Increased triacylglycerol production in oleaginous microalga Neochloris oleoabundans by overexpression of plastidial lysophosphatidic acid acyltransferase
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Microalgae are promising sources of lipid triacylglycerol (TAG) for sustainable production of natural edible oils and biofuels. Nevertheless, products derived from microalgal TAG are not yet economically feasible; increasing TAG content via targeted genetic engineering of genes in TAG biosynthesis pathway are important to achieve economic viability. To increase TAG content, oleaginous microalga Neochloris oleoabundans was genetically engineered with the endogenous enzyme lysophosphatidic acid acyltransferase (NeoLPAAT1) responsible for plastidial TAG biosynthesis
NeoLPAAT1 was found to contain all canonical motifs attributed to LPAAT proteins, two hypothetical membrane-spanning domains and a putative chloroplast transit peptide, indicating as a member of plastidial LPAAT type 1 subfamily. The NeoLPAAT1-expression cassette integrated in N. oleoabundans transformant was confirmed by PCR. The neutral lipid content in the transformant detected by Nile red staining was 1.6-fold higher than in wild type. The NeoLPAAT1 transcript was twofold higher in the transformant than wild type. Considerably higher lipid quantity was found in the transformant than wild type: total lipid content increased 1.8- to 1.9-fold up to 78.99 ± 1.75% dry cell weight (DCW) and total lipid productivity increased 1.8- to 2.4-fold up to 16.06 ± 2.68 mg/L/day; while TAG content increased 2.1- to 2.2-fold up to 55.40 ± 5.56% DCW and TAG productivity increased 1.9- to 2.8-fold up to 10.67 ± 2.37 mg/L/day. A slightly altered fatty acid composition was detected in the transformant compared to wild type; polyunsaturated fatty acid (C18:2) increased to 19% from 11%. NeoLPAAT1-overexpression stability was observed in the transformant continuously maintained in solid medium over 150 generations in a period of about 6 years.
Our results demonstrate the considerably increased TAG content and productivity in N. oleoabundans by overexpression of plastidial NeoLPAAT1 that are important for products derived from microalgal TAG to achieve economic viability. Plastidial LPAAT1 can be a candidate for target genetic manipulation to increase TAG content in other microalgal species with desired characteristics for production of natural edible oils and biofuels.
KeywordsBiofuels Lysophosphatidic acid acyltransferase (LPAAT) 1-Acyl-sn-glycero-3-phosphate acyltransferase (AGPAT) Microalgae Lipids Edible oils
lysophosphatidic acid acyltransferase
dry cell weight
gas chromatography–mass spectrometry
quantitative real-time PCR
fatty acid methyl ester
monounsaturated fatty acid
polyunsaturated fatty acid
saturated fatty acid
Microalgae are promising sources of lipid triacylglycerol (TAG) for sustainable production of natural edible oils as an alternative to plant derived oil [1, 2] and biofuels as an environmentally safe alternative to fossil fuels [3, 4]; because they possess short life cycles, perform photosynthesis, require non-arable land and absorb a large amount of CO2. Nevertheless, there are several challenges that need to be overcome before products derived from microalgal TAG can be economically produced at a commercial scale, one of which is the lack of microalgal strains with high TAG content [3, 5]. Increasing TAG content in microalgae could be achieved by targeted genetic engineering of genes in TAG biosynthesis pathway [4, 6, 7].
The TAG biosynthesis pathway in microalgae is not yet fully understood but considered to be most similar to that operating in higher plants . In the model plant Arabidopsis thaliana and the model microalga Chlamydomonas reinhardtii, two sets of homologous enzymes catalyze two distinct and parallel TAG biosynthesis pathways, one in the plastid (prokaryotic pathway) and the other in the endoplasmic reticulum (ER; eukaryotic pathway) [9-13]. The ER pathway has been shown as an important route of TAG biosynthesis, however, increasing evidence suggests that the plastidial pathway also plays an important role in TAG biosynthesis in C. reinhardtii [13, 14]. In TAG biosynthesis pathway, lysophosphatidic acid acyltransferase (LPAAT or LPAT; EC 18.104.22.168) also known as 1-acyl-sn-glycero-3-phosphate acyltransferase (AGPAT) catalyzes the acylation of the sn-2 position of lysophosphatidic acid to generate a key intermediate, phosphatidic acid . C. reinhardtii has been shown to possess CrLPAAT2 localized to ER membranes and CrLPAAT1 localized to plastid [11, 16]. Overexpression of LPAAT1 for enhancing TAG accumulation has been attempted so far in very few microalgal species. CrLPAAT1 overexpression in C. reinhardtii led to > 20% increase in oil content  and LPAAT1 (AGPAT1) overexpression in diatom Phaeodactylum tricornutum led to increase in lipid content by 1.81-fold . However, no LPAAT1 overexpression has been reported so far in oleaginous microalga Neochloris oleoabundans.
