Engineering a <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis> biosynthesis pathway into <Emphasis Type="Italic">Escherichia coli</Emphasis> for high yield triglyceride production

Background

Microbial lipid production represents a potential alternative feedstock for the biofuel and oleochemical industries. Since Escherichia coli exhibits many genetic, technical, and biotechnological advantages over native oleaginous bacteria, we aimed to construct a metabolically engineered E. coli strain capable of accumulating high levels of triacylglycerol (TAG) and evaluate its neutral lipid productivity during high cell density fed-batch fermentations.

Results

The Streptomyces coelicolor TAG biosynthesis pathway, defined by the acyl-CoA:diacylglycerol acyltransferase (DGAT) Sco0958 and the phosphatidic acid phosphatase (PAP) Lppβ, was successfully reconstructed in an E. coli diacylglycerol kinase (dgkA) mutant strain. TAG production in this genetic background was optimized by increasing the levels of the TAG precursors, diacylglycerol and long-chain acyl-CoAs. For this we carried out a series of stepwise optimizations of the chassis by 1) fine-tuning the expression of the heterologous SCO0958 and lpp β genes, 2) overexpression of the S. coelicolor acetyl-CoA carboxylase complex, and 3) mutation of fadE, the gene encoding for the acyl-CoA dehydrogenase that catalyzes the first step of the β-oxidation cycle in E. coli. The best producing strain, MPS13/pET28-0958-ACC/pBAD-LPPβ rendered a cellular content of 4.85% cell dry weight (CDW) TAG in batch cultivation. Process optimization of fed-batch fermentation in a 1-L stirred-tank bioreactor resulted in cultures with an OD_600nm of 80 and a product titer of 722.1 mg TAG L^-1 at the end of the process.

Conclusions

This study represents the highest reported fed-batch productivity of TAG reached by a model non-oleaginous bacterium. The organism used as a platform was an E. coli BL21 derivative strain containing a deletion in the dgkA gene and containing the TAG biosynthesis genes from S. coelicolor. The genetic studies carried out with this strain indicate that diacylglycerol (DAG) availability appears to be one of the main limiting factors to achieve higher yields of the storage compound. Therefore, in order to develop a competitive process for neutral lipid production in E. coli, it is still necessary to better understand the native regulation of the carbon flow metabolism of this organism, and in particular, to improve the levels of DAG biosynthesis.

     

Overexpression of <Emphasis Type="Italic">SsDGAT2</Emphasis> from <Emphasis Type="Italic">Sapium sebiferum</Emphasis> (L.) Roxb Increases Seed Oleic Acid Level in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Sapium sebiferum (L.) Roxb is one of the most important oil trees in China. Diacylglycerol acyltransferases (DGATs) esterify sn-1, 2-diacylglycerol with a long-chain fatty acyl-CoA, the last step and the rate-limiting step of triacylglycerol (TAG) biosynthesis in prokaryotic and eukaryotic organisms. At least 74 DGAT2 sequences from 61 organisms have been identified, but the SsDGAT2 gene had not been reported to date. To clarify the function of SsDGAT2, we cloned the CDS (rapid amplification of cDNA end) of SsDGAT2 by RACE technology. The full-length CDS of SsDGAT2 contains 1011 bp and encodes a protein of 336 amino acids. Recombinant SsDGAT2 restored TAG biosynthesis to the yeast strain Saccharomyces cerevisiae H1246 TAG-deficient mutant and preferentially incorporated unsaturated C18 fatty acids into lipids. To investigate the biotechnological potential of SsDGAT2, it was expressed under the control of the 35S promoter in Arabidopsis Col-4. The oleic acid content increased by 50 % in transgenic plants relative to the control. The results indicated that most of the oleic acid increase was at the expense of linolenic acid (18:3) content, which suggests that high-oleic-acid-content seeds can be created by the overexpression of SsDGAT2 in S. sebiferum (L.) Roxb.     

