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The ecological footprint and economic performance of the current suite of biofuel production methods
make them insufficient to displace fossil fuels and reduce their impact on the inventory of Green House
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Gas (GHG) in the global atmosphere. Algae metabolic engineering forms the basis for 4th generation
biofuel production which can meet this need. The first generation biofuels are known to be made from
agricultural products such as corn or sugarcane. The second generation biofuels use all forms of (lingo)
cellulosic biomass. The third and fourth generation of biofuel production involves ‘‘algae-to-biofuels’’
technology: the former is basically processing of algae biomass for biofuel production, while the latter is
about metabolic engineering of algae for producing biofuels from oxygenic photosynthetic
microorganisms. Our review focuses on the research achievement of metabolic engineering of algae for
biofuel production. It is concluded that 4th generation biofuel production has introduced the ‘‘cell
factory’’ concept in this field, and shifted the research paradigm. There still exists several technical
bottlenecks in algae biofuel research and development, which can only be solved by the use of post-
genome tools on these photosynthetic organisms.
Broader context
The energy crisis and climate change have become the two main topics in all summit conferences since the beginning of this
millennium. It has been found that algae may be an ideal production system for renewable biofuels since these photosynthetic
organisms are easy to grow in fresh water, sea water or brackish water, and consume CO2 as their carbon source to convert solar
energy into chemical energy for cellular activities. With the aid of metabolic engineering, we are able to modify algae to produce
biofuels continuously while they are grown in ponds or closed photobioreactor systems. This approach possesses great potential in
providing sustainable and clean energy for our society to replace fossil fuels. Our review article concludes that the typical amount of
process steps required for biofuel production using 4th generation biofuel production methods is much less than the prior methods,
thereby avoiding large capital and operational expenditures.
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cyanobacterium Anacystis nidulans R2 in 1987.9 More recently, fusions to highly expressed endogenous proteins,145 or to highly
the genomic revolution has significantly advanced metabolic expressed recombinant proteins in the chloroplast.146
engineering for many photosynthetic organisms. As a milestone, Besides Chlamydomonas reinhardtii, Chlorella is another
Synechocystis sp. PCC 6803 (Synechocystis) has become the first unicellular green algae transformation system.96 Jarvis97 has
photosynthetic organism for which the genome was completely described the development of a transient expression system for
sequenced. The length of this circular genome is 3 573 471 bp.10 Chlorella ellipsoidea using a heterologous gene, or firefly lucif-
A total of 3317 protein coding genes was assigned (http:// erase. El-Sheekh98 has created a transgenic expression system of
genome.kazusa.or.jp/cyanobase/Synechocystis). Synechocystis is Chlorella kessleri by using the gene for b-glucuronidase (GUS).
a freshwater, non-filamentous, non-nitrogen fixing cyanobac- The stable transformants exhibited GUS activity. Hawkins101 has
teria capable of both photoautotrophic and heterotrophic developed the PEG method to use Chlorella (C. vulgaris C-27 and
growth. The genomic information, coupled with the biochem- C. sorokiniana) to express a recombinant heterologous protein
istry and physiological information available for Synechocystis consisting of an extracellular secretion signal sequence inserted
sp. PCC 6803, has made this strain one of the most popular between a promoter region and a gene for human growth
hormone (hGH). In 2002, Kim et al. 147 transformed the proto-
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of oxygenic photosynthesis of higher plants since the size of its growth hormone gene (fGH), and stable FGH protein expression
genome is relatively small compared to any higher plant systems. was detected in the engineered microalgae.
Marine diatoms have been a new research frontier due to their
widespread existence on the Earth and their adaptability to
a varying environment, and their substantial biomass production
2.2 Eukaryotic microalgae
in water. Establishment of the diatom genome program and
The biotechnology of eukaryotic microalgae has entered into transgenic technology has laid a sound foundation for diatomic
a rapid developing phase in recent years. The availability of genetic manipulation.148 The recombinant diatoms have found
genomic information for eukaryotic microalgae has greatly applications in both fundamental studies and industrial
facilitated fundamental study and industrial applications. Table production.149,137 Using recombinant DNA technology, Duna-
111–95 is the list for microalgal genome sequences which have been hay132,149 has engineered two species of diatoms to insert chime-
completed or are to be completed. rical plasmid vectors containing a bacterial antibiotic resistance
Transgenic technology of eukaryotic microalgae for exoge- neomycin phosphotransferase II (nptII) gene into the diatoms
nous gene transformation and expression began in the 1980s. It Cyclotella cryptica and Navicula saprophila.
