# Patent

## Title
Designer organisms for photobiological butanol production from carbon dioxide and water

## Abstract

The present invention provides a biosafety-guarded photobiological butanol production technology based on designer transgenic plants, designer algae, designer blue-green algae (cyanobacteria and oxychlorobacteria), or designer plant cells. The designer photosynthetic organisms are created such that the endogenous photobiological regulation mechanism is tamed, and the reducing power (NADPH) and energy (ATP) acquired from the photosynthetic process are used for synthesis of butanol (CH3CH2CH2CH2OH) directly from carbon dioxide (CO2) and water (H2O). The butanol production methods of the present invention completely eliminate the problem of recalcitrant lignocellulosics by bypassing the bottleneck problem of the biomass technology. The photobiological butanol-production technology of the present invention is expected to have a much higher solar-to-butanol energy-conversion efficiency than the current technology and could also help protect the Earth's environment from the dangerous accumulation of CO2 in the atmosphere.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of co-pending U.S. patent application Ser. No. 12/918,784, filed Aug. 20, 2010, which is a U.S. National Stage Application of International Patent Application No. PCT/US2009/034801, filed Feb. 21, 2009, which claimed the benefit of U.S. Provisional Application Numbers U.S. 61/066,845 and U.S. 61/066,835 filed on Feb. 23, 2008. The entire disclosures of all of these applications are incorporated herein by reference.


FIELD OF THE INVENTION
The present invention generally relates to biosafety-guarded biofuel energy production technology. More specifically, the present invention provides a photobiological butanol production methodology based on designer transgenic plants, such as transgenic algae, blue-green algae (cyanobacteria and oxychlorobacteria), or plant cells that are created to use the reducing power (NADPH) and energy (ATP) acquired from the photosynthetic process for immediate synthesis of butanol (CH3CH2CH2CH2OH) directly from carbon dioxide (CO2) and water (H2O).
BACKGROUND OF THE INVENTION
Butanol (CH3CH2CH2CH2OH), a four-carbon alcohol, can be used as a liquid fuel to run engines such as cars. Butanol can replace gasoline and the energy contents of the two fuels are nearly the same (110,000 Btu per gallon for butanol; 115,000 Btu per gallon for gasoline). Butanol has many superior properties as an alternative fuel when compared to ethanol as well. These include: 1) Butanol has higher energy content (110,000 Btu per gallon butanol) than ethanol (84,000 Btu per gallon ethanol); 2) Butanol is six times less “evaporative” than ethanol and 13.5 times less evaporative than gasoline, making it safer to use as an oxygenate and thereby eliminating the need for very special blends during the summer and winter seasons; 3) Butanol can be transported through the existing fuel infrastructure including the gasoline pipelines whereas ethanol must be shipped via rail, barge or truck; and 4) Butanol can be used as replacement for gasoline gallon for gallon e.g. 100% or any other percentage, whereas ethanol can only be used as an additive to gasoline up to about 85% (E-85) and then only after significant modification to the engine (while butanol can work as a 100% replacement fuel without having to modify the current car engine).
A significant potential market for butanol as a liquid fuel already exists in the current transportation and energy systems. Butanol is also used as an industrial solvent. In the United States, currently, butanol is manufactured primarily from petroleum. Historically (1900s-1950s), biobutanol was manufactured from corn and molasses in a fermentation process that also produced acetone and ethanol and was known as an ABE (acetone, butanol, ethanol) fermentation typically with certain butanol-producing bacteria such as Clostridium acetobutylicum and Clostridium beijerinckii. When the USA lost its low-cost sugar supply from Cuba around 1954, however, butanol production by fermentation declined mainly because the price of petroleum dropped below that of sugar. Recently, there is renewed R&D interest in producing butanol and/or ethanol from biomass such as corn starch using Clostridia- and/or yeast-fermentation process. However, similarly to the situation of “cornstarch ethanol production,” the “cornstarch butanol production” process also requires a number of energy-consuming steps including agricultural corn-crop cultivation, corn-grain harvesting, corn-grain starch processing, and starch-to-sugar-to-butanol fermentation. The “cornstarch butanol production” process could also probably cost nearly as much energy as the energy value of its product butanol. This is not surprising, understandably because the cornstarch that the current technology can use represents only a small fraction of the corn crop biomass that includes the corn stalks, leaves and roots. The cornstovers are commonly discarded in the agricultural fields where they slowly decompose back to CO2, because they represent largely lignocellulosic biomass materials that the current biorefinery industry cannot efficiently use for ethanol or butanol production. There are research efforts in trying to make ethanol or butanol from lignocellulosic plant biomass materials—a concept called “cellulosic ethanol” or “cellulosic butanol”. However, plant biomass has evolved effective mechanisms for resisting assault on its cell-wall structural sugars from the microbial and animal kingdoms. This property underlies a natural recalcitrance, creating roadblocks to the cost-effective transformation of lignocellulosic biomass to fermentable sugars. Therefore, one of its problems known as the “lignocellulosic recalcitrance” represents a formidable technical barrier to the cost-effective conversion of plant biomass to fermentable sugars. That is, because of the recalcitrance problem, lignocellulosic biomasses (such as cornstover, switchgrass, and woody plant materials) could not be readily converted to fermentable sugars to make ethanol or butanol without certain pretreatment, which is often associated with high processing cost. Despite more than 50 years of R&D efforts in lignocellulosic biomass pretreatment and fermentative butanol-production processing, the problem of recalcitrant lignocellulosics still remains as a formidable technical barrier that has not yet been eliminated so far. Furthermore, the steps of lignocellulosic biomass cultivation, harvesting, pretreatment processing, and cellulose-to-sugar-to-butanol fermentation all cost energy. Therefore, any new technology that could bypass these bottleneck problems of the biomass technology would be useful.
Oxyphotobacteria (also known as blue-green algae including cyanobacteria and oxychlorobacteria) and algae (such as Chlamydomonas reinhardtii, Platymonas subcordiformis, Chlorella fusca, Dunaliella salina, Ankistrodesmus braunii, and Scenedesmus obliquus), which can perform photosynthetic assimilation of CO2 with O2 evolution from water in a liquid culture medium with a maximal theoretical solar-to-biomass energy conversion of about 10%, have tremendous potential to be a clean and renewable energy resource. However, the wild-type oxygenic photosynthetic green plants, such as blue-green algae and eukaryotic algae, do not possess the ability to produce butanol directly from CO2 and H2O. The wild-type photosynthesis uses the reducing power (NADPH) and energy (ATP) from the photosynthetic water splitting and proton gradient-coupled electron transport process through the algal thylakoid membrane system to reduce CO2 into carbohydrates (CH2O)n such as starch with a series of enzymes collectively called the “Calvin cycle” at the stroma region in an algal or green-plant chloroplast. The net result of the wild-type photosynthetic process is the conversion of CO2 and H2O into carbohydrates (CH2O)n and O2 using sunlight energy according to the following process reaction:

nCO2+nH2O→(CH2O)n+nO2  [1]

The carbohydrates (CH2O)n are then further converted to all kinds of complicated cellular (biomass) materials including proteins, lipids, and cellulose and other cell-wall materials during cell metabolism and growth.