Neochloris oleoabundans, a taxonomic synonym of Ettlia oleoabundans , is a promising source of TAG; because under nitrogen starvation condition, it produces lipids 36–54% of its cell dry weight and up to 80% of its total lipids is TAG . However, the knowledge concerning N. oleoabundans is very limited; no genomic sequences are available. To enable targeted genetic manipulation of TAG biosynthesis, the stable nuclear transformation system of N. oleoabundans has been established  and the cDNA encoding LPAAT1 of N. oleoabundans (NeoLPAAT1) has been cloned .
In this study, we tested whether overexpression of endogenous plastidial LPAAT1 would affect TAG biosynthesis in oleaginous microalga. The plastidial LPAAT1 cDNA sequence of N. oleoabundans (NeoLPAAT1) was characterized. The NeoLPAAT1-overexpressing N. oleoabundans was generated and characterized with regards to growth and neutral lipid accumulation in the cells, lipid content and productivity, and fatty acid composition.
Comparative homologue of NeoLPAAT1
Selection of N. oleoabundans transformants
Detection of NeoLPAAT1‑expression cassette integration
The integration of NeoLPAAT1-expression cassettes in N. oleoabundans was analyzed using genomic PCR with primers specific to NeoLPAAT1 coding sequence. The expected 943-bp amplicon was detected in the selected transformants: AR-LPAAT-48, AR-LPAAT-90, B2-LPAAT-38 and B2-LPAAT-46, but not in wild type (Fig. 2b). The 943-bp amplicon subjected to DNA sequencing was confirmed to be NeoLPAAT1 coding sequence. Therefore, the NeoLPAAT1-expression cassettes were successfully introduced into the transformants. The amplicon from the resident NeoLPAAT1 gene including introns was 1865 bp. Because one of the two primers used in this PCR was located on two exons, the resident NeoLPAAT1 gene was not amplified. The PCR-positive transformants were further analyzed for growth characteristics.
Growth of the transformants
Neutral lipids of the transformants
To investigate the potential high-lipid production of the selected transformants, neutral lipids in the cells during +N growth condition were monitored by Nile red staining. The exponential growth of N. oleoabundans has been shown to accompany the decrease in N concentration; N-limited growth can stimulate the cells to produce more lipids . The levels of neutral lipid accumulation in transformants AR-LPAAT-48, AR-LPAAT-90, B2-LPAAT-38 and B2-LPAAT-46 were different; they were higher than that in wild type (Fig. 3b). Whether the different levels of neutral lipid accumulation in the transformant clones are due to copy number or integration positional effect of the NeoLPAAT1-expression cassettes remains to be investigated. Among the transformants, B2-LPAAT-46 was found to reach maximum neutral lipid content (day 33) earlier than wild type (day 38) and have the highest neutral lipid content which increased to 1.6-fold compared to the maximum content in wild type (Fig. 3b). Therefore, transformant B2-LPAAT-46 was selected for subsequent experiments.
Evaluation of NeoLPAAT1 transcript
Lipid productivity analysis
Fatty acid composition analysis
Long‑term stability of transformants
Transformants AR-LPAAT and B2-LPAAT were subcultured (every 2 weeks) in solid BBM over 150 generations in a period of about 6 years. Neutral lipid accumulation in the transformants were periodically checked by Nile red staining; higher lipid-accumulation than wild-type trait was observed in all transformants used in this study, indicating the NeoLPAAT1 overexpression stability.