generally resulted in the random integration of exogenous genes
into the nuclear genome. Selection markers, promoters, reporter
2.3 Manipulation of microalgal metabolism
genes, transformation technology and other genetic tools or
methods have been successfully applied to several microalgae. The recombinant DNA technique for algae has proven to be
More than 30 different microalgal species have been successfully capable of creating constructs for both prokaryotes and
engineered by gene transformation into the cellular nucleus, eukaryotes which may replicate and possess novel functions. In
chloroplasts and mitochondria. Table 2 lists the eukaryotic addition to direct metabolic pathway modification, algal meta-
microalgae which have been investigated with gene trans- bolic engineering also involves targeted improvement of cellular
formation.96–139 activities by manipulation of enzymatic, transport, and regula-
Metabolic engineering research of eukaryotic microalgae was tory functions of the photosynthetic cells using other biological
mainly focused on unicellular green algae (i.e. Chlamydomonas and engineering approaches. Algae are subjected to a wide range
reinhardtii, and chlorella vulgaris) and marine diatoms. Chla- of environmental stresses, such as temperature elevation,
mydomonas reinhardtii is the most studied eukaryotic microalgae. nutrient depletion, or other adverse external factors in their
It is an ideal model organism for the understanding of various growth environment.150 Consequently, cells will respond with
fundamental mechanisms of biological processes, such as altered metabolic programming to adapt to the varying envi-
oxygenic photosynthesis, circadian rhythms, and flagella ronment. Environmental stress has been successfully used as
biogenesis. Recently, C. reinhardtii has also been studied as a means to manipulate microalgal metabolism in favor of lipid
a potential algal system for anaerobic biohydrogen produc- accumulation during the cell cultures. For instance, Liu et al.151
tion.140 The chloroplast DNA map of C. reinhardtii was estab- demonstrated that a high initial iron concentration in the
lished in 1978.141 Successful genetic transformation has also been medium has induced elevated lipid accumulation in marine strain
conducted in the C. reinhardtii chromosome, chloroplast142 and C. vulgaris. Illman et al.152 found that nitrogen deficiency resulted
mitochondrial genome.143 It is obvious that algae possess in an increase in the cellular lipid contents for all five investigated
a number of advantages over higher plant systems for the Chlorella strains. Among them, C. emersonii, C. minutissima and
production of recombinant proteins.144 In particular, Chlamy- C. vulgaris showed an increase in lipid content of 63%, 56% and
domonas has been demonstrated to be capable of producing 40% of their dry weight, respectively. Thomas et al.153 observed
recombinant proteins, even those complex mammalian thera- the effect of nitrogen stress on the algae lipid fraction for
peutic proteins and monoclonal antibodies are available at Botryococcus, Isochrysis and Dunaliella species. They found that
commercially viable levels with existing production platforms.144 nitrate deficiency could cause the protein content and the chlo-
Further research efforts have been undertaken to improve rophyll level to decrease while carbohydrate and lipids would
protein accumulation and stability by the expression of cleavable exhibit a species-specific change. Santos et al.154 have shown that
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Table 1 List for microalgal genome sequences which have been completed or are to be completed
Condition Phylum Species Strain GenBank Length (nt) Genes Proteins References
Chlorophyta
Chaetosphaeridium globosum M1311 AF494279 56,574 77 46 22
Chara vulgaris AY267353 67,737 76 46 23
Chlamydomonas eugametos CCAP11/6A AF008237 22,897 20 14 24
Chlamydomonas reinhardtii CC-503 cw92 mt+ U03843 15,758 25 8 12,25
Chlorokybus atmophyticus SAG 48.80 EF463011 201,763 89 58 26
Dunaliella salina CCAP19/18 GQ250045 28,331 21 9 27
Mesostigma viride NIES-296 AF353999 42,424 70 41 28
Oltmannsiellopsis viridis NIES 360 DQ365900 56,761 63 36 29
Prototheca wickerhamii UTEX 1553 U02970 55,328 63 36 30
Pseudendoclonium akinetum UTEX 1912 AY359242 95,880 94 72 31
Scenedesmus obliquus KS3/2 UTEX 393 X17375 42,781 53 20 32
Cryptophyta
Rhodomonas salina CCMP1319 AF288090 48,063 73 44 33
Haptophyta
Emiliania huxleyi 1516 AY342361 29,013 48 21 34
Hemiselmis andersenii CCMP644 EU651892 60,553 74 44 35
Ochrophyta (Phaeophyceae)
Chattonella marina KA11-m-1 AB546636 44,772 69 41 36