In certain alga such as Chlamydomonas reinhardtii, some of the organic reserves such as starch could be slowly metabolized to ethanol (but not to butanol) through a secondary fermentative metabolic pathway. The algal fermentative metabolic pathway is similar to the yeast-fermentation process, by which starch is breakdown to smaller sugars such as glucose that is, in turn, transformed into pyruvate by a glycolysis process. Pyruvate may then be converted to formate, acetate, and ethanol by a number of additional metabolic steps (Gfeller and Gibbs (1984) “Fermentative metabolism of Chlamydomonas reinhardtii,” Plant Physiol. 75:212-218). The efficiency of this secondary metabolic process is quite limited, probably because it could use only a small fraction of the limited organic reserve such as starch in an algal cell. Furthermore, the native algal secondary metabolic process could not produce any butanol. As mentioned above, butanol has many superior physical properties to serve as a replacement for gasoline as a fuel. Therefore, a new photobiological butanol-producing mechanism with a high solar-to-butanol energy efficiency is needed.
The present invention provides revolutionary designer photosynthetic organisms, which are capable of directly synthesizing butanol from CO2 and H2O using sunlight. The photobiological butanol-production system provided by the present invention could bypass all the bottleneck problems of the biomass technology mentioned above.
SUMMARY OF THE INVENTION
The present invention provides photobiological butanol production methods based on designer transgenic plants (such as algae and oxyphotobacteria) or plant cells. The designer photosynthetic organisms are created through genetic engineering such that the endogenous photosynthesis regulation mechanism is tamed, and the reducing power (NADPH) and energy (ATP) acquired from the photosynthetic water splitting and proton gradient-coupled electron transport process are used for synthesis of butanol (CH3CH2CH2CH2OH) directly from carbon dioxide (CO2) and water (H2O). The photobiological butanol-production methods of the present invention completely eliminate the problem of recalcitrant lignocellulosics by bypassing the bottleneck problem of the biomass technology. The photosynthetic butanol-production technology of the present invention is expected to have a much higher solar-to-butanol energy-conversion efficiency than the current technology.
A fundamental feature of the present photosynthetic butanol production methodology is to create designer plants (such as algae) or plant cells that contain transgenes coding for a set of enzymes that can act on an intermediate product of the Calvin cycle and convert the intermediate product immediately into butanol, instead of making starch and other complex biomass materials. Accordingly, the present invention provides, inter alia, methods for producing butanol based on a designer plant or plant cells, DNA constructs encoding genes of a designer butanol-production pathway, as well as the designer plants and designer plant cells created.
In one aspect, the present invention provides a method for photosynthetic production of butanol by growing a designer plant (such as a designer alga or designer blue-green alga) or plant cells in a liquid culture medium, wherein the plant or plant cells are genetically engineered to express a set of enzymes that act on an intermediate product of the Calvin cycle and convert the intermediate product into butanol.
According to the present invention, a designer plant, such as a designer alga, or designer plant cell for use in the photosynthetic butanol production can be created utilizing essentially any plant, plant tissue, or plant cells as host, so long as such plant, plant tissue and cells have a photosynthetic capability and can be cultured in a liquid medium. In a preferred embodiment, an aquatic plant (hydrophytes) is utilized to create a designer plant, which includes, but not limited to, submersed aquatic herbs (such as Hydrilla verticillata, Elodea densa, Aponogeton boivinianus, Hygrophila difformmis), duckweeds (such as Spirodela polyrrhiza, Wolffia globosa, Landoltia punctata), water cabbage (Pistia stratiotes), buttercups (Ranunculus), water caltrop (Trapa natans and Trapa bicornis), water lily (such as Nymphaea lotus), water hyacinth (Eichhornia crassipes), seagrasses (such as Heteranthera Zosterifolia), and algae.
In an especially preferred embodiment, algae are used as host to create designer algae for photosynthetic butanol production. Algae suitable for use in the present invention can be either unicellular or multicellular algae (the latter including, but not limited to, seaweeds such as Ulva latissima (sea lettuce), Ascophyllum nodosum, and Porphyra tenera), and include green algae (Chlorophyta), red algae (Rhodophyta), brown algae (Phaeophyta), diatoms (Bacillariophyta), and blue-green algae (Oxyphotobacteria including Cyanophyta (cyanobacteria) and Prochlorophytes (oxychlorobacteria)). Both the prokaryotic blue-green algae (oxyphotobacteria) and the eukaryotic algae are highly suitable for use in this invention. A particularly preferred species of algae for use in the present invention is a species of green algae, Chlamydomonas reinhardtii, of which the genome has recently been sequenced.
The selection of the enzymes appropriate for use to create a designer butanol-production pathway in a host depends on from which intermediate product of the Calvin cycle the designer pathway branches off from the Calvin cycle. In one embodiment, the designer pathway branches off from the point of glyceraldehydes 3-phosphate and converts it into butanol by using, for example, the set of enzymes consisting of glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, pyruvate kinase, pyruvate-ferredoxin oxidoreductase (or pyruvate-NADP+ oxidoreductase), thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase. In this designer pathway, for conversion of two molecules of glyceraldehyde-3-phosphate to butanol, two NADH molecules are generated from NAD+ at the step from glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate catalyzed by glyceraldehyde-3-phosphate dehydrogenase; meanwhile two molecules of NADH are converted to NAD+: one at the step catalyzed by 3-hydroxybutyryl-CoA dehydrogenase to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA and another at the step catalyzed by butyryl-CoA dehydrogenase to reduce crotonyl-CoA to butyryl-CoA. Consequently, in this designer pathway, the number of NADH molecules consumed is balanced with the number of NADH molecules generated. Furthermore, both the step catalyzed by butyraldehyde dehydrogenase in reducing butyryl-CoA to butyraldehyde and the terminal step catalyzed by butanol dehydrogenase in reducing butyraldehyde to butanol can use NADPH, which can be regenerated by the photosynthetic water splitting and proton gradient-coupled electron transport process. Therefore, this designer butanol-production pathway can operate continuously.
In another example, a designer pathway is created that takes the intermediate product, 3-phosphoglycerate, and converts it into butanol by using, for example, a set of enzymes consisting of phosphoglycerate mutase, enolase, pyruvate kinase, pyruvate-ferredoxin oxidoreductase, thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase.
In order for this 3-phosphoglycerate-branched butanol-production pathway to operate, it is important to use a 3-hydroxybutyryl-CoA dehydrogenase and a butyryl-CoA dehydrogenase that can use NADPH which can be supplied by the photo-driven electron transport process. Alternatively, when a 3-hydroxybutyryl-CoA dehydrogenase and a butyryl-CoA dehydrogenase that can use only NADH are employed, it is preferably here to use an additional embodiment that can confer an NADPH/NADH conversion mechanism to supply NADH by converting NADPH to NADH to facilitate photosynthetic production of butanol through the 3-phosphoglycerate-branched designer pathway.
In still another example, a designer pathway is created that takes fructose-1,6-diphosphate and converts it into butanol by using, for example, a set of enzymes consisting of aldolase, triose phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, pyruvate kinase, pyruvate-NADP+ oxidoreductase (or pyruvate-ferredoxin oxidoreductase), thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase. The addition of yet one more enzyme in the designer organism, phosphofructose kinase, permits the creation of another designer pathway which branches off from the point of fructose-6-phosphate for the production of butanol. Like the glyceraldehyde-3-phosphate-branched butanol-production pathway, both the fructose-1,6-diphosphate-branched pathway and the fructose-6-phosphate-branched pathway can themselves generate NADH for use in the pathway at the step catalyzed by 3-hydroxybutyryl-CoA dehydrogenase to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA and another at the step catalyzed by butyryl-CoA dehydrogenase to reduce crotonyl-CoA to butyryl-CoA. In each of these designer butanol-production pathways, the numbers of NADH molecules consumed are balanced with the numbers of NADH molecules generated; and both the butyraldehyde dehydrogenase (catalyzing the step in reducing butyryl-CoA to butyraldehyde) and the butanol dehydrogenase (catalyzing the terminal step in reducing butyraldehyde to butanol) can all use NADPH, which can be regenerated by the photosynthetic water splitting and proton gradient-coupled electron transport process. Therefore, these designer butanol-production pathways can operate continuously. It can be noted that certain sets of designer enzymes may permit two or more designer pathways, i.e., pathways that branches off from two or more points of the Calvin cycle for the production of butanol.
According to the present invention, nucleic acids encoding for these enzymes are genetically engineered such that the enzymes expressed are inserted into the chloroplasts of the host to achieve targeted cellular localization. The targeted insertion of designer butanol-production-pathway enzymes can be accomplished through use of a nucleotide sequence that encodes for a stroma “signal” peptide, placed in an operable linkage to the nucleotide sequence encoding for a designer enzyme. A number of transit peptide sequences are suitable for use for the targeted insertion of the designer butanol-production enzymes into chloroplast, including but not limited to the transit peptide sequences of the hydrogenase apoproteins (such as Hyd1), ferredoxin apoprotein (Frx1), thioredoxin m apoprotein (Trx2), glutamine synthase apoprotein (Gs2), LhcII apoproteins, PSII-T apoprotein (PsbT), PSII-S apoprotein (PsbS), PSII-W apoprotein (PsbW), CF0CF1 subunit-apoprotein (AtpC), CF0CF1 subunit-apoprotein (AtpD), CFoCF1 subunit-II apoprotein (AtpG), photosystem I (PSI) apoproteins (such as, of genes PsaD, PsaE, PsaF, PsaG, PsaH, and PsaK), and Rubisco small-subunit (SSU) apoproteins (such as RbcS2). Preferred transit peptide sequences include the Hyd1 transit peptide, the Frx1 transit peptide, and the Rubisco SSU transit peptides (such as RbcS2).
Further in accordance with the present invention, the expression of the designer butanol-producing pathway is controlled through the use of an externally inducible promoter so that the designer transgenes are inducibly expressed under certain specific conditions. In one embodiment, the inducible promoter used to control the expression of designer genes is a promoter that is inducible by anaerobiosis, including, for example, the promoters of the hydrogenase gene (Hyd1), the Cyc6 gene encoding the apoprotein of Cytochrome C6, and the Cpx1 gene encoding coprogen oxidase. Additional inducible promoters suitable for use in the present invention include the nitrate reductase (Nia1) promoter, heat-shock protein promoter HSP70A, CabII-1 promoter, Ca1 promoter, Ca2 promoter, nitrite-reductase-gene (nirA) promoters, bidirectional-hydrogenase-gene hox promoters, light- and heat-responsive groE promoters, Rubisco-operon rbcL promoters, metal (zinc)-inducible smt promoter, iron-responsive idiA promoter, redox-responsive crhR promoter, heat-shock-gene hsp16.6 promoter, small heat-shock protein (Hsp) promoter, CO2-responsive carbonic-anhydrase-gene promoters, green/red light responsive cpcB2A2 promoter, UV-light responsive lexA, recA and ruvB promoters, nitrate-reductase-gene (narB) promoters, and combinations thereof.
In another aspect of the present invention, designer DNA constructs are provided, which contain one or more nucleotide sequences encoding one or more designer butanol-production-pathway enzymes, each of which is placed in an operable linkage to an inducible promoter, and to a nucleotide sequence encoding for an appropriate chloroplast-targeting transit peptide. The constructs may contain additional appropriate sequences, such as a selection marker gene to facilitate the screening and identification of transformants. Nucleic acid constructs carrying designer genes can be delivered into a host alga, plant organism or plant tissue or cells using the available gene-transformation techniques, such as electroporation, natural transformation, conjugation, PEG induced uptake, and ballistic delivery of DNA, and Agrobacterium-mediated transformation.
The designer plants (e.g., designer algae), plant tissues, and plant cells that have been created to contain one or more designer construct, form another embodiment of the present invention. In a further aspect, the present invention provides additional methods for enhanced photosynthetic butanol production, the related designer constructs and designer plants, plant tissues and cells.
In a specific embodiment, a photosynthetic butanol-producing designer plant (for example, a designer alga), plant tissue or cell(s), as described above, has been further modified to contain additional designer transgenes to inducibly express one or more enzymes to facilitate the NADPH/NADH conversion, such as the NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase, NADPH phosphatase and NAD kinase. Alternatively, the 3-hydroxybutyryl-CoA dehydrogenase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase of the designer plant, plant tissue or cell(s) can be selected and modified so that they can use NADPH as well.
In another embodiment, a photosynthetic butanol-producing designer plant or plant tissue, or cell(s) has been further modified to inactivate starch-synthesis activity. In a specific embodiment, such further modification includes introduction of a designer DNA construct that encodes and inducibly expresses an interfering RNA (iRNA) molecule that specifically inhibits the synthesis of a starch-synthesis-pathway enzyme, for example, starch synthase, glucose-1-phosphate adenylyltransferase, glucose-phosphate-isomerase and/or phosphoglucomutase for enhanced photobiological production of butanol.
In still another embodiment, a photosynthetic butanol-producing designer plant or plant tissue or cell(s) has been further modified to contain an additional set of designer genes that facilitate starch degradation and glycolysis in the stroma. Such additional designer genes include, for example, genes coding for amylase, starch phosphorylase, hexokinase, phosphoglucomutase, and glucose-phosphate-isomerase.
In yet another embodiment, a photobiological butanol-production pathway(s) is distributed in parts in both chloroplast and cytoplasm. The distribution of the designer butanol-production-pathway enzymes between chloroplast and cytoplasm is controlled by the use and/or deletion of the transit peptide sequences in the designer DNA constructs.
In still another embodiment, a photobiological butanol-production pathway(s) is distributed entirely in cytoplasm as in the case of designer oxyphotobacteria (blue-green algae) including designer cyanobacteria and designer oxychlorobacteria.
This invention also provides a biosafety-guarded photobiological biofuel-production technology based on cell-division-controllable designer transgenic plants, algae, blue-green algae (cyanobacteria and oxychlorobacteria), or plant cells. The cell-division-controllable designer photosynthetic organisms contain two key functions: a designer biosafety mechanism(s) and a designer biofuel-production pathway(s). The designer biosafety feature(s) is conferred by a number of mechanisms including: (1) the inducible insertion of designer proton-channels into cytoplasm membrane to permanently disable any cell division and/or mating capability, (2) the selective application of designer cell-division-cycle regulatory protein or interference RNA (iRNA) to permanently inhibit the cell division cycle and preferably keep the cell at the G1 phase or G0 state, and (3) the innovative use of a high-CO2-requiring host photosynthetic organism for expression of the designer biofuel-production pathway(s). The designer cell-division-control technology can help ensure biosafety in using the designer organisms for photosynthetic biofuel production.
The present invention further provides a process of using a designer photosynthetic organism (such as a designer cyanobacterium or alga), in combination with a photobiological reactor system and a butanol separation/harvesting process for photobiological production of butanol and O2 directly from CO2 and H2O using sunlight. Both industrial CO2 sources and/or atmospheric CO2 from the environment may be used in the photobiological butanol-production process.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 presents designer butanol-production pathways branched from the Calvin cycle using the reducing power (NADPH) and energy (ATP) from the photosynthetic water splitting and proton gradient-coupled electron transport process to reduce carbon dioxide (CO2) into butanol CH3CH2CH2CH2OH with a series of enzymatic reactions.
FIG. 2A presents a DNA construct for designer butanol-production-pathway gene(s).
FIG. 2B presents a DNA construct for NADPH/NADH-conversion designer gene for NADPH/NADH inter-conversion.
FIG. 2C presents a DNA construct for a designer iRNA starch/glycogen-synthesis inhibitor(s) gene.
FIG. 2D presents a DNA construct for a designer starch-degradation-glycolysis gene(s).
FIG. 2E presents a DNA construct of a designer butanol-production-pathway gene(s) for cytosolic expression.
FIG. 2F presents a DNA construct of a designer butanol-production-pathway gene(s) with two recombination sites for integrative genetic transformation in oxyphotobacteria.
FIG. 2G presents a DNA construct of a designer biosafety-control gene(s).
FIG. 2H presents a DNA construct of a designer proton-channel gene(s).
FIG. 3A illustrates a cell-division-controllable designer organism that contains two key functions: designer biosafety mechanism(s) and designer biofuel-production pathway(s).
FIG. 3B illustrates a cell-division-controllable designer organism for photobiological production of butanol (CH3CH2CH2CH2OH) from carbon dioxide (CO2) and water (H2O) with designer biosafety mechanism(s).
FIG. 3C illustrates a cell-division-controllable designer organism for biosafety-guarded photobiological production of other biofuels such as ethanol (CH3CH2OH) from carbon dioxide (CO2) and water (H2O).