Increasing seed oil content and altering oil quality of <Emphasis Type="Italic">Brassica napus</Emphasis> L. by over-expression of diacylglycerol acyltransferase 1 (<Emphasis Type="Italic">SsDGAT1</Emphasis>) from <Emphasis Type="Italic">Sapium sebiferum</Emphasis> (L.) Roxb.

Sapium sebiferum (L.) Roxb. [S. sebiferum] is one of the most important woody oil trees and traditional herbal medicines in China. Diacylglycerol acyltransferases (DGATs) esterify sn-1,2-diacylglycerol with a long-chain fatty acyl-CoA acting as a key enzyme at the last and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. Although at least 61 DGAT1 sequences from 48 organisms have been identified, until now there have been almost no reports on the DGAT1 gene in S. sebiferum (SsDGAT1). In an attempt to clarify SsDGAT1’s function, we cloned the CDS (coding sequence) of SsDGAT1 by RACE (rapid amplification of cDNA ends) technology. The full-length CDS of SsDGAT1 contains 1524 bp, encoding a protein of 507 amino acids. Even recombinant SsDGAT1 was able to restore TAG biosynthesis in the yeast strain S. cerevisiae H1246 TAG-deficient mutant. Moreover, when SsDGAT1 was placed under the control of 35S promoter in Brassica napus L. W10, the total oil content of transgenic rape plants showed an increase of 12.3–14.7 % compared with the wild type. In addition, the transgenic rapeseed with heterologous expression of SsDGAT1 showed an alteration in seed oil composition overall: a significant decrease in oleic acid levels but a tendency towards an increase in linolenic acid levels. The result confirmed that SsDGAT1 may be involved in flux control of oil biosynthesis and could be used specifically to manipulate and improve oil content and composition in plants. These experimental findings suggest that we might be able to develop a plant high in industrial oils by over-expression of SsDGAT1 in S. sebiferum.     

Changes in the fatty acid composition of symbiotic dinoflagellates from the hermatypic coral <Emphasis Type="Italic">Echinopora lamellosa</Emphasis> during adaptation to the irradiance level

The composition of fatty acids (FAs) of symbiotic dinoflagellates isolated from the hermatypic coral Echinoporal lamellosa adapted to the irradiance of 95, 30, 8, and 2% PAR was studied. Polar lipids and triacylglycerols (TAG) differed between them in FA composition. Polar lipids were enriched in unsaturated FAs, whereas TAG, in saturated FAs. Light exerted a substantial influence on the FA composition in both polar lipids and TAG. The elevation of irradiance resulted in the accumulation of 16:0 acid in both lipid groups and 16:1(n-7) acid in TAG. It seems likely that de novo synthesis of 16:0 acid occurred actively in the cells of symbiotic dinoflagellates in high light. Since these processes are energy-consuming ones, they utilize excessive energy. When light intensity declined, 18:4(n-3) and 20:5(n-3) acids accumulated in polar lipids, which was accompanied by the increase in the content of chlorophyll a in the cells of zooxanthellae, whereas the levels of 22:6(n-3) and 20:4(n-6) acids reduced. Although the relative content of particular FAs varied substantially in dependence of irradiance, the balance between the sum of saturated and unsaturated FAs changed insignificantly. We concluded that the role of photoadaptation could not be limited only to changes in the degree of lipid unsaturation and membrane fluidity. It is supposed that light-induced changes in the FA composition reflect the interrelation between photosynthesis and FA biosynthesis.     

DGAT1 from the arachidonic-acid-producing microalga <Emphasis Type="Italic">Lobosphaera incisa</Emphasis> shows late gene expression under nitrogen starvation and substrate promiscuity in a heterologous system