This study is based on the overexpression of endogenous plastidial NeoLPAAT1 in N. oleoabundans to increase TAG accumulation for sustainable production of natural edible oils and biofuels. The plastidial LPAAT of C. reinhardtii and the putative plastidial LPAAT of other microalgae with sequenced genomes, including Volvox carteri, Ostreococcus lucimarinus and Coccomyxa subellipsoidea, belongs to the same subcluster as LPAAT1 from cyanobacteria and plants, suggesting a common origin of the plastidal isoform of LPAAT1 [11, 32]. Similar to the well characterized CrLPAAT1 of the model microalga C. reinhardtii  and AtLPAAT1 of the model plant Arabidopsis thaliana , plastidial NeoLPAAT1 was found to contain all four canonical motifs attributed to LPAAT proteins, two hypothetical membrane-spanning domains and a putative chloroplast transit peptide (Fig. 1a). NeoLPAAT1 had the closest evolutionary relationship with CvLPAAT1 of Treboxiophycean C. variabilis but was quite distantly related to CrLPAAT1 of Chlorophycean C. reinhardtii (Fig. 1b). This result is consistent with previous report that diacylglycerol acyltransferase type 2 (NeoDGAT2) of N. oleoabundans has the closest evolutionary relationship with CvDGAT2 of C. variabilis but is quite distantly related to CrDGAT2A (DGTT4) of C. reinhardtii . However, N. oleoabundans has been classified based on uninucleate cell morphology to class Chlorophyceae . Classification of N. oleoabundans using 18S and 28S rDNA sequence remains to be verified. N. oleoabundans possesses ER-located NeoDGAT2  and plastidial NeoLPAAT1 (in this study), suggesting the existence of two distinct and parallel TAG biosynthesis pathways. Similar incidents of duplicated sets of TAG assembly enzymes have been observed in C. reinhardtii: CrLPAAT1 and CrDGAT1 located in plastid [11, 35], and CrLPAAT2 and CrDGAT2 located in ER [16, 36].
Among the NeoLPAAT1-overexpressing transformants, B2-LPAAT-46 exhibited the highest neutral lipid content which increased to 1.6-fold compared to the maximum content in wild type (Fig. 3b). The lipid content and productivity were dramatically increased under –N condition when compared to +N condition: in transformant B2-LPAAT-46, total lipid content and productivity increased 3.8- and 1.9-fold, respectively, TAG content and productivity increased 4.8- and 2.2-fold, respectively; in wild type, total lipid content and productivity increased 3.9- and 2.5-fold, respectively, TAG content and productivity increased 4.9- and 3.2-fold, respectively (Fig. 5a, b). The results agreed well with previous report that N. oleoabundans begins accumulating lipids with the application of minimal N starvation, just following exhaustion of exogenous N. In addition, N. oleoabundans exhibits only a small decrease in growth and drastically higher lipid content under N starvation condition; concurrent growth and lipid accumulation result in higher lipid productivity . Lipid productivities of wild type and transformant B2-LPAAT-46 may further increase when the cells cultured under optimal conditions. The lipid productivities of N. oleoabundans have been reported with different experimental conditions resulting in large variations in performance, i.e. total lipid productivities vary from 9 to 134 mg/L/day [27, 29, 37, 38] and TAG productivities vary from 6 to 216 mg/L/day [27, 39], making it difficult to compare the reports with each other. The TAG content of 55.40 ± 5.56% DCW produced by the transformant in this study (Fig. 3b) was the highest in comparison to those produced by LPAAT1-overexpressing microalgae reported so far [11, 17] and also 20% higher than that (46.1 ± 1.6% DCW) produced by N. oleoabundans overexpressing NeoDGAT2 . The results suggest that the plastidial pathway also plays an important role in TAG biosynthesis in N. oleoabundans. The FA composition in transformant B2-LPAAT-46 was slightly altered; the linoleic acid (C18:2) increased to 19% from 11% when compared to wild type (Fig. 6). Whether C18:2-acyl-CoA is a preferred substrate of NeoLPAAT1 remains to be determined.
Silencing or down regulation of the non-required heterologous genes when expressed at high levels has been reported in C. reinhardtii [40, 41]. Heterologous gene silencing has also been observed in N. oleoabundans; when the transformants introduced with Gfp gene  continuously maintained in solid BBM medium for over a year, the green fluorescent protein activity seems to diminish . However, overexpression of endogenous NeoDGAT2 in N. oleoabundans has been shown to be stable . Therefore, to avoid heterologous gene silencing, endogenous NeoLPAAT1 was used in this study. Transformants AR-LPAAT and B2-LPAAT were continuously maintained in solid BBM over 150 generations in a period of about 6 years. All transformants used in this study were periodically checked for neutral lipid accumulation by Nile red staining and found to have higher lipid accumulation than wild-type, indicating the NeoLPAAT1 overexpression stability.
We characterized the plastidial NeoLPAAT1 sequence and successfully created N. oleoabundans transformant overexpressing NeoLPAAT1 with considerably increased TAG content and productivity. A slightly altered fatty acid composition was detected in the transformant compared to wild type. Stability of NeoLPAAT1 overexpression was observed in the transformant continuously maintained in solid medium over 150 generations in a period of about 6 years. The considerably increased TAG content and productivity in N. oleoabundans by overexpression of NeoLPAAT1 are important for products derived from microalgal TAG to achieve economic viability. Plastidial LPAAT1 can be a candidate for target genetic manipulation to increase TAG content in other microalgal species with desired characteristics for production of natural edible oils and biofuels.