DETAILED DESCRIPTION OF THE INVENTION
The present invention is directed to a photobiological butanol production technology based on designer photosynthetic organisms such as designer transgenic plants (e.g., algae and oxyphotobacteria) or plant cells. The designer plants and plant cells are created using genetic engineering techniques such that the endogenous photosynthesis regulation mechanism is tamed, and the reducing power (NADPH) and energy (ATP) acquired from the photosynthetic water splitting and proton gradient-coupled electron transport process can be used for immediate synthesis of butanol (CH3CH2CH2CH2OH) directly from carbon dioxide (CO2) and water (H2O) according to the following process reaction:

4CO2+5H2O→CH3CH2CH2CH2OH+6O2  [2]

The photobiological butanol-production methods of the present invention completely eliminate the problem of recalcitrant lignocellulosics by bypassing the bottleneck problem of the biomass technology. As shown in FIG. 1, the photosynthetic process in a designer organism effectively uses the reducing power (NADPH) and energy (ATP) from the photosynthetic water splitting and proton gradient-coupled electron transport process for immediate synthesis of butanol (CH3CH2CH2CH2OH) directly from carbon dioxide (CO2) and water (H2O) without being drained into the other pathway for synthesis of the undesirable lignocellulosic materials that are very hard and often inefficient for the biorefinery industry to use. This approach is also different from the existing “cornstarch butanol production” process. In accordance with this invention, butanol can be produced directly from carbon dioxide (CO2) and water (H2O) without having to go through many of the energy consuming steps that the cornstarch butanol-production process has to go through, including corn crop cultivation, corn-grain harvesting, corn-grain cornstarch processing, and starch-to-sugar-to-butanol fermentation. As a result, the photosynthetic butanol-production technology of the present invention is expected to have a much (more than 10-times) higher solar-to-butanol energy-conversion efficiency than the current technology. Assuming a 10% solar energy conversion efficiency for the proposed photosynthetic butanol production process, the maximal theoretical productivity (yield) could be about 72,700 kg of butanol per acre per year, which could support about 70 cars (per year per acre). Therefore, this invention could bring a significant capability to the society in helping to ensure energy security. The present invention could also help protect the Earth's environment from the dangerous accumulation of CO2 in the atmosphere, because the present methods convert CO2 directly into clean butanol energy.