We report the identification and characterization of an acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1)-encoding gene from the green oleaginous microalga Lobosphaera incisa (SAG 2468), a prolific photosynthetic producer of the n-6 very long chain polyunsaturated fatty acid (VLC-PUFA), arachidonic acid. The gene expression pattern of LiDGAT1 in L. incisa cells showed a weak increase in mRNA abundance in the course of nitrogen starvation under low light; however, LiDGAT1 expression was significantly upregulated with the progression of N-starvation under high light. Heterologous expression of LiDGAT1 in the neutral lipid-deficient mutant H1246 of Saccharomyces cerevisiae complemented the mutant phenotype and demonstrated an excelling TAG production compared to the yeast endogenous DGAT gene (DGA1). The TAG that formed in the LiDGAT1-expressing H1246 cells contained higher proportions of C16:0 and C18:0 fatty acids, suggesting that at least in a heterologous system, lacking PUFA biosynthesis, the enzyme seems to favor saturated over monounsaturated fatty acids. LiDGAT1 expression prompted an incorporation of several tested exogenous C18 PUFA and C20 VLC-PUFA into TAG. LiDGAT1-driven activity mediated the incorporation of either n-3 or n-6 VLC-PUFA, supplied as substrates for the TAG assembly; however, somewhat of a preference for 18:3n-3 over 20:4n-6 was demonstrated by lipidomics analysis. A structure-functional analysis of LiDGAT1 revealed that the N-terminal Pleckstrin homology (PH) domain is important but not essential for TAG generation in the yeast expression system. Deletion of the PH domain led to decreased TAG formation and ARA incorporation into TAG in yeast. Remarkably, we found the PH domain to be present in the DGAT1 of a number of chlorophytes, in a charophyceaen multicellular alga, in two diatoms and in the liverwort Marchantia polymorpha, but absent from those of red algae, higher plants and animals. Our findings indicate the promiscuity of LiDGAT1 for VLC-PUFA and suggest a specific role for this enzyme in the neutral lipid metabolism of L. incisa that needs to be further investigated by molecular engineering approaches.     

Identification and characterization of a novel diacylglycerol acyltransferase gene from <Emphasis Type="Italic">Mortierella alpina</Emphasis>

Objectives

To clone and express a diacylglycerol acyltransferase (DGAT) gene from Mortierella alpina in Saccharomyces cerevisiae and characterize oil production and fatty acid composition of the resulting recombinant

Results

A new, full-length cDNA, putatively encoding a DGAT, was cloned from M. alpina. We subsequently cloned the gene, except the transmembrane-encoding region, termed MaDGAT, its molecular mass was 31.3 kDa. MaDGAT shares 75% identity with a DGAT from Mortierella verticillata NRRL 6337. A recombinant vector expressing MaDGAT, pYES2-DGAT, was constructed and transformed into S. cerevisiae H1246, a neutral, lipid-deficient quadruple mutant. TLC analysis showed that the recombinant vector restored triacylglycerol biosynthesis and its content in the recombinant strain was 3.9%.

Conclusion

MaDGAT is a novel DGAT gene and could increase TAG biosynthesis in M. alpina or other filamentous fungi, thereby promoting the synthesis of polyunsaturated fatty acids.

     

<Emphasis Type="Italic">Rhodococcus</Emphasis> bacteria as a promising source of oils from olive mill wastes

The accumulation of triacylglycerols (TAG) is a common feature among actinobacteria belonging to Rhodococcus genus. Some rhodococcal species are able to produce significant amounts of those lipids from different single substrates, such as glucose, gluconate or hexadecane. In this study we analyzed the ability of different species to produce lipids from olive oil mill wastes (OMW), and the possibility to enhance lipid production by genetic engineering. OMW base medium prepared from alperujo, which exhibited high values of chemical oxygen demand (127,000 mg/l) and C/N ratio (508), supported good growth and TAG production by some rhodococci. R. opacus, R. wratislaviensis and R. jostii were more efficient at producing cell biomass (2.2–2.7 g/l) and lipids (77–83% of CDW, 1.8–2.2 g/l) from OMW than R. fascians, R. erythropolis and R. equi (1.1–1.6 g/l of cell biomass and 7.1–14.0% of CDW, 0.1–0.2 g/l of lipids). Overexpression of a gene coding for a fatty acid importer in R. jostii RHA1 promoted an increase of 2.2 fold of cellular biomass value with a concomitant increase in lipids production during cultivation of cells in OMW. This study demonstrates that the bioconversion of OMW to microbial lipids is feasible using more robust rhodococal strains. The efficiency of this bioconversion can be significantly enhanced by engineering strategies.     

