Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin

Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria

The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.

Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains

The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.

Extremophilic Solutions: The Role of Deinoxanthin in Counteracting UV-Induced Skin Harm

This research delved into the protective capacities of deinoxanthin, a carotenoid present in Deinococcus radiodurans, against UVA- and UVB-mediated skin damage using human fibroblast foreskin cells (HFF-1). Using the MTT assay, HFF-1 cells treated with 10 µM DNX displayed 20% and 31.7% higher viability than the positive (Vitamin C-treated) and negative (DNX-untreated) control groups, respectively, upon 100 mJ/cm2 UVB exposure. At 24 J/cm2 UVA, 20 µM DNX-treated cells showed 80.6% viability, exceeding the positive and negative control groups by 28.6% and 33.6%, respectively. Flow cytometry analysis revealed that cells treated with DNX and exposed to 24 J/cm2 UVA exhibited a 69.32% reduction in apoptotic processes compared to untreated cells. Similarly, when exposed to 100 mJ/cm2 UVB, DNX-treated cells demonstrated a 72.35% decrease in apoptotic processes relative to their untreated counterparts. DNX also displayed dose-dependent inhibition on tyrosinase activity. The study emphasized DNX's antioxidative capacity, evident in its modulation of superoxide dismutase activity and measurements of Malondialdehyde and intracellular reactive oxygen species levels. DNX-treated cells exhibited higher hydroxyproline levels, suggesting healthier collagen production. Additionally, the wound-healing assay method confirmed an accelerated healing rate in DNX-treated cells. Conclusively, DNX offers significant protection against UV-induced skin damage, emphasizing its potential for skincare and therapeutics.

Effective gene silencing using type I-E CRISPR system in the multiploid, radiation-resistant bacterium Deinococcus radiodurans

The extremely radiation-resistant bacterium, Deinococcus radiodurans, is a microbe of importance, both, for studying stress tolerance mechanisms and as a chassis for industrial biotechnology. However, the molecular tools available for use in this organism continue to be limiting, with its multiploid genome presenting an additional challenge. In view of this, the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas tools provide a large repertoire of applications for gene manipulation. We show the utility of the type I-E Cascade system for knocking down gene expression in this organism. A single-vector system was designed for the expression of the Cascade components as well as the crRNA. The type I-E Cascade system was better tolerated than the type II-A dCas9 system in D. radiodurans. An assayable acid phosphatase gene, phoN integrated into the genome of this organism could be knocked down to 10% of its activity using the Cascade system. Cascade-based knockdown of ssb, a gene important for radiation resistance resulted in poor recovery post-irradiation. Targeting the Radiation and Desiccation Response Motif (RDRM), upstream of the ssb, prevented de-repression of its expression upon radiation exposure. In addition to this, multi-locus targeting was demonstrated on the deinococcal genome, by knocking down both phoN and ssb expression simultaneously. The programmable CRISPR interference tool developed in this study will facilitate the study of essential genes, hypothetical genes, and cis-elements involved in radiation response as well as enable metabolic engineering in this organism. Further, the tool can be extended for implementing high-throughput approaches in such studies. IMPORTANCE Deinococcus radiodurans is a microbe that exhibits a very high degree of radiation resistance. In addition, it is also identified as an organism of industrial importance. We report the development of a gene-knockdown system in this organism by engineering a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-Cascade system. We used this system to silence an assayable acid phosphatase gene, phoN to 10% of its activity. The study further shows the application of the Cascade system to target an essential gene ssb, that caused poor recovery from radiation. We demonstrate the utility of CRISPR-Cascade to study the role of a regulatory cis-element in radiation response as well as for multi-gene silencing. This easy-to-implement CRISPR interference system would provide an effective tool for better understanding of complex phenomena such as radiation response in D. radiodurans and may also enhance the potential of this microbe for industrial application.

