serine proteases, and serine protease inhibitors (serpins). Due to their complexity, PPO activation mechanisms vary among insect species. Activated phenoloxidase (PO) oxidizes phenolic molecules to produce melanin around invading pathogens and wounds. The crystal structure of Manduca sexta PPO shows that a conserved amino acid, phenylalanine (F), can block the active site pocket. During activation, this blocker must be dislodged or even cleaved at the N-terminal sequence to expose the active site pockets and allow substrates to enter. Thanks to the crystal structure of M. sexta PPO, some domains and specific amino acids that affect PPO activities have been identified. Further studies of the relationship between PPO structure and enzyme activities will provide an opportunity to examine other type-3 copper proteins, and trace when and why their various physiological functions evolved. Recent researches show that insect PPO has a relationship with neuron activity, longevity, feces melanization (phytophagous insects) and development, which suggests that it is time for us to look back on insect PPO beyond the view of immunity in this review.