Enhanced production of fatty acids in three strains of microalgae using a combination of nitrogen starvation and chemical inhibitors of carbohydrate synthesis

Microalgae are attracting much attention as superior biodiesel producers. In particular, under stressful conditions, they accumulate organic compounds consisting entirely of carbon and hydrogen. The aim of this work was to increase intracellular fatty acid content in Dunaliella tertiolecta (Chlorophyceae), Nannochloropsis oculata (Eustigmatophyceae), and Porphyridium cruentum (Rhodophyceae) using a combination of nitrogen starvation and chemical inhibitors of carbohydrate biosynthesis. These microalgae were subjected to nitrogen starvation and their physiological changes were then observed over time. In D. tertiolecta, no significant change in total fatty acid content was detected on day 3.5 relative to the initial total fatty acid content (day 0), while total carbohydrate content dramatically increased as the nitrogen starvation period was extended. In N. oculata, total fatty acid content rapidly increased, reaching up to nearly 40% of the DCW at day 3.5. However, total carbohydrate content exhibited a gradual reduction throughout the experiment. In P. cruentum, total carbohydrate content increased up to 43% of DCW on day 3.5 and total fatty acid content increased slightly under nitrogen depletion. These data suggest that different eukaryotic microalgae use different storage products under stressful conditions. Among the three strains, D. tertiolecta showed decreased total carbohydrate content and enhanced total fatty acid content following inhibition of carbohydrate synthesis by dichlorophenyl dimethylurea and cyclohexane diamine tetra acetic acid. The results demonstrate the possibility of furthering our understanding of the fatty acid and carbohydrate biosynthesis metabolic network that responds to environmental changes in microalgae.     

The combined effects of blue light and dilution rate on lipid class and fatty acid composition of <Emphasis Type="Italic">Tisochrysis lutea</Emphasis>

The lipid class and the fatty acid compositions of microalgae highly influence bivalve larval and post-larval development. Light is an essential environmental factor for microalgal culture, and quantity and quality of light may induce changes in the biochemical composition of the algae. The objective of this study was to investigate the effect of light spectrum (blue vs. white light) on lipid class and fatty acid compositions of Tisochrysis lutea cultured in a chemostat. Two different dilution rates (D) were assayed for each light spectrum: 0.2 and 0.7 day^?1. Triacylglycerol (TAG), sterol, and hydrocarbon (HC) content increased sharply at low D. The proportion of alkenones was significantly reduced under blue light. Polyunsaturated fatty acids (PUFA), and particularly n-3 PUFA, content in phospholipids (PL) increased under blue light compared to white light at low D. Thus, blue light raised 22:6(n-3) levels in total lipids of T. lutea at low D. The cultivation of T. lutea in a chemostat at low D under blue light may improve nutritional value as feed for bivalve larvae by modifying the PUFA profile, especially increasing 22:6(n-3).     

Drastic anthocyanin increase in response to <Emphasis Type="Italic">PAP1</Emphasis> overexpression in <Emphasis Type="Italic">fls1</Emphasis> knockout mutant confers enhanced osmotic stress tolerance in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Key message

pap1 - D/fls1ko double mutant plants that produce substantial amounts of anthocyanin show tolerance to abiotic stress.

Abstract

Anthocyanins are flavonoids that are abundant in various plants and have beneficial effects on both plants and humans. Many genes in flavonoid biosynthetic pathways have been identified, including those in the MYB-bHLH-WD40 (MBW) complex. The MYB gene Production of Anthocyanin Pigment 1 (PAP1) plays a particularly important role in anthocyanin accumulation. PAP1 expression in many plant systems strongly increases anthocyanin levels, resulting in a dark purple color in many plant organs. In this study, we generated double mutant plants that harbor fls1ko in the pap1-D background (i.e., pap1-D/fls1ko plants), to examine whether anthocyanins can be further enhanced by blocking flavonol biosynthesis under PAP1 overexpression. We also wanted to examine whether the increased anthocyanin levels contribute to defense against osmotic stresses. The pap1-D/fls1ko mutants accumulated higher anthocyanin levels than pap1-D plants in both control and sucrose-treated conditions. However, flavonoid biosynthesis genes were slightly down-regulated in the pap1-D/fls1ko seedlings as compared to their expression in pap1-D seedlings. We also report the performance of pap1-D/fls1ko seedlings in response to plant osmotic stresses.