Desmarestia viridis CCAP1306/14 AY500367 39,049 68 39 37
Dictyota dichotoma AY500368 31,617 66 38 37
Fucus vesiculosus 1753 AY494079 36,392 67 38 37
Laminaria digitata CCAP1321 AJ344328 38,007 67 39 38
Ochromonas danica CCAP933 AF287134 41,035 75 44 39
Pylaiella littoralis Kjellam AJ277126 58,507 79 52 40
Saccharina angustata SANGU AP011498 37,605 66 38 41
Saccharina coriacea SCORI AP011499 37,500 66 38 42
Saccharina diabolica SDIAB AP011496 37,657 66 38 43
Saccharina japonica SJAPO AP011493 37,657 66 38 44
Saccharina longipedalis SLOPE AP011497 37,657 66 38 45
Saccharina ochotensis SOCHO AP011495 37,656 66 38 46
Saccharina religiosa SRELI AP011494 37,657 66 38 47
Synedra acus (Kutz.) Skabitsch GU002153 46,657 62 35 48
Thalassiosira pseudonana CCMP1335 DQ186202 43,827 61 35 19
Prasinophyta
Micromonas sp. RCC299 FJ859351 47,425 79 39 49
Nephroselmis olivacea NIES-484 AF110138 45,223 70 40 50
Ostreococcus tauri OTH95 CR954200 44,237 78 43 51
Pedinomonas minor CCAP1965 AF116775 25,137 23 11 50
Polytomella capuana SAG 63-5 EF645804 12,998 21 7 52
Pycnococcus provasolii CCMP1203 GQ497137 24,321 36 18 53
Rhodophyta
Cyanidioschyzon merolae 10D D89861 32,211 62 34 54
Chondrus crispus Nova Scotia Z47547 25,836 57 29 55
Gracilariopsis andersonii HQ586060 27,036 47 27 56
Gracilariophila oryzoides HQ586059 25,161 44 23 56
Plocamiocolax pulvinata HQ586061 25,894 46 24 56
Porphyra purpurea AF114794 36,753 57 31 57
Completed (chloroplast genomes sequenced)
Bacillariophyta
Phaeodactylum tricornutum CCAP1055/1 EF067920 117,369 170 132 58
Chlorophyta
Bryopsis hypnoides SAG 7.86 GQ892829 153,429 111 69 59
Chara vulgaris DQ229107 184,933 148 105 60
Chlamydomonas reinhardtii CC3269 BK000554 203,828 109 69 25
Chlorokybus atmophyticus SAG 48.80 DQ422812 152,254 157 114 61
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Table 1 (Contd. )
Condition Phylum Species Strain GenBank Length (nt) Genes Proteins References
Cryptophyta
Cryptomonas paramecium CCAP977/2a GQ358203 77,717 115 82 74
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Table 1 (Contd. )
Condition Phylum Species Strain GenBank Length (nt) Genes Proteins References
Table 2 Eukaryotic microalgae which have been investigated with gene transformation
Chlorophyta
Chlorella ellipsoidea Nuclear NP-1 96
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the lipid content in Spirulina increased by approximately three 633 genes, 704 metabolites and 831 metabolic reactions for the
times with the decrease of both nitrogen concentration and study of optimal Synechocystis growth, network capacity and
temperature. functions. The Synechocystis model was used for in silico
Improvement of solar conversion efficiency is of critical predictions of heterotrophic, photoautotrophic and mixotrophic
importance for the development of algae-to-biofuel technologies. growth conditions, and of the insertion of an ethanol fermenta-
Through their billion years of evolution, microalgae have tion pathway. Simulation results were also compared with actual
developed effective light-harvesting antennae complexes (LHCs) metabolic measurements which showed satisfactory agreement.
to capture light energy. Under strong light, their photosystems I More recently, two more papers on Synechocystis metabolic
and II can be overwhelmed by high light intensity which leads to models for photoautotrophic growth have been established in the
photoinhibition.155 In order to manipulate microalgal photo- literature.169,170
synthesis and metabolism, the Melis lab has worked on Chla- The metabolic network for green alga, C. reinhardtii, was
mydomonas cells with a truncated antenna size to create a C. reconstructed,171 accounting for the intracellular localization of
reinhardtii DNA insertional mutant, tla1.156 It was concluded enzymes to three compartments (mitochondria, chloroplastic
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that fully pigmented cells would over-absorb the light and and cytosol). The C. reinhardtii model consists of 484 metabolic
wastefully dissipate heat which might reduce photosynthetic reactions and 458 intracellular metabolites. FBA was used to
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efficiency, and that truncated Chl antenna cells permit greater estimate intracellular metabolic flux distributions under auto-
transmittance of light and a better overall solar utilization by the trophic, heterotrophic and mixotrophic growth conditions. The
microalgal cell cultures. Another group of researchers have used modeling efforts also provide a comprehensive method for
RNA interference technology to down-regulate the expression of annotation of genome databases.
