Putative carotenoid genes expressed under the regulation of Shine–Dalgarno regions in Escherichia coli for efficient lycopene production

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.

Bacillus subtilis: current and future modification strategies as a protein secreting factory

Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.

Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway

Lycopene is a common carotenoid found mainly in ripe red fruits and vegetables that is widely used in the food industry due to its characteristic color and health benefits. Microbial synthesis of lycopene is gradually replacing the traditional methods of plant extraction and chemical synthesis as a more economical and productive manufacturing strategy. The biosynthesis of lycopene is a typical multienzyme cascade reaction, and it is important to understand the characteristics of each key enzyme involved and how they are regulated. In this paper, the catalytic characteristics of the key enzymes involved in the lycopene biosynthesis pathway and related studies are first discussed in detail. Then, the strategies applied to the key enzymes of lycopene synthesis, including fusion proteins, enzyme screening, combinatorial engineering, CRISPR/Cas9-based gene editing, DNA assembly, and scaffolding technologies are purposefully illustrated and compared in terms of both traditional and emerging multienzyme regulatory strategies. Finally, future developments and regulatory options for multienzyme synthesis of lycopene and similar secondary metabolites are also discussed.

Draft genome sequence of a new carotenoid-producing strain Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China

Some species of the genus Brevibacterium are orange bacteria involved in cheese ripening, synthesis of odoriferous compounds, and carotenoids with aromatic end groups. Here, we report the genome sequence of Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. The genome of XU54 consists of 4,899,099 base pairs with a GC content of 62.2%. The genome sequence was annotated with 4453 genes, encoding 4260 proteins, 13 rRNAs, and 49 tRNAs. 16S rRNA BLAST and comparative genomic analysis both indicated that XU54 may be a new species of Brevibacterium. In addition, compared to the type strains, some enzymes related to sulfur metabolism showed a low similarity of 66.85, 79.53 and 14.61%, respectively. The carotenoids biosynthesis gene cluster was identified and analyzed according to the genomic data, which revealed relatively low identity (5-85%) with existing strains. The optimum conditions for its growth and carotenoid production were then discussed. The whole-genome sequence of Brevibacterium sp. XU54 will be beneficial for utilizing these newly identified genes in carotenoid biosynthesis and regulation of sulfur metabolism pathway to promote the production of novel carotenoids and other structurally diverse compounds through combinatorial biosynthesis, which facilitates cheese ripening and coloration.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03366-1.

Tailoring the Tag/Catcher System by Integrating Covalent Bonds and Noncovalent Interactions for Highly Efficient Protein Self-Assembly

Covalent bonds and noncovalent interactions play crucial roles in enzyme self-assembly. Here, we designed a Tag/Catcher system named NGTag/NGCatcher in which the Catcher is a highly charged protein that can bind proteins with positively charged tails and rapidly form a stable isopeptide bond with NGTag. In this study, we present a multienzyme strategy based on covalent bonds and noncovalent interactions. In vitro, mCherry, YFP, and GFP can form protein-rich three-dimensional networks based on NGCatcher, NGTag, and RK (Arginine/Lysine) tails, respectively. Furthermore, this technology was applied to improve lycopene production in Escherichia coli. Three key enzymes were involved in lycopene production variants from Deinococcus wulumuqiensis R12 of NGCatcher_CrtE, NGTag_Idi, and RKIspARK, where the multienzyme complexes were clearly observed in vivo and in vitro, and the lycopene production in vivo was 17.8-fold higher than that in the control group. The NGTag/NGCatcher system will provide new opportunities for in vivo and in vitro multienzyme catalysis.