     

The atf2 gene is involved in triacylglycerol biosynthesis and accumulation in the oleaginous Rhodococcus opacus PD630

Rhodococcus opacus PD630 is an oleaginous bacterium able to accumulate large amounts of triacylglycerols (TAG) in different carbon sources. The last reaction for TAG biosynthesis is catalyzed by the bifunctional wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) enzymes encoded by atf genes. R. opacus PD630 possesses at least 17 putative atf homologous genes in its genome, but only atf1 and atf2 exhibited a significant DGAT activity when expressed in E. coli, as revealed in a previous study. The contribution of atf1 gene to TAG accumulation by strain PD630 has been demonstrated previously, although additional Atfs may also contribute to lipid accumulation, since the atf1-disrupted mutant is still able to produce significant amounts of TAG (Alvarez et al., Microbiology 154:2327–2335, 2008). In this study, we investigated the in vivo role of atf2 gene in TAG accumulation by R. opacus PD630 by using different genetic strategies. The atf2-disrupted mutant exhibited a decrease in TAG accumulation (up to 25–30 %, w/w) and an approximately tenfold increase in glycogen formation in comparison with the wild-type strain. Surprisingly, in contrast to single mutants, a double mutant generated by the disruption of atf1 and atf2 genes only showed a very low effect in TAG and in glycogen accumulation under lipid storage conditions. Overexpression of atf1 and atf2 genes in strain PD630 promoted an increase of approximately 10 % (w/w) in TAG accumulation, while heterologous expression of atf2 gene in Mycobacterium smegmatis caused an increase in TAG accumulation during cultivation in nitrogen-rich media. This study demonstrated that, in addition to atf1 gene, atf2 is actively involved in TAG accumulation by the oleaginous R. opacus PD630.     

Both epiphytic and endophytic strains of <Emphasis Type="Italic">Rhodococcus fascians</Emphasis> influence transporter gene expression and cytokinins in infected <Emphasis Type="Italic">Pisum sativum</Emphasis> L. seedlings

Some strains of the soil bacterium Rhodococcus fascians maintain an epiphytic life style while others become endophytic. Virulent, endophytic strains cause multiple shoot growth and inhibit root growth of seed-inoculated Pisum sativum L. We were interested in assessing, at the molecular level, the impact of strains of contrasting niche on the emerging shoots and roots of inoculated seeds. The presence of R. fascians was monitored microscopically, endogenous cytokinin and chlorophyll levels were measured, and the expression of genes monitored by RT-qPCR. The expression of the pea sugar transporter genes (SWEET and SUT), amino acid (AAP) transporters and cell wall invertase gene family members, as well as expression of plant and bacterial cytokinin biosynthesis (IPT), activation (LOG) and degradation (CKX) genes were monitored. Both the virulent strain and the epiphytic strain affected the expression of the transporter genes, with less obvious differences between the strains on the shoot compared with the effect on the root. Strong expression of the R. fascians genes, RfIPT, RfLOG and RfCKX, in pea seedlings at 15 days post inoculation was mirrored by increased expression of transporter gene family members in the plant. However, the elevated levels of isopentenyl adenine-type and zeatin-type cytokinins were not consistently associated with the virulent strain. In conclusion, while both the virulent strain and the epiphytic strain impacted the expression of transporter genes in the shoots and roots, only the virulent strain affected morphology. The inhibited root growth, the greening of the roots, and the expression of the pea response regulators in the infected roots are indicative of a response to cytokinin, but a role for the ‘classical’ cytokinins as virulence determinants was not established.