Highly Water-Dispersed and Stable Deinoxanthin Nanocapsule for Effective Antioxidant and Anti-Inflammatory Activity

Introduction

Deinoxanthin (DX), a carotenoid, has excellent antioxidant and anti-inflammatory properties. However, owing to its lipophilicity, it is unfavorably dispersed in water and has low stability, limiting its application in cosmetics, food, and pharmaceuticals. Therefore, it is necessary to study nanoparticles to increase the loading capacity and stability of DX.

Methods

In this study, DX-loaded nanocapsules (DX@NCs) were prepared by nanoprecipitation by loading DX into nanocapsules. The size, polydispersity index, surface charge, and morphology of DX@NCs were confirmed through dynamic light scattering and transmission electron microscopy. The loading content and loading efficiency of DX in DX@NCs were analyzed using high-performance liquid chromatography. The antioxidant activity of DX@NCs was evaluated by DPPH assay and in vitro ROS. The biocompatibility of DX@NCs was evaluated using an in vitro MTT assay. In vitro NO analysis was performed to determine the effective anti-inflammatory efficacy of DX@NCs.

Results

DX@NCs exhibited increased stability and antioxidant efficacy owing to the improved water solubility of DX. The in situ and in vitro antioxidant activity of DX@NCs was higher than that of unloaded DX. In addition, it showed a strong anti-inflammatory effect by regulating the NO level in an in vitro cell model.

Conclusion

This study presents a nanocarrier to improve the water-soluble dispersion and stability of DX. These results demonstrate that DX@NC is a carrier with excellent stability and has a high potential for use in cosmetic and pharmaceutical applications owing to its antioxidant and anti-inflammatory effects.

Technological advances in the production of carotenoids and their applications- A critical review

Carotenoids are naturally occurring pigments that are widely distributed in algae, fungi, bacteria, and plants. Carotenoids play a significant role in the food, feed, cosmetic, nutraceutical, and pharmaceutical industries. These pigments are effectively considered as a health-promoting compounds, which are widely used in our daily diet to reduce the risk of chronic diseases such as cardiovascular diseases, cancer, acute lung injury, cataracts, neural disorders, etc. In this context, this review paper demonstrates the synthesis of carotenoids and their potential application in the food and pharmaceutical industries. However, the demand for carotenoid production is increasing overtime, and the extraction and production are expensive and technically challenging. The recent developments in carotenoid biosynthesis, and key challenges, bottlenecks, and future perspectives were also discussed to enhance the circular bioeconomy.

iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C6+ heavy ion irradiation

Background

Deinococcus radiodurans (D. radiodurans) is best known for its extreme resistance to diverse environmental stress factors, including ionizing radiation (IR), ultraviolet (UV) irradiation, oxidative stress, and high temperatures. Robust DNA repair system and antioxidant system have been demonstrated to contribute to extreme resistance in D. radiodurans. However, practically all studies on the mechanism underlying D. radiodurans’s extraordinary resistance relied on the treated strain during the post-treatment recovery lag phase to identify the key elements involved. The direct gene or protein changes of D. radiodurans after stress have not yet been characterized.

Results

In this study, we performed a proteomics profiling on D. radiodurans right after the heavy ion irradiation treatment, to discover the altered proteins that were quickly responsive to IR in D. radiodurans. Our study found that D. radiodurans shown exceptional resistance to ¹²C⁶⁺ heavy ion irradiation, in contrast to Escherichia coli (E.coli) strains. By using iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-based quantitative mass spectrometry analysis, the kinetics of proteome changes induced by various dosages of ¹²C⁶⁺ heavy ion irradiation were mapped. The results revealed that 452 proteins were differentially expressed under heavy ion irradiation, with the majority of proteins being upregulated, indicating the upregulation of functional categories of translation, TCA cycle (Tricarboxylic Acid cycle), and antioxidation regulation under heavy ion irradiation.