A fundamental feature of the present methodology is utilizing a plant (e.g., an alga or oxyphotobacterium) or plant cells, introducing into the plant or plant cells nucleic acid molecules encoding for a set of enzymes that can act on an intermediate product of the Calvin cycle and convert the intermediate product into butanol as illustrated in FIG. 1, instead of making starch and other complicated cellular (biomass) materials as the end products by the wild-type photosynthetic pathway. Accordingly, the present invention provides, inter alia, methods for producing butanol based on a designer plant (such as a designer alga and a designer oxyphotobacterium), designer plant tissue, or designer plant cells, DNA constructs encoding genes of a designer butanol-production pathway, as well as the designer algae, designer oxyphotobacteria (including designer cyanobacteria), designer plants, designer plant tissues, and designer plant cells created. The various aspects of the present invention are described in further detail hereinbelow.
Host Photosynthetic Organisms
According to the present invention, a designer organism or cell for the photosynthetic butanol production of the invention can be created utilizing as host, any plant (including alga and oxyphotobacterium), plant tissue, or plant cells that have a photosynthetic capability, i.e., an active photosynthetic apparatus and enzymatic pathway that captures light energy through photosynthesis, using this energy to convert inorganic substances into organic matter. Preferably, the host organism should have an adequate photosynthetic CO2 fixation rate, for example, to support photosynthetic butanol production from CO2 and H2O at least about 1,450 kg butanol per acre per year, more preferably, 7,270 kg butanol per acre per year, or even more preferably, 72,700 kg butanol per acre per year.
In a preferred embodiment, an aquatic plant is utilized to create a designer plant. Aquatic plants, also called hydrophytic plants, are plants that live in or on aquatic environments, such as in water (including on or under the water surface) or permanently saturated soil. As used herein, aquatic plants include, for example, algae, blue-green algae (cyanobacteria and oxychlorobacteria), submersed aquatic herbs (Hydrilla verticillata, Elodea densa, Hippuris vulgaris, Aponogeton Boivinianus Aponogeton Rigidifolius, Aponogeton Longiplumulosus, Didiplis Diandra, Vesicularia Dubyana, Hygrophilia Augustifolia, Micranthemum Umbrosum, Eichhornia Azurea, Saururus Cernuus, Cryptocoryne Lingua, Hydrotriche Hottoniiflora Eustralis Stellata, Vallisneria Rubra, Hygrophila Salicifolia, Cyperus Helferi, Cryptocoryne Petchii, Vallisneria americana, Vallisneria Torta, Hydrotriche Hottoniiflora, Crassula Helmsii, Limnophila Sessiliflora, Potamogeton Perfoliatus, Rotala Wallichii, Cryptocoryne Becketii, Blyxa Aubertii, Hygrophila Difformmis), duckweeds (Spirodela polyrrhiza, Wolffia globosa, Lemna trisulca, Lemna gibba, Lemna minor, Landoltia punctata), water cabbage (Pistia stratiotes), buttercups (Ranunculus), water caltrop (Trapa natans and Trapa bicornis), water lily (Nymphaea lotus, Nymphaeaceae and Nelumbonaceae), water hyacinth (Eichhornia crassipes), Bolbitis heudelotii, Cabomba sp., seagrasses (Heteranthera Zosterifolia, Posidoniaceae, Zosteraceae, Hydrocharitaceae, and Cymodoceaceae). Butanol produced from an aquatic plant can diffuse into water, permitting normal growth of the plants and more robust production of butanol from the plants. Liquid cultures of aquatic plant tissues (including, but not limited to, multicellular algae) or cells (including, but not limited to, unicellular algae) are also highly preferred for use, since the butanol molecules produced from a designer butanol-production pathway can readily diffuse out of the cells or tissues into the liquid water medium, which can serve as a large pool to store the product butanol that can be subsequently harvested by filtration and/or distillation/evaporation techniques.
Although aquatic plants or cells are preferred host organisms for use in the methods of the present invention, tissue and cells of non-aquatic plants, which are photosynthetic and can be cultured in a liquid culture medium, can also be used to create designer tissue or cells for photosynthetic butanol production. For example, the following tissue or cells of non-aquatic plants can also be selected for use as a host organism in this invention: the photoautotrophic shoot tissue culture of wood apple tree Feronia limonia, the chlorophyllous callus-cultures of corn plant Zea mays, the green root cultures of Asteraceae and Solanaceae species, the tissue culture of sugarcane stalk parenchyma, the tissue culture of bryophyte Physcomitrella patens, the photosynthetic cell suspension cultures of soybean plant (Glycine max), the photoautotrophic and photomixotrophic culture of green Tobacco (Nicofiana tabacum L.) cells, the cell suspension culture of Gisekia pharmaceoides (a C4 plant), the photosynthetic suspension cultured lines of Amaranthus powellii Wats., Datura innoxia Mill., Gossypium hirsutum L., and Nicotiana tabacum×Nicotiana glutinosa L. fusion hybrid.
By “liquid medium” is meant liquid water plus relatively small amounts of inorganic nutrients (e.g., N, P, K etc, commonly in their salt forms) for photoautotrophic cultures; and sometimes also including certain organic substrates (e.g., sucrose, glucose, or acetate) for photomixotrophic and/or photoheterotrophic cultures.
In an especially preferred embodiment, the plant utilized in the butanol production method of the present invention is an alga or a blue-green alga. The use of algae and/or blue-green algae has several advantages. They can be grown in an open pond at large amounts and low costs. Harvest and purification of butanol from the water phase is also easily accomplished by distillation/evaporation or membrane separation.
Algae suitable for use in the present invention include both unicellular algae and multi-unicellular algae. Multicellular algae that can be selected for use in this invention include, but are not limited to, seaweeds such as Ulva latissima (sea lettuce), Ascophyllum nodosum, Codium fragile, Fucus vesiculosus, Eucheuma denticulatum, Gracilaria gracilis, Hydrodictyon reticulatum, Laminaria japonica, Undaria pinntifida, Saccharina japonica, Porphyra yezoensis, and Porphyra tenera. Suitable algae can also be chosen from the following divisions of algae: green algae (Chlorophyta), red algae (Rhodophyta), brown algae (Phaeophyta), diatoms (Bacillariophyta), and blue-green algae (Oxyphotobacteria including Cyanophyta and Prochlorophytes). Suitable orders of green algae include Ulvales, Ulotrichales, Volvocales, Chlorellales, Schizogoniales, Oedogoniales, Zygnematales, Cladophorales, Siphonales, and Dasycladales. Suitable genera of Rhodophyta are Porphyra, Chondrus, Cyanidioschyzon, Porphyridium, Gracilaria, Kappaphycus, Gelidium and Agardhiella. Suitable genera of Phaeophyta are Laminaria, Undaria, Macrocystis, Sargassum and Dictyosiphon. Suitable genera of Cyanophyta (also known as Cyanobacteria) include (but not limited to) Phoridium, Synechocystis, Syncechococcus, Oscillatoria, and Anabaena. Suitable genera of Prochlorophytes (also known as oxychlorobacteria) include (but not limited to) Prochloron, Prochlorothrix, and Prochlorococcus. Suitable genera of Bacillariophyta are Cyclotella, Cylindrotheca, Navicula, Thalassiosira, and Phaeodactylum. Preferred species of algae for use in the present invention include Chlamydomonas reinhardtii, Platymonas subcordiformis, Chlorella fusca, Chlorella sorokiniana, Chlorella vulgaris, Chlorella ellipsoidea, Chlorella spp., Dunaliella salina, Dunaliella viridis, Dunaliella bardowil, Haematococcus pluvialis; Parachlorella kessleri, Betaphycus gelatinum, Chondrus crispus, Cyanidioschyzon merolae, Cyanidium caldarium, Galdieria sulphuraria, Gelidiella acerosa, Gracilaria changii, Kappaphycus alvarezii, Porphyra miniata, Ostreococcus tauri, Porphyra yezoensis, Porphyridium sp., Palmaria palmata, Gracilaria spp., Isochrysis galbana, Kappaphycus spp., Laminaria japonica, Laminaria spp., Monostroma spp., Nannochloropsis oculata, Porphyra spp., Porphyridium spp., Undaria pinnatifida, Ulva lactuca, Ulva spp., Undaria spp., Phaeodactylum Tricornutum, Navicula saprophila, Crypthecodinium cohnii, Cylindrotheca fusiformis, Cyclotella cryptica, Euglena gracilis, Amphidinium sp., Symbiodinium microadriaticum, Macrocystis pyrifera, Ankistrodesmus braunii, and Scenedesmus obliquus. 
Preferred species of blue-green algae (oxyphotobacteria including cyanobacteria and oxychlorobacteria) for use in the present invention include Thermosynechococcus elongatus BP-1, Nostoc sp. PCC 7120, Synechococcus elongatus PCC 6301, Syncechococcus sp. strain PCC 7942, Syncechococcus sp. strain PCC 7002, Syncechocystis sp. strain PCC 6803, Prochlorococcus marinus MED4, Prochlorococcus marinus MIT 9313, Prochlorococcus marinus NATL1A, Prochlorococcus SS120, Spirulina platensis (Arthrospira platensis), Spirulina pacifica, Lyngbya majuscule, Anabaena sp., Synechocystis sp., Synechococcus elongates, Synechococcus (MC-A), Trichodesmium sp., Richelia intracellularis, Synechococcus WH7803, Synechococcus WH8102, Nostoc punctiforme, Syncechococcus sp. strain PCC 7943, Synechocyitis PCC 6714 phycocyanin-deficient mutant PD-1, Cyanothece strain 51142, Cyanothece sp. CCY0110, Oscillatoria limosa, Lyngbya majuscula, Symploca muscorum, Gloeobacter violaceus, Prochloron didemni, Prochlorothrix hollandica, Synechococcus (MC-A), Trichodesmium sp., Richelia intracellularis, Prochlorococcus marinus, Prochlorococcus SS120, Synechococcus WH8102, Lyngbya majuscula, Symploca muscorum, Synechococcus bigranulatus, cryophilic Oscillatoria sp., Phormidium sp., Nostoc sp.-1, Calothrix parietina, thermophilic Synechococcus bigranulatus, Synechococcus lividus, thermophilic Mastigocladus laminosus, Chlorogloeopsis fritschii PCC 6912, Synechococcus vulcanus, Synechococcus sp. strain MA4, Synechococcus sp. strain MA19, and Thermosynechococcus elongatus. 
Proper selection of host photosynthetic organisms for their genetic backgrounds and certain special features is also beneficial. For example, a photosynthetic-butanol-producing designer alga created from cryophilic algae (psychrophiles) that can grow in snow and ice, and/or from cold-tolerant host strains such as Chlamydomonas cold strain CCMG1619, which has been characterized as capable of performing photosynthetic water splitting as cold as 4° C. (Lee, Blankinship and Greenbaum (1995), “Temperature effect on production of hydrogen and oxygen by Chlamydomonas cold strain CCMP1619 and wild type 137c,” Applied Biochemistry and Biotechnology 51/52:379-386), permits photobiological butanol production even in cold seasons or regions such as Canada. Meanwhile, a designer alga created from a thermophilic/thermotolerant photosynthetic organism such as thermophilic algae Cyanidium caldarium and Galdieria sulphuraria and/or thermophilic cyanobacteria (blue-green algae) such as Thermosynechococcus elongatus BP-1 and Synechococcus bigranulatus may permit the practice of this invention to be well extended into the hot seasons or areas such as Mexico and the Southwestern region of the United States including Nevada, California, Arizona, New Mexico and Texas, where the weather can often be hot. Furthermore, a photosynthetic-butanol-producing designer alga created from a marine alga, such as Platymonas subcordiformis, permits the practice of this invention using seawater, while the designer alga created from a freshwater alga such as Chlamydomonas reinhardtii can use freshwater. Additional optional features of a photosynthetic butanol-producing designer alga include the benefits of reduced chlorophyll-antenna size, which has been demonstrated to provide higher photosynthetic productivity (Lee, Mets, and Greenbaum (2002). “Improvement of photosynthetic efficiency at high light intensity through reduction of chlorophyll antenna size,” Applied Biochemistry and Biotechnology, 98-100: 37-48) and butanol-tolerance that allows for more robust and efficient photosynthetic production of butanol from CO2 and H2O. By use of a phycocyanin-deficient mutant of Synechocystis PCC 6714, it has been experimentally demonstrated that photoinhibition can be reduced also by reducing the content of light-harvesting pigments (Nakajima, Tsuzuki, and Ueda (1999) “Reduced photoinhibition of a phycocyanin-deficient mutant of Synechocystis PCC 6714”, Journal of Applied Phycology 10: 447-452). These optional features can be incorporated into a designer alga, for example, by use of a butanol-tolerant and/or chlorophyll antenna-deficient mutant (e.g., Chlamydomonas reinhardtii strain DS521) as a host organism, for gene transformation with the designer butanol-production-pathway genes. Therefore, in one of the various embodiments, a host alga is selected from the group consisting of green algae, red algae, brown algae, blue-green algae (oxyphotobacteria including cyanobacteria and prochlorophytes), diatoms, marine algae, freshwater algae, unicellular algae, multicellular algae, seaweeds, cold-tolerant algal strains, heat-tolerant algal strains, light-harvesting-antenna-pigment-deficient mutants, butanol-tolerant algal strains, and combinations thereof.