Strain and growth conditions
Neochloris oleoabundans strain UTEX 1185, obtained from the Algal Culture Collection at the University of Texas, was cultured in liquid or in solid (1.5% Difco Bacto agar) Bold’s basal medium (BBM) [42, 43] under constant illumination of 55–60 μmol photons/m2/s at 30 °C. Cultures in liquid medium started with cells at density of ~ 1.5 × 107 cells/mL (OD750 = 0.3). For cell growth under nitrogen-sufficient ( +N) condition, cultures were maintained in 500 mL Erlenmeyer flasks containing 200 mL of BBM; the flasks were sealed and shaken at 100 rpm. Cell density of the cultures was evaluated using hemocytometer for cell counting and spectrophotometer for OD750. Doubling time of the cells was calculated as described . For nitrogen-starvation (−N) condition, the cells grown in BBM at exponential phase were harvested, washed and resuspended in 200 mL of BBM without NaNO3 (BBM-N) in 500 mL Erlenmeyer flasks, shaken at 50 rpm and supplied with 50 L/h bubbling-filtered air.
NeoLPAAT1 sequence analysis
The 1,023-bp LPAAT cDNA sequence of N. oleoabundans encoding 340 amino acids (GenBank: MF706164; protein id: AUS8446) has been cloned previously as plasmid pYES2-FLPAT34 . We designated this protein as NeoLPAAT1. To further analyze the NeoLPAAT1 sequence, various methods were performed as follows. The NeoLPAAT1 was aligned with other LPAAT1 using ClustalW multiple alignment program . The membrane-spanning domains were predicted by TMHMM v2.0 . The chloroplast transit peptide of the NeoLPAAT1 was predicted using PredAlgo . The phylogenetic tree of NeoLPAAT1 was constructed using the neighbor-joining method in MEGA 7 .
Construction of transformation vectors
To construct NeoLPAAT1 cDNA under the control of promoters HSP70-RBCS2 (AR)  and β2-tubulin (β2-Tub)  of C. reinhardtii, plasmids pAR-LPAAT and pB2-LPAAT harboring the gene cassettes AR-NeoLPAAT1-3′rbcS2 and (β2-Tub)-NeoLPAAT1-3′rbcS2, respectively (Fig. 2a), were constructed by replacing the AR-ChGfp-3′rbcS2 fragment of pChGFP-Hyg3  with the PCR fragments containing: (i) AR promoter from pCB740  or β2-Tub promoter from pHyg3  (ii) NeoLPAAT1 cDNA (GenBank: MF706164) from pYES2-FLPAT34 , and (iii) 3′UTR of 3′rbcS2 from pCrGFP . Both pAR-LPAAT and pB2-LPAAT contained hygromycin B resistance gene Hyg3 [20, 46] used as a selectable marker.
Transformation of N. oleoabundans
To generate transformants overexpressing NeoLPAAT1, plasmids pAR-LPAAT and pB2-LPAAT were transformed into the N. oleoabundans nuclear genome using electroporation as described previously . N. oleoabundans cells were electroporated using a Gene Pulser (Bio-Rad Labs) set electric field strength at 1000 V/cm, capacitance at 25 μF and resistance at 200 Ω. The electroporated cells were spread on a BBM agar plate containing 5 μg/mL hygromycin B. After incubation for 2 weeks, the resulting transformants AR-LPAAT and B2-LPAAT appeared.
Genomic PCR analysis
The integration of NeoLPAAT1-expression cassettes in the nuclear genome of N. oleoabundans were verified using genomic PCR. The genomic DNA of N. oleoabundans was isolated as described . PCR was performed with primers specific to NeoLPAAT1 coding sequence: LPAAT-F1 (CGGGATCCTAGCTAGCATGCTGTGCCCCACTGTCG) and LPAAT-R10 (GATGGCAGGGTGAATCACGAGTTTAACTTTGCCTGG). The touchdown PCR was carried out 11 cycles for the first phase (denature at 98 °C for 10 s, annealing at 80 °C for 30 s with a 1 °C decrease in every successive cycle, extension at 72 °C for 30 s) and 25 cycles for second phase (denature at 98 °C for 10 s, annealing at 70 °C for 30 s, extension at 72 °C for 30 s, including initial denaturation at 98 °C for 3 min and final extension at 72 °C for 7 min). The PCR product was investigated in a 1.5% agarose gel and further verified by DNA sequencing analysis. The amplicon of the NeoLPAAT1 coding sequence was 943 bp.