LHC proteins in C. reinhardtii to reduce photodamage and
increase light penetration in microalgal cell growth.157 The
resulting LHC mutant was seen to show more efficient conver- 3. Case studies
sion of solar energy to biomass.
3.1 Gaseous biofuels
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last step in the biosynthesis of isoprene, cleavage of pyrophos- synthase in the cyanobacterium Anabeana 7120, wherein the
phate from isopentyl diphopshate (IPP) and dimethyl allyl gene lspS is maintained as a plasmid, has already been demon-
diphosphate (DMAPP) is carried out by a single enzyme, strated. Recently, Lindberg et al.184 have engineered a platform
isoprene synthase. for bioisoprene production using Synechocystis PCC 6803. They
There is precedence for the cloning of plant isoprene genes into have applied synthetic biology to the synthesis of the native
bacteria. For example, a cDNA clone for isoprene synthase has kudzu (kIspS) and Synechocystis codon-optimized kudzu IspS
been cloned from poplar.180 Expression of this foreign gene, lspS, (SkIspS) genes using the nucleotide sequence of the P. montana
in E. coli, and production of isoprene from the recombinant (kudzu) isoprene synthase gene (IspS)185 without its predicted
organism, has also been demonstrated.180 The class of enzymes to chloroplast transit peptide. These newly designed DNA
which isoprene synthase belongs, terpene cyclases, has been sequences were synthesized to encode isoprene synthase and
relatively well-studied. The 3D structures of the homologs 5-epi- catalyze the biochemical conversion of DMAPP to isoprene. The
aristolochene synthase181 and bornyl diphosphate synthase182 genes were transformed into Synechocystis PCC 6803 under the
have been determined. control of a light driven promoter psbAII. The over-expression of
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As illustrated in Fig. 2, cyanobacteria are known to lack a gene ispS protein with high lighting intensity resulted in the accumu-
for isoprene synthase but can synthesize the penultimate isoprene lation of isoprene at a rate of 50 mg day1 per g dry cell mass.184
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precursors (IPP and DMAPP) via the 2-C-methyl-D-erythritol-4- The metabolic flux relationship was analyzed to investigate the
phosphate (MEP) pathway rather than the mevalonic acid intracellular pathway utilization. The authors have thus found
pathway.183 Like plants, the carbon source for IPP and DMAPP that photosynthetic carbon partitioning among the sugar,
in cyanobacteria is obtained through the photosynthetic fixation terpenoid and fatty acid biosynthetic pathways needs to be
of carbon dioxide. Hence, a cyanobacterium metabolically reprogrammed in order to increase the carbon flow toward the
engineered to incorporate an expressible isoprene synthase gene isoprene synthesis via the terpenoid pathway. This work has
could generate isoprene directly from CO2 and water in the shown that green isoprene can be produced by photosynthetic
presence of sunlight. Cloning and expression of active isoprene cyanobacteria, through heterologous expression of the gene
encoding for the isoprene synthase (IspS), in a reaction of the
MEP pathway, driven by solar energy.184
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recombinant cyanobacteria would produce ethanol with the yield protein) and the lowest Km (0.24 mM). Similarly, the adh gene is
in an order of magnitude of 54 nmol OD730 unit1 litre1 day1. commonly found in many organisms. In 1988 Youngleson et al.
In the same study, ethanol concentrations of approximately 5 cloned an adhII gene into a recombinant plasmid, pCADH100,
mM were reached after 4 weeks of growth. A later patent from Clostridium acetobutylicum.192
describes yields of 1.7 mmol of ethanol per mg of chlorophyll per
hour with the CI-PL temperature inducible promoter (US Patent
3.3 Algal butanol and four carbon alcohols
No. 6699696, 5/21/2001).
More recently, Dexter and Fu (2009)190 have reported their Butanol is one of the four carbon alcohols that may be used as
metabolic engineering work on Synechocystis sp. PCC 6803 that a liquid biofuel. Compared to ethanol, butanol possesses a heat
can photoautotrophically convert CO2 to bioethanol (Fig. 3). content per weight similar to that of gasoline. It also has lower
Transformation was performed using a double homologous vapor pressure, and is hydrophobic.193 Therefore butanol may
recombination system to integrate the pyruvate decarboxylase become a potential transportation fuel to supplement gasoline.