Creating a Designer Butanol-Production Pathway in a Host
Selecting Appropriate Designer Enzymes
One of the key features in the present invention is the creation of a designer butanol-production pathway to tame and work with the natural photosynthetic mechanisms to achieve the desirable synthesis of butanol directly from CO2 and H2O. The natural photosynthetic mechanisms include (1) the process of photosynthetic water splitting and proton gradient-coupled electron transport through the thylakoid membrane, which produces the reducing power (NADPH) and energy (ATP), and (2) the Calvin cycle, which reduces CO2 by consumption of the reducing power (NADPH) and energy (ATP).
In accordance with the present invention, a series of enzymes are used to create a designer butanol-production pathway that takes an intermediate product of the Calvin cycle and converts the intermediate product into butanol as illustrated in FIG. 1. A “designer butanol-production-pathway enzyme” is hereby defined as an enzyme that serves as a catalyst for at least one of the steps in a designer butanol-production pathway. According to the present invention, a number of intermediate products of the Calvin cycle can be utilized to create designer butanol-production pathway(s); and the enzymes required for a designer butanol-production pathway are selected depending upon from which intermediate product of the Calvin cycle the designer butanol-production pathway branches off from the Calvin cycle.
In one example, a designer pathway is created that takes glyceraldehydes-3-phosphate and converts it into butanol by using, for example, a set of enzymes consisting of, as shown with the numerical labels 01-12 in FIG. 1, glyceraldehyde-3-phosphate dehydrogenase 01, phosphoglycerate kinase 02, phosphoglycerate mutase 03, enolase 04, pyruvate kinase 05, pyruvate-ferredoxin oxidoreductase 06, thiolase 07, 3-hydroxybutyryl-CoA dehydrogenase 08, crotonase 09, butyryl-CoA dehydrogenase 10, butyraldehyde dehydrogenase 11, and butanol dehydrogenase 12. In this glyceraldehydes-3-phosphate-branched designer pathway, for conversion of two molecules of glyceraldehyde-3-phosphate to butanol, two NADH molecules are generated from NAD+ at the step from glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate catalyzed by glyceraldehyde-3-phosphate dehydrogenase 01; meanwhile two molecules of NADH are converted to NAD+: one at the step catalyzed by 3-hydroxybutyryl-CoA dehydrogenase 08 in reducing acetoacetyl-CoA to 3-hydroxybutyryl-CoA and another at the step catalyzed by butyryl-CoA dehydrogenase 10 in reducing crotonyl-CoA to butyryl-CoA. Consequently, in this glyceraldehydes-3-phosphate-branched designer pathway (01-12), the number of NADH molecules consumed is balanced with the number of NADH molecules generated. Furthermore, both the pathway step catalyzed by butyraldehyde dehydrogenase 11 (in reducing butyryl-CoA to butyraldehyde) and the terminal step catalyzed by butanol dehydrogenase 12 (in reducing butyraldehyde to butanol) can use NADPH, which can be regenerated by the photosynthetic water splitting and proton gradient-coupled electron transport process. Therefore, this glyceraldehydes-3-phosphate-branched designer butanol-production pathway can operate continuously.
In another example, a designer pathway is created that takes the intermediate product, 3-phosphoglycerate, and converts it into butanol by using, for example, a set of enzymes consisting of (as shown with the numerical labels 03-12 in FIG. 1) phosphoglycerate mutase 03, enolase 04, pyruvate kinase 05, pyruvate-ferredoxin oxidoreductase 06, thiolase 07, 3-hydroxybutyryl-CoA dehydrogenase 08, crotonase 09, butyryl-CoA dehydrogenase 10, butyraldehyde dehydrogenase 11, and butanol dehydrogenase 12. It is worthwhile to note that the last ten enzymes (03-12) of the glyceraldehydes-3-phosphate-branched designer butanol-producing pathway (01-12) are identical with those utilized in the 3-phosphoglycerate-branched designer pathway (03-12). In other words, the designer enzymes (01-12) of the glyceraldehydes-3-phosphate-branched pathway permit butanol production from both the point of 3-phosphoglycerate and the point glyceraldehydes 3-phosphate in the Calvin cycle. These two pathways, however, have different characteristics. Unlike the glyceraldehyde-3-phosphate-branched butanol-production pathway, the 3-phosphoglycerate-branched pathway which consists of the activities of only ten enzymes (03-12) could not itself generate any NADH that is required for use at two places: one at the step catalyzed by 3-hydroxybutyryl-CoA dehydrogenase 08 in reducing acetoacetyl-CoA to 3-hydroxybutyryl-CoA, and another at the step catalyzed by butyryl-CoA dehydrogenase 10 in reducing crotonyl-CoA to butyryl-CoA. That is, if (or when) a 3-hydroxybutyryl-CoA dehydrogenase and/or a butyryl-CoA dehydrogenase that can use strictly only NADH but not NADPH is employed, it would require a supply of NADH for the 3-phosphoglycerate-branched pathway (03-12) to operate. Consequently, in order for the 3-phosphoglycerate-branched butanol-production pathway to operate, it is important to use a 3-hydroxybutyryl-CoA dehydrogenase 08 and a butyryl-CoA dehydrogenase 10 that can use NADPH which can be supplied by the photo-driven electron transport process. Therefore, it is a preferred practice to use a 3-hydroxybutyryl-CoA dehydrogenase and a butyryl-CoA dehydrogenase that can use NADPH or both NADPH and NADH (i.e., NAD(P)H) for this 3-phosphoglycerate-branched designer butanol-production pathway (03-12 in FIG. 1). Alternatively, when a 3-hydroxybutyryl-CoA dehydrogenase and a butyryl-CoA dehydrogenase that can use only NADH are employed, it is preferably here to use an additional embodiment that can confer an NADPH/NADH conversion mechanism (to supply NADH by converting NADPH to NADH, see more detail later in the text) in the designer organism to facilitate photosynthetic production of butanol through the 3-phosphoglycerate-branched designer pathway.
In still another example, a designer pathway is created that takes fructose-1,6-diphosphate and converts it into butanol by using, as shown with the numerical labels 20-33 in FIG. 1, a set of enzymes consisting of aldolase 20, triose phosphate isomerase 21, glyceraldehyde-3-phosphate dehydrogenase 22, phosphoglycerate kinase 23, phosphoglycerate mutase 24, enolase 25, pyruvate kinase 26, pyruvate-NADP+ oxidoreductase (or pyruvate-ferredoxin oxidoreductase) 27, thiolase 28, 3-hydroxybutyryl-CoA dehydrogenase 29, crotonase 30, butyryl-CoA dehydrogenase 31, butyraldehyde dehydrogenase 32, and butanol dehydrogenase 33, with aldolase 20 and triose phosphate isomerase 21 being the only two additional enzymes relative to the glyceraldehydes-3-phosphate-branched designer pathway. The use of a pyruvate-NADP+ oxidoreductase 27 (instead of pyruvate-ferredoxin oxidoreductase) in catalyzing the conversion of a pyruvate molecule to acetyl-CoA enables production of an NADPH, which can be used in some other steps of the butanol-production pathway. The addition of yet one more enzyme in the designer organism, phosphofructose kinase 19, permits the creation of another designer pathway which branches off from the point of fructose-6-phosphate of the Calvin cycle for the production of butanol. Like the glyceraldehyde-3-phosphate-branched butanol-production pathway, both the fructose-1,6-diphosphate-branched pathway (20-33) and the fructose-6-phosphate-branched pathway (19-33) can themselves generate NADH for use in the pathway at the step catalyzed by 3-hydroxybutyryl-CoA dehydrogenase 29 to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA and at the step catalyzed by butyryl-CoA dehydrogenase 31 to reduce crotonyl-CoA to butyryl-CoA. In each of these designer butanol-production pathways, the numbers of NADH molecules consumed are balanced with the numbers of NADH molecules generated; and both the butyraldehyde dehydrogenase 32 (catalyzing the step in reducing butyryl-CoA to butyraldehyde) and the butanol dehydrogenase 33 (catalyzing the terminal step in reducing butyraldehyde to butanol) can all use NADPH, which can be regenerated by the photosynthetic water splitting and proton gradient-coupled electron transport process. Therefore, these designer butanol-production pathways can operate continuously.
Table 1 lists examples of the enzymes including those identified above for construction of the designer butanol-production pathways. Throughout this specification, when reference is made to an enzyme, such as, for example, any of the enzymes listed in Table 1, it includes their isozymes, functional analogs, and designer modified enzymes and combinations thereof. These enzymes can be selected for use in construction of the designer butanol-production pathways (such as those illustrated in FIG. 1). The “isozymes or functional analogs” refer to certain enzymes that have the same catalytic function but may or may not have exactly the same protein structures. The most essential feature of an enzyme is its active site that catalyzes the enzymatic reaction. Therefore, certain enzyme-protein fragment(s) or subunit(s) that contains such an active catalytic site may also be selected for use in this invention. For various reasons, some of the natural enzymes contain not only the essential catalytic structure but also other structure components that may or may not be desirable for a given application. With techniques of bioinformatics-assisted molecular designing, it is possible to select the essential catalytic structure(s) for use in construction of a designer DNA construct encoding a desirable designer enzyme. Therefore, in one of the various embodiments, a designer enzyme gene is created by artificial synthesis of a DNA construct according to bioinformatics-assisted molecular sequence design. With the computer-assisted synthetic biology approach, any DNA sequence (thus its protein structure) of a designer enzyme may be selectively modified to achieve more desirable results by design. Therefore, the terms “designer modified sequences” and “designer modified enzymes” are hereby defined as the DNA sequences and the enzyme proteins that are modified with bioinformatics-assisted molecular design. For example, when a DNA construct for a designer chloroplast-targeted enzyme is designed from the sequence of a mitochondrial enzyme, it is a preferred practice to modify some of the protein structures, for example, by selectively cutting out certain structure component(s) such as its mitochondrial transit-peptide sequence that is not suitable for the given application, and/or by adding certain peptide structures such as an exogenous chloroplast transit-peptide sequence (e.g., a 135-bp Rubisco small-subunit transit peptide (RbcS2)) that is needed to confer the ability in the chloroplast-targeted insertion of the designer protein. Therefore, one of the various embodiments flexibly employs the enzymes, their isozymes, functional analogs, designer modified enzymes, and/or the combinations thereof in construction of the designer butanol-production pathway(s).
As shown in Table 1, many genes of the enzymes identified above have been cloned and/or sequenced from various organisms. Both genomic DNA and/or mRNA sequence data can be used in designing and synthesizing the designer DNA constructs for transformation of a host alga, oxyphotobacterium, plant, plant tissue or cells to create a designer organism for photobiological butanol production (FIG. 1). However, because of possible variations often associated with various source organisms and cellular compartments with respect to a specific host organism and its chloroplast/thylakoid environment where the butanol-production pathway(s) is designed to work with the Calvin cycle, certain molecular engineering art work in DNA construct design including codon-usage optimization and sequence modification is often necessary for a designer DNA construct (FIG. 2) to work well. For example, in creating a butanol-producing designer eukaryotic alga, if the source sequences are from cytosolic enzymes (sequences), a functional chloroplast-targeting sequence may be added to provide the capability for a designer unclear gene-encoded enzyme to insert into a host chloroplast to confer its function for a designer butanol-production pathway. Furthermore, to provide the switchability for a designer butanol-production pathway, it is also important to include a functional inducible promoter sequence such as the promoter of a hydrogenase (Hyd1) or nitrate reductase (Nia1) gene, or nitrite reductase (nirA) gene in certain designer DNA construct(s) as illustrated in FIG. 2A to control the expression of designer gene(s). In addition, as mentioned before, certain functional derivatives or fragments of these enzymes (sequences), chloroplast-targeting transit peptide sequences, and inducible promoter sequences can also be selected for use in full, in part or in combinations thereof, to create the designer organisms according to various embodiments of this invention. The arts in creating and using the designer organisms are further described hereinbelow.