Nile red fluorescence assay
To analyze the level of neutral lipids, cells grown under +N condition ( ~ 1.5 × 107 cells/mL) was stained with fluorescent dye Nile red dissolved in acetone to final concentration of 1 μg/mL and incubated in the dark for 10 min. The fluorescence intensity of the stained cells in a 96-well plate was determined using a spectrofluorometer (Beckman Coulter DTX-880, USA) with excitation at 535 nm and emission at 574 nm. Specific fluorescence intensities were obtained by subtracting the autofluorescence of the unstained cells and normalized by cell numbers.
Quantitative real time PCR analysis
Relative NeoLPAAT1 transcript abundance was quantified using quantitative real-time PCR (qPCR). Total RNA was extracted from cells cultured under −N condition for 1 day using TRI Solution (GeneMark, Taiwan). The cDNA was prepared from the total RNA with oligo (dT)18 primer using RevertAid H Minus First Strand cDNA Synthesis Kit (Thermo Scientific, Canada). The cDNA was amplified using KAPA SYBR FAST qPCR Kit (Kababiosystems, USA) with NeoLPAAT1-gene specific primers: LPAAT-RT-F1 (GAGCTTCCTGGACATTTACACGC) and LPAAT-RT-R1 (CAGCTCGCTGCATTGTTTTAGG); and endogenous Actin (NeoActin)-gene specific primers: NeoActin-F1 (ACACTGTGCCCATCTATGAGGG) and NeoActin-R1 (CTTGATGTCACGCACGATTTCG). Quantitative RT-PCR analysis was performed using Mastercycler realplex4 and realplex software (Eppendorf, Germany). The NeoLPAAT1 transcript level was normalized to a reference, NeoActin transcript.
Lipid extraction and quantification
Total lipids of N. oleoabundans grown under +N and −N condition were extracted based on modified Bligh and Dyer method . The cell pellet of approximately 80 mg (50 OD750) was suspended in chloroform:methanol (1:2, v/v). The cells were lysed using vortexing at 2700 rpm (Vortex Genie2 G560E, Scientific Industries, USA) including 0.5 mm glass beads, then chloroform:water (1:1, v/v) was added to the mixture. Chloroform phase was collected and evaporated using nitrogen gas. Total lipids were determined gravimetrically. The TAG was subsequently separated from total lipids using thin-layer chromatography (TLC) with solvent hexane:diethyl ether:acetic acid (70:30:1, v/v/v) and a reference substance, glyceryl trioleate (92860 Sigma-Aldrich, USA). TAG was quantified using iodine staining and Quantity One 1-D analysis software (Bio-Rad Labs., USA). Total lipid and TAG content was calculated as percentage of dry cell weight (% DCW). DCW of a sample was determined gravimetrically after drying the cells. The lipid productivity was calculated using the formula PLipid (mg/L/day) = [CLipid (mg/mg) × DCW (mg/L)]/Time (day), where CLipid is lipid content of cells, DCW is dry cell weight, and Time is the cultivation period, as described [27, 38].
Fatty acid composition analysis
To generate fatty acid methyl esters (FAME) by transesterification, TAG extracted from TLC was incubated with 5% (v/v) sulfuric acid in methanol at 70 °C for 3 h in the presence of an internal standard, glyceryl trinonadecanoate (91988 Sigma-Aldrich). FAME analysis was carried out using GC–MS (Agilent 7890A GC system and Agilent 5975C inert XL MSD with Triple-Axis Detector) equipped with Agilent DB-WAX column (30 m length, 0.25 mm i.d., 0.25 μm film thickness). The oven temperature was increased from 50 to 250 °C at a rate of 3 °C/min, the injector and detector temperature were 240 °C and 250 °C, respectively. Helium was used as the carrier gas at flow rate of 1 mL/min. The mass spectra were analyzed using MSD ChemStation software (version E.02.00.493, Agilent) and compared with the NIST08.L database. Fatty acid composition was calculated as percentage of the total fatty acids present in the sample.
The statistical differences between wild type (used as control) and transformant samples were analyzed using two-tailed student’s t test of SPSS Base 16.0 software (SPSS, USA).
WC conceived of the study, designed the experiments, analyzed the data, performed the in silico analysis and wrote the manuscript, KA and SF performed the experiments. All authors read and approved the final manuscript.
We thank Kusol Pootanakit (Institute of Molecular Biosciences, Mahidol University) for providing plasmid pYES2-FLPAT34 and Sitthisak Ketkhunthod for helping lipid evaluation.
The authors declare that they have no competing interests.
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