Back to nature, microbial production of pigments and colorants for food use

Pigments-producing microorganisms are quite common in Nature. However, there is a long journey from the Petri dish to the market place. Twenty-five years ago, scientists wondered if such productions would remain a scientific oddity or become an industrial reality. The answer is not straightforward as processes using fungi, bacteria or yeasts can now indeed provide carotenoids or phycocyanin at an industrial level. Another production factor to consider is peculiar as Monascus red colored food is consumed by more than one billion Asian people; however, still banned in many other countries. European and American consumers will follow as soon as "100%-guaranteed" toxin-free strains (molecular engineered strains, citrinin gene deleted strains) will be developed and commercialized at a world level. For other pigmented biomolecules, some laboratories and companies invested and continue to invest a lot of money as any combination of new source and/or new pigment requires a lot of experimental work, process optimization, toxicological studies, and regulatory approval. Time will tell whether investments in pigments such as azaphilones or anthraquinones were justified. Future trends involve combinatorial engineering, gene knock-out, and the production of niche pigments not found in plants such as C50 carotenoids or aryl carotenoids.

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.

Study of the properties of carotenoids and key carotenoid biosynthesis genes from Deinococcus xibeiensis R13

To investigate the properties of carotenoids from the extremophile Deinococcus xibeiensis R13, the factors affecting the stability of carotenoids extracted from D. xibeiensis R13, including temperature, illumination, pH, redox chemicals, metal ions, and food additives, were investigated. The results showed that low temperature, neutral pH, reducing agents, Mn²⁺ , and food additives (xylose and glucose) can effectively improve the stability of Deinococcus carotenoids. The carotenoids of D. xibeiensis R13 exhibited strong antioxidant activity, with the scavenging rate of hydroxyl radicals reaching 71.64%, which was higher than the scavenging efficiency for 1,1-diphenyl-2-picrylhydrazyl free radicals and 2,2'-azino-bis (3-ethyl-benzothiazoline-6-sulfonic acid) free radicals (44.55 and 27.65%, respectively). In addition, the total antioxidant capacity reached 0.60 U/ml, which was 2.61-fold that of carotenoids from the model strain Deinococcus radiodurans R1. Finally, we predicted the gene clusters encoding carotenoid biosynthesis pathways in the genome of R13 and identified putative homologous genes. The key enzyme genes (crtE, crtB, crtI, crtLm, cruF, crtD, and crtO) in carotenoid synthesis of D. xibeiensis R13 were cloned to construct the multigene coexpression plasmids pET-EBI and pRSF-LmFDO. The carotenoid biosynthesis pathway was heterologously introduced into engineered Escherichia coli EBILmFDO, which exhibited a higher yield (7.14 mg/L) than the original strain. These analysis results can help us to better understand the metabolic synthesis of carotenoids in extremophiles.

Modular engineering for microbial production of carotenoids

There is an increasing demand for carotenoids due to their applications in the food, flavor, pharmaceutical and feed industries, however, the extraction and synthesis of these compounds can be expensive and technically challenging. Microbial production of carotenoids provides an attractive alternative to the negative environmental impacts and cost of chemical synthesis or direct extraction from plants. Metabolic engineering and synthetic biology approaches have been widely utilized to reconstruct and optimize pathways for carotenoid overproduction in microorganisms. This review summarizes the current advances in microbial engineering for carotenoid production and divides the carotenoid biosynthesis building blocks into four distinct metabolic modules: 1) central carbon metabolism, 2) cofactor metabolism, 3) isoprene supplement metabolism and 4) carotenoid biosynthesis. These four modules focus on redirecting carbon flux and optimizing cofactor supplements for isoprene precursors needed for carotenoid synthesis. Future perspectives are also discussed to provide insights into microbial engineering principles for overproduction of carotenoids.

Engineering a growth-phase-dependent biosynthetic pathway for carotenoid production in Saccharomyces cerevisiae

Metabolic engineering is usually focused on static control of microbial cell factories to efficient production of interested chemicals, though heterologous pathways compete with endogenous metabolism. However, products like carotenoids may cause metabolic burden on engineering strains, thus limiting product yields and influencing strain growth. Herein, a growth-phase-dependent regulation was developed to settle this matter, and its efficiency was verified using the heterogenous biosynthesis of lycopene in Saccharomyces cerevisiae as an example. Through growth-phase-dependent control of the lycopene biosynthetic pathway, limited step in MVA pathway, and competitive squalene pathway, production yield was increased by approximately 973-fold (from 0.034- to 33.1-mg/g CDW) and 1.48 g/L of production was obtained by one-stage fermentation in a 5-L bioreactor. Our study not only introduces an economically approach to the production of carotenoids, but also provides an example of dynamic regulation of biosynthetic pathways for metabolic engineering.