TABLE 1







lists examples of enzymes for construction of designer butanol-production pathways.











GeGenBank Accession Number,


Enzyme
Source (Organism)
JGI Protein ID or Citation





Butanol 
Clostridium saccharoperbutylacetonicum;
GeGenBank: AB257439; AJ508920;


dehydrogenase
Propionibacterium freudenreichii;
AF112135; AF388671; AF157307;



Trichomonas vaginalis; Aeromonas
M96946, M96945



hydrophila; Clostridium beijerinckii;




Clostridium acetobutylicum



Butyraldehyde
Clostridium saccharoperbutylacetonicum
GenBank: AY251646


dehydrogenase




Butyryl-CoA
Clostridium beijerinckii; Butyrivibrio
GenBank: AF494018; AB190764;


dehydrogenase
fibrisolvens; Butyrate-producing 
DQ987697; Z92974



bacterium L2-50; Thermoanaerobacterium




thermosaccharolyticum;



Crotonase
Clostridium beijerinckii; Butyrivibrio
GenBank: AF494018; AB190764;



fibrisolvens; Butyrate-producing 
DQ987697; Z92974



bacterium L2-50; Thermoanaerobacterium




thermosaccharolyticum;



3-Hydroxybutyryl-
Clostridium beijerinckii; Butyrivibrio
GenBank: AF494018; AB190764;


CoA dehydro-
fibrisolvens; Ajellomyces capsulatus;
XM_001537366; XM_741533;


genase
Aspergillus fumigatus; Aspergillus
XM_001274776; XM_001262361;



clavatus; Neosartorya fischeri; Butyrate-
DQ987697; BT001208; Z92974



producing bacterium L2-50; Arabidopsis




thaliana; Thermoanaerobacterium




thermosaccharolyticum;



Thiolase
Butyrivibrio fibrfibrisolvens; butyrate-
GenBank: AB190764; DQ987697;



producing bacterium L2-50;
Z2974



Thermoanaerobacterium




thermosaccharolyticum;



Glyceraldehyde-3-
Mesostigma viride cytosol; Triticum
GenBank: DQ873404; EF592180;


phosphate 
aestivum cytosol; Chlamydomonas
L27668; XM_001549497; J01324;


dehydrogenase
reinhardtii chloroplast; Botryotinia
M18802; EU078558;



fuckeliana; Saccharomyces cerevisiae;
XM_1001539393; XM_001386423,



Zymomonas mobilis; Karenia brevis;
XM_1001386568; XM_001485596;



Ajellomyces capsulatus; Pichia stipitis;
DQ681075; EF592180;



Pichia guilliermondii; Kluyveromyces
NM_101214; U45857, 



marxianus, Triticum aestivum; 
ZMU45856, U45855



Arabidopsisthaliana; Zea mays cytosolic



Phosphoglycerate 
Chlamydomonas reinhardtii chloroplast;
GenBank: U14912, AF244144;


kinase
Plasmodium vivax; Babesia bovis;
XM_001614707; XM_001610679;



