Homologous gene targeting of a carotenoids biosynthetic gene in Rhodosporidium toruloides by Agrobacterium-mediated transformation

Introducing CCD1 into isolated Rhodotorula strain enhances flavor production and improves cigar fermentation

Introduction

The fermentation process plays an important role in enhancing the quality of cigar tobacco leaves. Through fermentation, microbial metabolism can degrade aromatic precursors and macromolecules, which increases the content of aroma compounds and reduces irritancy of tobacco leaves.

Methods

To further enhance the fermentation effect of cigar tobacco leaves, a Rhodotorula strain (Rh3), capable of producing carotenoids and improving fermentation quality, was isolated from cigar tobacco leaves. Subsequent genetic engineering techniques introduced the carotenoid cleavage dioxygenase 1 (CCD1) gene into the isolated Rh3.

Results

The modified Rh3 exhibits a significant increase in carotenoid degradation products compared with the original Rh3 in culture medium (from 0.29 μg/mg to 15 μg/mg). Subsequent cigar tobacco leaf fermentation experiments revealed that the modified Rh3 produced 65.9% more carotenoid degradation products compared to the control group, outperforming the original strain, which achieved a 41.4% increase. Furthermore, the modified strain preserves its ability to improve the intrinsic chemical composition of cigar tobacco leaves.

Discussion

We show here that modified Rh3 can increase the content of carotenoid degradation products, thereby enhancing the fermentation effect of cigar tobacco leaves. This study presents a beneficial exploration to improve the quality of cigar tobacco leaves for future use and offers a promising strategy for producing flavor compounds from discarded tobacco leaves.

De Novo Biosynthesis of 2-Phenylethanol by Metabolic Engineering the Oleaginous Yeast Rhodotorula toruloides

Microbial production offers a sustainable route to plant- and chemical-based manufacturing. 2-Phenylethanol (2-PE) has been widely used in foods, flavors, and pharmaceuticals. Herein, de novo biosynthesis of 2-PE was achieved for the first time by rewiring the non-native producer Rhodotorula toruloides. Our results showed that the generation of phenylalanine (Phe) and the recycling of the amino group could be bypassed since the Ehrlich pathway outperformed the phenylacetaldehyde-dependent one in de novo biosynthesis of 2-PE when the adenosine 5'-triphosphate (ATP) citrate synthase (ACL) was inactivated. The 2-PE titer was enhanced to 151.7 mg/L in a shake flask by alleviating feedback inhibition, enhancing precursor availability and cofactor balance. Finally, the production of 2-PE was elevated to 1.06 g/L with a yield of 8.5 mg/g glucose and productivity of 8 mg/L/h in a 3 L bioreactor. Our results should shed light on the microbial production of other aromatic derivatives with R. toruloides.

Pioneering DNA assembling techniques and their applications in eukaryotic microalgae

Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.

Molecular characterization and expression profiling of two flavohemoglobin genes play essential roles in dissolved oxygen and NO stress in Saitozyma podzolica zwy2-3

Flavohemoglobins (Fhbs) are key enzymes involved in microbial nitrosative stress resistance and nitric oxide degradation. However, the roles of Fhbs in fungi remain largely unknown. In this study, SpFhb1 and SpFhb2, two flavohemoglobin-encoding genes in Saitozyma podzolica zwy2-3 were characterized. Protein structure analysis and molecular docking showed that SpFhbs were conserved in bacteria and fungi. Phylogenetic analysis revealed that SpFhb2 may be acquired through the transfer event of independent horizontal genes from bacteria. The expression levels of SpFhb1 and SpFhb2 showed opposite trend under high/low dissolved oxygen, implying that they may exhibited different functions. Through deletion and overexpression of SpFhbs, we confirmed that SpFhbs were conducive to lipid accumulation under high stress. The sensitivities of ΔFhb mutants to NO stress were significantly increased compared with that in the WT, indicating that they were required for NO detoxification and nitrosative stress resistance in S. podzolica zwy2-3. Furthermore, SpAsg1 was identified that simultaneously regulates SpFhbs, which functions in the lipid accumulation under high/low dissolved oxygen and NO stress in S. podzolica zwy2-3. Overall, two different SpFhbs were identified in this study, providing new insights into the mechanism of lipid accumulation in fungi under high/low dissolved oxygen and NO stress.