Design and tailoring of an artificial DNA scaffolding system for efficient lycopene synthesis using zinc-finger-guided assembly

A highly efficient lycopene production system was constructed by assembling enzymes fused to zinc-finger motifs on DNA scaffolds in vitro and in vivo. Three key enzymes of the lycopene synthesis pathway, geranylgeranyl diphosphate synthase, phytoene synthase, and phytoene desaturase, were fused with zinc-finger proteins, expressed and purified. Recombinant plasmids of the pS series containing DNA scaffolds that the zinc-finger proteins can specifically bind to were constructed. In the in vitro system, the production efficiency of lycopene was improved greatly after the addition of the scaffold plasmid pS231. Subsequently, the plasmid pET-AEBI was constructed and introduced into recombinant Escherichia coli BL21 (DE3) for expression, together with plasmids of the pS series. The lycopene production rate and content of the recombinant strain pp231 were higher than that of all strains carrying the DNA scaffold and the control. With the addition of cofactors and substrates in the lycopene biosynthesis pathway, the lycopene yield of pp231 reached 632.49 mg/L at 40 h, representing a 4.7-fold increase compared to the original recombinant strain pA1A3. This DNA scaffold system can be used as a platform for the construction and production of many biochemicals synthesized via multi-enzyme cascade reactions.

The diversity and commonalities of the radiation-resistance mechanisms of Deinococcus and its up-to-date applications

Deinococcus is an extremophilic microorganism found in a wide range of habitats, including hot springs, radiation-contaminated areas, Antarctic soils, deserts, etc., and shows some of the highest levels of resistance to ionizing radiation known in nature. The highly efficient radiation-protection mechanisms of Deinococcus depend on a combination of passive and active defense mechanisms, including self-repair of DNA damage (homologous recombination, MMR, ER and ESDSA), efficient cellular damage clearance mechanisms (hydrolysis of damaged proteins, overexpression of repair proteins, etc.), and effective clearance of reactive oxygen species (ROS). Due to these mechanisms, Deinococcus cells are highly resistant to oxidation, radiation and desiccation, which makes them potential chassis cells for wide applications in many fields. This article summarizes the latest research on the radiation-resistance mechanisms of Deinococcus and prospects its biotechnological application potentials.

Combinatorial expression of different β-carotene hydroxylases and ketolases in Escherichia coli for increased astaxanthin production

In natural produced bacteria, β-carotene hydroxylase (CrtZ) and β-carotene ketolase (CrtW) convert β-carotene into astaxanthin. To increase astaxanthin production in heterologous strain, simple and effective strategies based on the co-expression of CrtZ and CrtW were applied in E. coli. First, nine artificial operons containing crtZ and crtW genes from different sources were constructed and, respectively, introduced into E. coli ZF237T, a β-carotene producing host. Among the nine resulting strains, five accumulated detectable amounts of astaxanthin ranging from 0.49 to 8.07 mg/L. Subsequently, the protein fusion CrtZ to CrtW using optimized peptide linkers further increased the astaxanthin production. Strains expressing fusion proteins with CrtZ rather than CrtW attached to the N-terminus accumulated much more astaxanthin. The astaxanthin production of the best strain ZF237T/CrtZ_As-(GS)₁-W_Bs was 127.6% and 40.2% higher than that of strains ZF237T/crtZ_AsW_Bs and ZF237T/crtZ_BsW_Ps, respectively. The strategies depicted here also will be useful for the heterologous production of other natural products.

Effects of lipopolysaccharide structure on lycopene production in Escherichia coli

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The heterogenous crtEBI operon was overexpressed in 10 LPS mutant strains of E. coli W3110.

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ΔwaaC/pWSK29-crtEBI and ΔwaaF/pWSK29-crtEBI produced more lycopene than others.

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Overexpressing dxr, dxr, ispA and idi in ΔwaaC/pWSK29-crtEBI and ΔwaaF/pWSK29-crtEBI enhanced lycopene production.