Botryotinia fuckeliana;
XM_001548271; DQ665858;



Monocercomonoides sp.; Lodderomyces
XM_001523843; XM_001484377;



elongisporus; Pichia guilliermondii;
NM_179576;



Arabidopsis thaliana; Helianthus annuus;
DQ835564; EF122488; AF316577;



Oryza sativa; Dictyostelium discoideum;
AY647236; AY029776; AF108452;



Euglena gracilis; Chondrus crispus;
AF073473



Phaeodactylum tricornutum; Solanum




tuberosum



Phosphoglycerate 
Chlamydomonas reinhardtii cytoplasm;
JGI Chlre2 protein ID 161689,


mutase (phospho-
Aspergillus fumigatus; Coccidioides
GenBank: AF268078; XM_747847;


glyceromutase)
immitis; Leishmania braziliensis;
XM_749597; XM_001248115;



Ajellomyces capsulatus;
XM_001569263; XM_001539892;



Monocercomonoides sp.; Aspergillus
DQ665859; XM_001270940;



clavatus; Arabidopsis thaliana; Zea mays
NM_117020; M80912


Enolase
Chlamydomonas reinhardtii cytoplasm;
GenBank: X66412, P31683;



Arabidopsis thaliana; Leishmania
AK222035; DQ221745;



Mexicana; Lodderomyces elongisporus;
XM_001528071; XM_001611873;



Babesia bovis; Sclerotinia sclerotiorum;
XM_001594215; XM_001483612;



Pichia guilliermondii; Spirotrichonympha
AB221057; EF122486, U09450;



leidyi; Oryza sativa; Trimastix pyriformis;
DQ845796; AB088633; U82438;



Leuconostoc mesenteroides; Davidiella
D64113; U13799; AY307449;



tassiana; Aspergillus oryzae;
U17973



Schizosaccharomyces pombe; Brassica




napus; Zea mays



Pyruvate kinase
Chlamydomonas reinhardtii cytoplasm;
JGI Chlre3 protein ID 138105;



Arabidopsis thaliana; Saccharomyces
GenBank: AK229638; AY949876,



cerevisiae; Babesia bovis; Sclerotinia
AY949890, AY949888;



sclerotiorum; Trichomonas vaginalis;
XM_001612087; XM_001594710;



Pichia guilliermondii; Pichia stipitis;
XM_001329865; XM_001487289;



Lodderomyces elongisporus; Coccidioides
XM_001384591; XM_001528210;



immitis; Trimastix pyriformis; Glycine
XM_001240868; DQ845797; 



max (soybean)
L08632


Phosphofructose 
Chlamydomonas reinhardtii; Arabidopsis
JGI Chlre2 protein ID 159495;


kinase
thaliana; Ajellomyces capsulatus; Yarrowia
GenBank: NM_001037043,



lipolytica; Pichia stipitis; Dictyostelium
NM_179694, NM_119066,



discoideum; Tetrahymena thermophila;
NM_125551; XM_001537193;



Trypanosoma brucei; Plasmodium
AY142710; XM_001382359,



falciparum; Spinacia oleracea;
XM_001383014; XM_639070;




XM_001017610; XM_838827;




XM_001347929; DQ437575;


Fructose-diphos-
Chlamydomonas reinhardtii chloroplast;
GenBank: X69969; AF308587;


phate aldolase
Fragaria x ananassa cytoplasm; Homo
NM_005165; XM_001609195;



sapiens; Babesia bovis; Trichomonas
XM_001312327, XM_001312338;



vaginalis; Pichia stipitis; Arabidopsis
XM_001387466; NM_120057,



thaliana
NM_001036644


Triose phosphate 
Arabidopsis thaliana; Chlamydomonas
GenBank: NM_127687, AF247559;


isomerase
reinhardtii; Sclerotinia sclerotiorum;
AY742323; XM_001587391;



Chlorella pyrenoidosa; Pichia
AB240149; XM_001485684;



guilliermondii; Euglena intermedia;
DQ459379; AY742325; L36387;



Euglena longa; Spinacia oleracea;
AY438596; U83414; EF575877;



Solanum chacoense; Hordeum vulgare;




Oryza sativa



Glucose-1-
Arabidopsis thaliana; Zea mays;
GenBank: NM_127730, 


phosphate 
Chlamydia trachomatis; Solanum
NM_124205, XM_121927, 


adenylyl
tuberosum (potato); Shigella flexneri;
AY059862; EF694839,


transferase
Lycopersicon esculentum
EF694838; AF087165; P55242;




NP_709206; T07674


Starch synthase
Chlamydomonas reinhardtii; Phaseolus
GenBank: AF026422, AF026421,



vulgaris; Oryza sativa; Arabidopsis
DQ019314, AF433156; AB293998;



thaliana; Colocasia esculenta; Amaranthus
D16202, AB115917, AY299404;



cruentus; Parachlorella kessleri; Triticum
AF121673, AK226881; NM_101044;



aestivum; Sorghum bicolor; Astragalus
AY225862, AY142712; DQ178026;



membranaceus; Perilla frutescens; Zea
AB232549; Y16340; AF168786;



mays; Ipomoea batatas
AF097922; AF210699; AF019297;




AF068834


Alpha-amylase
Hordeum vulgare aleurone cells;
GenBank: J04202; XM_001319100;



Trichomonas vaginalis; Phanerochaete
EF143986; AY324649; NM_129551;



chrysosporium; Chlamydomonas
X07896



reinhardtii; Arabidopsis thaliana;




Dictyoglomus thermophilum heat-stable




amylase gene;



Beta-amylase
Arabidopsis thaliana; Hordeum vulgare;
GenBank: NM_113297; D21349;



Musa acuminata
DQ166026


Starch phos-
Citrus hybrid cultivar root; Solanum
Gennbank: AY098895; P53535;


phorylase
tuberosum chloroplast; Arabidopsis
NM_113857, NM_114564;



thaliana; Triticum aestivum; Ipomoea
AF275551; M64362



batatas



Phosphoglu-
Oryza sativa plastid; Ajellomyces
GenBank: AC105932, AF455812;


comutase
capsulatus; Pichia stipitis; Lodderomyces
XM_001536436; XM_001383281;



elongisporus; Aspergillus fumigatus;
XM_001527445; XM_749345;



Arabidopsis thaliana; Populus tomentosa;
NM_124561, NM_180508,



Oryza sativa; Zea mays
AY128901; AY479974; AF455812;




U89342, U89341


Glucosephosphate 
Chlamydomonas reinhardtii;
JGI Chlre3 protein ID 135202;


(glucose- 
Saccharomyces cerevisiae; Pichia stipitis;
GenBank: M21696;


phosphate)
Ajellomyces capsulatus; Spinacia oleracea
XM_001385873 ; XM_001537043;


isomerase
cytosol; Oryza sativa cytoplasm;
T09154; P42862; NM_123638,



Arabidopsis thaliana; Zea mays
NM_118595; U17225


Hexokinase 
Ajellomyces capsulatus; Pichia stipitis;
GenBank: XM_001541513;


(glucokinase)
Pichia angusta; Thermosynechococcus
XM_001386652, AY278027;



elongates; Babesia bovis; Solanum
XM_001386035; NC_004113;



chacoense; Oryza sativa; Arabidopsis
XM_001608698; DQ177440;



thaliana
DQ116383; NM_112895


NADP(H) 
Methanococcus jannaschii
The Journal Of Biological


phosphatase

Chemistry 280 (47): 




39200-39207 (2005)


NAD kinase
Babesia bovis; Trichomonas vaginalis
GenBank: XM_001609395;




XM_001324239


Pyruvate-NADP+
Peranema trichophorum; 
GenBank: EF114757; AB021127,


oxidoreductase
Euglena gracilis
AJ278425


Pyruvate-
Mastigamoeba balamuthi; Desulfovibrio
GenBank: AY101767; Y09702;


ferredoxin
africanus; Entamoeba histolytica;
U30149; XM_001582310,


oxidoreductase
Trichomonas vaginalis; Cryptosporidium
XM_001313670, XM_001321286,



parvum; Cryptosporidium baileyi; Giardia
XM_001307087,



lamblia; Entamoeba histolytica;
XM_001311860, XM_001314776,



Hydrogenobacter thermophilus;
XM_001307250; EF030517;



Clostridium pasteurianum;
EF030516; XM_764947;