(pdc) and alcohol dehydrogenase II (adh) genes from obligately Among the anaerobic microbes that are capable of butanol
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ethanol producing Zymomonas mobilis into the Synechocystis production, Clostridium acetobylicum is a well known bacterium
chromosome under the control of the strong, light driven psbAII for sugar fermentation to produce butanol.194 The enzymes
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promoter. The engineered Synechocystis has shown an average participating in the formation of butanol have been well char-
yield of 5.2 mmol OD730 unit1 liter1 day1 with no required acterized and the regulating genes been cloned.195 Genome
antibiotic/selective agent during the photobioreactor cultures. information regarding C. acetobylicum is also available. A rele-
Comparison of the mass balances for ethanol production by both vant genome-scale model using flux balance analysis and a linear
the yeast Saccharomyces cerevisiae and the cyanobacterium program can also be used to understand the structure and
Synechocystis PCC 6803 indicates that the theoretical yield of function of the C. acetobylicum metabolic network.196
ethanol from glucose for S. cerevisiae is 0.51 g ethanol/g glucose, After successful metabolic engineering of E. coli for the
while the theoretical yield of ethanol from CO2 for Synechocystis production of butanol and high carbon alcohols, the Liao group
is 0.696 g ethanol/g CO2. has moved on to metabolic engineering of the photosynthetic
It is obvious that pdc and adhII genes play an important role in organism, Synechococcus elongatus PCC7942 to produce
the construction of bioethanol-producing cyanobacteria by butanol, isobutyraldehyde and isobutanol directly from CO2.
metabolic engineering. Therefore, algal ethanol yield and effi- The genetically engineered S. elongatus was active for 8 days and
ciency may be improved by transformation and expression of produced isobutyraldehyde at a higher rate than those reported
these two genes from other organisms. Raj et al.191 have for ethanol, hydrogen or lipid production by cyanobacteria or
compared the biochemical and kinetic properties of the pyruvate algae.197 Fig. 4 shows the butanol production pathway created
decarboxylase enzyme from Zymobacter palmae with purified for the bioconversion of CO2 to butanol by photosynthetic
pdc from three other bacteria. It was found that the Z. palmae organisms. The kivd gene for ketoacid decarboxylase from
enzyme exhibited the highest specific activity (130U per mg of Lactococcus lactis was transformed into S. elongatus by an
expression cassette under the control of the isopropyl-b-D-thio-
galactoside (IPTG) inducible promoter Ptrc.197
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The ACCase gene was then successfully transformed into the The main difference between 4th generation biofuel production
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diatoms C. cryptica and Navicula saprophila. However, the lipid and the previous approaches is that only the former one applies
content of the microalgae was not increased significantly.149 the ‘‘cell factory’’ concept for the production of gaseous and
Nevertheless, Beer et al. have designed strategies to engineer fatty liquid biofuels. The photosynthetic organisms are thus driven by
acid (FA) biosynthesis in plants as follows: Firstly, to over- solar energy from the sun for continuous production of biofuels
express FA biosynthetic enzymes; secondly, to increase the using CO2 as the raw material. The common feature of 4th
availability of precursor molecules, such as acetyl-CoA; thirdly, generation biofuel production methods is that they will secrete
to down-regulate FA catabolism by inhibiting b-oxidation, or the end products out of the cells, which will avoid the costly
lipase hydrolysis; fourthly, to introduce the desaturases to alter fermentation and/or processing of biomass feedstock applied in
saturation profiles; and finally, to optimize FA chain length with current biofuel production.
thioesterases.176 It should be noted that the most critical benefit in 4th gener-
ation biofuel production is the minimization of the number of
process steps between the sun providing energy and the trans-
formation of this energy into a fungible biofuel and capturing
CO2 prior to its emission into the environment. This benefit will
need to be matched to an appropriate biofuel type so that it
exploits the existing fossil fuel distribution infrastructure. It is
evident from Fig. 5 that the typical process steps required for
biofuel production using 4th generation methods are much less
than with the prior methods, thereby avoiding large capital and
operational expenditures.
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Published on 19 April 2011 on http://pubs.rsc.org | doi:10.1039/C0EE00593B
Fig. 5 Comparison of the typical bioprocess steps required for four generations of biofuels production.
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Abbreviations
Acknowledgements
3HBCOA 3-Hydroxybutyryl-CoA This work is supported by the National Basic Research Program
AACoA Acetoacetyl CoA of China (973 program) under grant No. 2011CB200902. This
ACAL Acetaldehyde work is also partially funded by PetroChina Company Ltd. in
ACCoA Acetyl-CoA China. The authors are grateful to the three anonymous
adh Alcohol dehydrogenase reviewers for their critical and constructive comments which
AdhE2 Aldehyde/alcoholdehydrogenase have improved this manuscript.
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