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The maximum yield of 5.39 mg/g was produced in ΔwaaC/pWSK29-crtEBI-SRA.

Lipopolysaccharides, the major molecules in the outer membrane of Escherichia coli, affect the behavior of bacteria including outer membrane permeability, but its influence on lycopene production in E. coli has never been reported. In this study, the effects of lipopolysaccharides with different structures on lycopene biosynthesis were investigated. Firstly, the heterogenous crtEBI operon were overexpressed in 10 LPS mutant strains of E. coli W3110 (ΔwaaC, ΔwaaF, ΔwaaY, ΔwaaG, ΔwaaR, ΔwaaO, ΔwaaU, ΔwaaP, ΔwaaY and ΔwaaB), and their ability to produce lycopene were compared. ΔwaaC/pWSK29-crtEBI, ΔwaaF/pWSK29-crtEBI and ΔwaaY/pWSK29-crtEBI produced 4.19, 4.20, and 3.81 mg/g lycopene, respectively, while the control W3110/pWSK29-crtEBI produced 3.71 mg/g lycopene; the other strains produced less lycopene than the control. In order to enhance lycopene production, genes dxr, dxr, ispA, and idi were overexpressed in ΔwaaC/pWSK29-crtEBI, ΔwaaF/pWSK29-crtEBI individually or in combination, and the lycopene production in each strain was analyzed. The maximum yield of 5.39 mg/g was achieved in ΔwaaC/pWSK29-crtEBI-SRA, which is 142% higher than that in W3110/pWSK29-crtEBI. The results indicate that the length of lipopolysaccharide affects lycopene biosynthesis in E. coli, and the shorter lipopolysaccharide and higher outer membrane permeability might be beneficial to lycopene biosynthesis.

High yields and soluble expression of superoxide dismutases in Escherichia coli due to the HIV-1 Tat peptide via increases in mRNA transcription

This study aimed to validate the high yield and soluble expression of proteins carrying the transactivator of transcription (Tat) peptide tag, and further explored the potential mechanism by which the Tat tag increases expression. Escherichia coli superoxide dismutase (SOD) proteins, including SodA, SodB and SodC, were selected for analysis. As expected, the yields and the solubility of Tat-tagged proteins were higher than those of Tat-free proteins, and similar results were observed for the total SOD enzyme activity. Bacterial cells that overexpressed Tat-tagged proteins exhibited increased anti-paraquat activity compared with those expressing Tat-free proteins that manifested as SodA>SodC>SodB. When compared with an MG1655 wild-type strain, the growth of a ΔSodA mutant strain was found to be inhibited after paraquat treatment; the growth of ΔSodB and ΔSodC mutant strains was also slightly inhibited. The mRNA transcript level of genes encoding Tat-tagged proteins was higher than that of genes encoding Tat-free proteins. Furthermore, the α-helix and turn of Tat-tagged proteins were higher than those of Tat-free proteins, but the β-sheet and random coil content was lower. These results indicated that the incorporation of the Tat core peptide as a significant basic membrane transduction peptide in fusion proteins could increase mRNA transcripts and promote the high yield and soluble expression of heterologous proteins in E. coli.

Expression of lycopene biosynthesis genes fused in line with Shine-Dalgarno sequences improves the stress-tolerance of Lactococcus lactis

OBJECTIVES

Lycopene biosynthetic genes from Deinococcus radiodurans were co-expressed in Lactococcus lactis to produce lycopene and improve its tolerance to stress.

RESULTS

Lycopene-related genes from D. radiodurans, DR1395 (crtE), DR0862 (crtB), and DR0861 (crtI), were fused in line with S hine-Dalgarno (SD) sequences and co-expressed in L. lactis. The recombinant strain produced 0.36 mg lycopene g^-1 dry cell wt after 48 h fermentation. The survival rate to UV irradiation of the recombinant strain was higher than that of the non-transformed strain.

CONCLUSION

The L. lactis with co-expressed genes responsible for lycopene biosynthesis from D. radiodurans produced lycopene and exhibited increased resistance to UV stress, suggesting that the recombinant strain has important application potential in food industry.