Conclusions

This study shows how D. radiodurans reacts to exposure to ¹²C⁶⁺ heavy ion irradiation in terms of its overall protein expression profile. Most importantly, comparing the proteome profiling of D. radiodurans directly after heavy ion irradiation with research on the post-irradiation recovery phase would potentially provide a better understanding of mechanisms underlying the extreme radioresistance in D. radiodurans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02676-x.

Comprehensive utilization of sucrose resources via chemical and biotechnological processes: A review

Sucrose, one of the most widespread disaccharides in nature, has been available in daily human life for many centuries. As an abundant and cheap sweetener, sucrose plays an essential role in our diet and the food industry. However, it has been determined that many diseases, such as obesity, diabetes, hyperlipidemia, etc., directly relate to the overconsumption of sucrose. It arouses many explorations for the conversion of sucrose to high-value chemicals. Production of valuable substances from sucrose by chemical methods has been studied since a half-century ago. Compared to chemical processes, biotechnological conversion approaches of sucrose are more environmentally friendly. Many enzymes can use sucrose as the substrate to generate functional sugars, especially those from GH68, GH70, GH13, and GH32 families. In this review, enzymatic catalysis and whole-cell fermentation of sucrose for the production of valuable chemicals were reviewed. The multienzyme cascade catalysis and metabolic engineering strategies were addressed.

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes)

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.

Conjugation-Based Genome Engineering in Deinococcus radiodurans

Deinococcus radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based DNA transfer method from E. coli to D. radiodurans, allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by targeting restriction-modification genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facilitate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.

Isolation and Characterization of a Yellow Xanthophyll Pigment-Producing Marine Bacterium, Erythrobacter sp. SDW2 Strain, in Coastal Seawater

Xanthophylls, a yellow pigment belonging to the carotenoid family, have attracted much attention for industrial applications due to their versatile nature. We report the isolation of a homo xanthophyll pigment-producing marine bacterium, identified as the Erythrobacter sp. SDW2 strain, from coastal seawater. The isolated Erythrobacter sp. SDW2 strain can produce 263 ± 12.9 mg/L (89.7 ± 5.4 mg/g dry cell weight) of yellow xanthophyll pigment from 5 g/L of glucose. Moreover, the xanthophyll pigment produced by the SDW2 strain exhibits remarkable antioxidative activities, confirmed by the DPPH (73.4 ± 1.4%) and ABTS (84.9 ± 0.7%) assays. These results suggest that the yellow xanthophyll pigment-producing Erythrobacter sp. SDW2 strain could be a promising industrial microorganism for producing marine-derived bioactive compounds with potential for foods, cosmetics, and pharmaceuticals.

Metabolic engineering of Deinococcus radiodurans for pinene production from glycerol

BACKGROUND

The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceutical products, and jet engine biofuels. Our objective was to produce pinene from glycerol, an abundant by-product of various industries.

RESULTS

To enable pinene production in D. radiodurans, we expressed the pinene synthase from Abies grandis, the geranyl pyrophosphate (GPP) synthase from Escherichia coli, and overexpressed the native 1-deoxy-D-xylulose 5-phosphate synthase. Further, we disrupted the deinoxanthin pathway competing for the substrate GPP by either inactivating the gene dr0862, encoding phytoene synthase, or substituting the native GPP synthase with that of E. coli. These manipulations resulted in a D. radiodurans strain capable of producing 3.2 ± 0.2 mg/L pinene in a minimal medium supplemented with glycerol, with a yield of 0.13 ± 0.04 mg/g glycerol in shake flask cultures. Additionally, our results indicated a higher tolerance of D. radiodurans towards pinene as compared to E. coli.

CONCLUSIONS

In this study, we successfully engineered the extremophile bacterium D. radiodurans to produce pinene. This is the first study demonstrating the use of D. radiodurans as a cell factory for the production of terpenoid molecules. Besides, its high resistance to pinene makes D. radiodurans a suitable host for further engineering efforts to increase pinene titer as well as a candidate for the production of the other terpenoid molecules.