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Rhodotorula toruloides is receiving significant attention as a novel cell factory because of its high production of lipids and carotenoids, fast growth and high cell density, as well as the ability to utilize a wide variety of substrates. These attractive traits of R. toruloides make it possible to become a low-cost producer that can be engineered for the production of various fuels and chemicals. However, the lack of understanding and genetic engineering tools impedes its metabolic engineering applications. A number of research efforts have been devoted to filling these gaps. This review focuses on recent developments in genetic engineering tools, advances in systems biology for improved understandings, and emerging engineered strains for metabolic engineering applications. Finally, future trends and barriers in developing R. toruloides as a cell factory are also discussed.

Red yeasts and their carotenogenic enzymes for microbial carotenoid production

Carotenoids are C40 isoprene-based compounds with significant commercial interests that harbor diverse bioactivities. Prominent examples of carotenoids are beta-carotene, a precursor to vitamin A essential for proper eye health, and lycopene and astaxanthin, powerful antioxidants implicated in preventing cancers and atherosclerosis. Due to their benefits to human health, the market value for carotenoids is rapidly increasing and is projected to reach USD 1.7 billion by 2025. However, their production now relies on chemical synthesis and extraction from plants that pose risks to food management and numerous biological safety issues. Thus, carotenoid production from microbes is considered a promising strategy for achieving a healthy society with more sustainability. Red yeast is a heterogeneous group of basidiomycetous fungi capable of producing carotenoids. It is a critical source of microbial carotenoids from low-cost substrates. Carotenogenic enzymes from red yeasts have also been highly efficient, invaluable biological resources for biotechnological applications. In this minireview, we focus on red yeast as a promising source for microbial carotenoids, strain engineering strategies for improving carotenoid production in red yeasts, and potential applications of carotenogenic enzymes from red yeasts in conventional and nonconventional yeasts.

Recent advances in genetic technology development of oleaginous yeasts

As important chemical raw materials and potential nutritional supplements, microbial lipids play an important role in ensuring economic development, food security, and energy security. Compared with non-natural hosts, oleaginous yeasts exhibit obvious advantages in lipid yield and productivity and have great potential to be genetically engineered into an oil cell factory. The main bottleneck in the current oleaginous yeasts engineering is the lack of genetic manipulation tools. Fortunately, the rapid development of synthetic biology has provided numerous new approaches, resources, and ideas for the field. Most importantly, gene editing technology mediated by CRISPR/Cas systems has been successfully applied to some oleaginous yeasts, almost completely rewriting the development pattern of genetic manipulation technology applicable. This paper reviews recent progress in genetic technology with regard to oleaginous yeasts, with a special focus on transformation methods and genome editing tools, discussing the effects of some important genetic parts. KEY POINTS: •Contribution of microbiotechnology in food safety and biofuel by oleaginous yeasts. •Advancement of genetic manipulation and transformation for oleaginous yeasts.

Engineering Rhodosporidium toruloides for limonene production

BACKGROUND

Limonene is a widely used monoterpene in the production of food, pharmaceuticals, biofuels, etc. The objective of this work was to engineer Rhodosporidium toruloides as a cell factory for the production of limonene.

RESULTS

By overexpressing the limonene synthase (LS), neryl pyrophosphate synthase (NPPS)/geranyl pyrophosphate synthase and the native hydroxy-methyl-glutaryl-CoA reductase (HMGR), we established a baseline for limonene production based on the mevalonate route in Rhodosporidium toruloides. To further enhance the limonene titer, the acetoacetyl-CoA thiolase/HMGR (EfMvaE) and mevalonate synthase (EfMvaS) from Enterococcus faecalis, the mevalonate kinase from Methanosarcina mazei (MmMK) and the chimeric enzyme NPPS-LS were introduced in the carotenogenesis-deficient strain. The resulting strains produced a maximum limonene titer of 393.5 mg/L.

CONCLUSION

In this study, we successfully engineered the carotenogenesis yeast R. toruloides to produce limonene. This is the first report on engineering R. toruloides toward limonene production based on NPP and the fusion protein SltNPPS-CltLS. The results demonstrated that R. toruloides is viable for limonene production, which would provide insights into microbial production of valuable monoterpenes.

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides. High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.

Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization

Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.

RNA interference in the oleaginous yeast Rhodosporidium toruloides

The red yeast Rhodosporidium toruloides is an excellent microbial host for production of carotenoids, neutral lipids and valuable enzymes. In recent years, genetic tools for gene expression and gene disruption have been developed for this red yeast. However, methods remain limited in terms of fine-tuning gene expression. In this study, we first demonstrated successful implementation of RNA interference (RNAi) in R. toruloides NP11, which was applied to down-regulate the expression of autophagy related gene 8 (ATG8), and fatty acid synthase genes (FAS1 and FAS2), respectively. Compared with the control strain, RNAi-engineered strains showed a silencing efficiency ranging from 11% to 92%. The RNAi approach described here ensures selective inhibition of the target gene expression, and should expand our capacity in the genetic manipulation of R. toruloides for both fundamental research and advanced cell factory development.

Developing a CRISPR/Cas9 System for Genome Editing in the Basidiomycetous Yeast Rhodosporidium toruloides

The basidiomycetous yeast Rhodosporidium toruloides (R. toruloides) has been explored as a promising host for the production of lipids and carotenoids. However, the rational manipulation of this yeast remains difficult due to lack of efficient genetic tools. Here, the development of a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas9) system for genome editing in R. toruloides is described. First, R. toruloides strains are generated with sufficient production of the Cas9 protein of Staphylococcus aureus origin by integrating a cassette containing a codon-optimized Cas9 gene into the genome. In parallel, two U6 genes are identified, predicting two U6 promoters and confirming better transcription of single-guide RNA (sgRNA) with the U6b promoter. Next, sgRNA cassettes are designed targeting CRTI, CAR2, and CLYBL gene, respectively, transforming into those Cas9-expressed strains, and finding over 60% transformants with successful insertion and deletion (indel) mutations. Furthermore, when the sgRNA cassette includes donor DNA flanked by two homologous arms of the gene CRTI, gene knockout occurs via homologous recombination. Thus, the CRISPR/Cas9 system is now established as a powerful genome-editing tool in R. toruloides, which should facilitate functional genomic study and advanced cell factory development.

Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems

Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.

Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis

Background

Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. Currently, information on the key metabolic pathways and their molecular basis of regulation remains scarce, severely limiting efforts to engineer it as an industrial host.

Results

We have adapted Agrobacterium tumefaciens-mediated transformation (ATMT) as a gene-tagging tool for the identification of novel genes in R. toruloides. Multiple factors affecting transformation efficiency in several species in the Pucciniomycotina subphylum were optimized. The Agrobacterium transfer DNA (T-DNA) showed predominantly single-copy chromosomal integrations in R. toruloides, which were trackable by high efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). To demonstrate the application of random T-DNA insertions for strain improvement and gene hunting, 3 T-DNA insertional libraries were screened against cerulenin, nile red and tetrazolium violet respectively, resulting in the identification of 22 mutants with obvious phenotypes in fatty acid or lipid metabolism. Similarly, 5 carotenoid biosynthetic mutants were obtained through visual screening of the transformants. To further validate the gene tagging strategy, one of the carotenoid production mutants, RAM5, was analyzed in detail. The mutant had a T-DNA inserted at the putative phytoene desaturase gene CAR1. Deletion of CAR1 by homologous recombination led to a phenotype similar to RAM5 and it could be genetically complemented by re-introduction of the wild-type CAR1 genome sequence.

Conclusions

T-DNA insertional mutagenesis is an efficient forward genetic tool for gene discovery in R. toruloides and related oleaginous yeast species. It is also valuable for metabolic engineering in these hosts. Further analysis of the 27 mutants identified in this study should augment our knowledge of the lipid and carotenoid biosynthesis, which may be exploited for oil and isoprenoid metabolic engineering.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1151-6) contains supplementary material, which is available to authorized users.

Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced Rhodotorula species. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications

Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.