XM_651927; AB042412; Y17727









Targeting the Designer Enzymes to the Stroma Region of Chloroplasts

Some of the designer enzymes discussed above, such as, pyruvate-ferredoxin oxidoreductase, thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase are known to function in certain special bacteria such as Clostridium; but wild-type plant chloroplasts generally do not possess these enzymes to function with the Calvin cycle. Therefore, in one of the various embodiments in creating a butanol-producing eukaryotic designer organism, designer nucleic acids encoding for these enzymes are expressed in the chloroplast(s) of a host cell. This can be accomplished by delivery of designer butanol-production-pathway gene(s) into the chloroplast genome of the eukaryotic host cell typically using a genegun. In certain extent, the molecular genetics of chloroplasts are similar to that of cyanobacteria. After being delivered into the chloroplast, a designer DNA construct that contains a pair of proper recombination sites as illustrated in FIG. 2F can be incorporated into the chloroplast genome through a natural process of homologous DNA double recombination.
In another embodiment, nucleic acids encoding for these enzymes are genetically engineered such that the enzymes expressed are inserted into the chloroplasts to operate with the Calvin cycle there. Depending on the genetic background of a particular host organism, some of the designer enzymes discussed above such as phosphoglycerate mutase and enolase may exist at some background levels in its native form in a wild-type chloroplast. For various reasons including often the lack of their controllability, however, some of the chloroplast background enzymes may or may not be sufficient to serve as a significant part of the designer butanol-production pathway(s). Furthermore, a number of useful inducible promoters happen to function in the nuclear genome. For example, both the hydrogenase (Hyd1) promoter and the nitrate reductase (Nia1) promoter that can be used to control the expression of the designer butanol-production pathways are located in the nuclear genome of Chlamydomonas reinhardtii, of which the genome has recently been sequenced. Therefore, in one of the various embodiments, it is preferred to use nuclear-genome-encodable designer genes to confer a switchable butanol-production pathway. Consequently, nucleic acids encoding for these enzymes also need to be genetically engineered with proper sequence modification such that the enzymes are controllably expressed and are inserted into the chloroplasts to create a designer butanol-production pathway.
According to one of the various embodiments, it is best to express the designer butanol-producing-pathway enzymes only into chloroplasts (at the stroma region), exactly where the action of the enzymes is needed to enable photosynthetic production of butanol. If expressed without a chloroplast-targeted insertion mechanism, the enzymes would just stay in the cytosol and not be able to directly interact with the Calvin cycle for butanol production. Therefore, in addition to the obvious distinctive features in pathway designs and associated approaches, another significant distinction is that one of the various embodiments innovatively employs a chloroplast-targeted mechanism for genetic insertion of many designer butanol-production-pathway enzymes into chloroplast to directly interact with the Calvin cycle for photobiological butanol production.
With a chloroplast stroma-targeted mechanism, the cells will not only be able to produce butanol but also to grow and regenerate themselves when they are returned to certain conditions under which the designer pathway is turned off, such as under aerobic conditions when designer hydrogenase promoter-controlled butanol-production-pathway genes are used. Designer algae, plants, or plant cells that contain normal mitochondria should be able to use the reducing power (NADH) from organic reserves (and/or some exogenous organic substrate such as acetate or sugar) to power the cells immediately after returning to aerobic conditions. Consequently, when the designer algae, plants, or plant cells are returned to aerobic conditions after use under anaerobic conditions for photosynthetic butanol production, the cells will stop making the butanol-producing-pathway enzymes and start to restore the normal photoautotrophic capability by synthesizing new and functional chloroplasts. Therefore, it is possible to use such genetically engineered designer alga/plant organisms for repeated cycles of photoautotrophic growth under normal aerobic conditions and efficient production of butanol directly from CO2 and H2O under certain specific designer butanol-producing conditions such as under anaerobic conditions and/or in the presence of nitrate when a Nia1 promoter-controlled butanol-production pathway is used.
The targeted insertion of designer butanol-production-pathway enzymes can be accomplished through use of a DNA sequence that encodes for a stroma “signal” peptide. A stroma-protein signal (transit) peptide directs the transport and insertion of a newly synthesized protein into stroma. In accordance with one of the various embodiments, a specific targeting DNA sequence is preferably placed in between the promoter and a designer butanol-production-pathway enzyme sequence, as shown in a designer DNA construct (FIG. 2A). This targeting sequence encodes for a signal (transit) peptide that is synthesized as part of the apoprotein of an enzyme in the cytosol. The transit peptide guides the insertion of an apoprotein of a designer butanol-production-pathway enzyme from cytosol into the chloroplast. After the apoprotein is inserted into the chloroplast, the transit peptide is cleaved off from the apoprotein, which then becomes an active enzyme.
A number of transit peptide sequences are suitable for use for the targeted insertion of the designer butanol-production-pathway enzymes into chloroplast, including but not limited to the transit peptide sequences of: the hydrogenase apoproteins (such as HydA1 (Hyd1) and HydA2, GenBank accession number AJ308413, AF289201, AY090770), ferredoxin apoprotein (Frx1, accession numbers L10349, P07839), thioredoxin m apoprotein (Trx2, X62335), glutamine synthase apoprotein (Gs2, Q42689), LhcII apoproteins (AB051210, AB051208, AB051205), PSII-T apoprotein (PsbT), PSII-S apoprotein (PsbS), PSII-W apoprotein (PsbW), CF0CF1 subunit-apoprotein (AtpC), CF0CF1 subunit-apoprotein (AtpD, U41442), CFoCF1 subunit-II apoprotein (AtpG), photosystem I (PSI) apoproteins (such as, of genes PsaD, PsaE, PsaF, PsaG, PsaH, and PsaK), Rubisco SSU apoproteins (such as RbcS2, X04472). Throughout this specification, when reference is made to a transit peptide sequence, such as, for example, any of the transit peptide sequence described above, it includes their functional analogs, modified designer sequences, and combinations thereof. A “functional analog” or “modified designer sequence” in this context refers to a peptide sequence derived or modified (by, e.g., conservative substitution, moderate deletion or addition of amino acids, or modification of side chains of amino acids) based on a native transit peptide sequence, such as those identified above, that has the same function as the native transit peptide sequence, i.e., effecting targeted insertion of a desired enzyme.
In certain specific embodiments, the following transit peptide sequences are used to guide the insertion of the designer butanol-production-pathway enzymes into the stroma region of the chloroplast: the Hyd1 transit peptide (having the amino acid sequence: msalylkpca aysirgsscr arqvaprapl aastvrvala tleaparrlg nvacaa (SEQ ID NO: 54)), the RbcS2 transit peptides (having the amino acid sequence: maaviakssv saavarpars svrpmaalkp avkaapvaap aqanq (SEQ ID NO: 55)), ferredoxin transit peptide (having the amino acid sequence: mamamrs (SEQ ID NO: 56)), the CF0CF1 subunit-δ transit peptide (having the amino acid sequence: mlaaksiagp rafkasavra apkagrrtvv vma (SEQ ID NO: 57)), their analogs, functional derivatives, designer sequences, and combinations thereof.
Use of a Genetic Switch to Control the Expression of a Designer Butanol-Producing Pathway.
Another key feature of the invention is the application of a genetic switch to control the expression of the designer butanol-producing pathway(s), as illustrated in FIG. 1. This switchability is accomplished through the use of an externally inducible promoter so that the designer transgenes are inducibly expressed under certain specific inducing conditions. Preferably, the promoter employed to control the expression of designer genes in a host is originated from the host itself or a closely related organism. The activities and inducibility of a promoter in a host cell can be tested by placing the promoter in front of a reporting gene, introducing this reporter construct into the host tissue or cells by any of the known DNA delivery techniques, and assessing the expression of the reporter gene.
In a preferred embodiment, the inducible promoter used to control the expression of designer genes is a promoter that is inducible by anaerobiosis, i.e., active under anaerobic conditions but inactive under aerobic conditions. A designer alga/plant organism can perform autotrophic photosynthesis using CO2 as the carbon source under aerobic conditions, and when the designer organism culture is grown and ready for photosynthetic butanol production, anaerobic conditions will be applied to turn on the promoter and the designer genes that encode a designer butanol-production pathway(s).
A number of promoters that become active under anaerobic conditions are suitable for use in the present invention. For example, the promoters of the hydrogenase genes (HydA1 (Hyd1) and HydA2, GenBank accession number: AJ308413, AF289201, AY090770) of Chlamydomonas reinhardtii, which is active under anaerobic conditions but inactive under aerobic conditions, can be used as an effective genetic switch to control the expression of the designer genes in a host alga, such as Chlamydomonas reinhardtii. In fact, Chlamydomonas cells contain several nuclear genes that are coordinately induced under anaerobic conditions. These include the hydrogenase structural gene itself (Hyd1), the Cyc6 gene encoding the apoprotein of Cytochrome C6, and the Cpx1 gene encoding coprogen oxidase. The regulatory regions for the latter two have been well characterized, and a region of about 100 bp proves sufficient to confer regulation by anaerobiosis in synthetic gene constructs (Quinn, Barraco, Ericksson and Merchant (2000). “Coordinate copper- and oxygen-responsive Cyc6 and Cpx1 expression in Chlamydomonas is mediated by the same element.” J Biol Chem 275: 6080-6089). Although the above inducible algal promoters may be suitable for use in other plant hosts, especially in plants closely related to algae, the promoters of the homologous genes from these other plants, including higher plants, can be obtained and employed to control the expression of designer genes in those plants.
In another embodiment, the inducible promoter used in the present invention is an algal nitrate reductase (Nia1) promoter, which is inducible by growth in a medium containing nitrate and repressed in a nitrate-deficient but ammonium-containing medium (Loppes and Radoux (2002) “Two short regions of the promoter are essential for activation and repression of the nitrate reductase gene in Chlamydomonas reinhardtii,” Mol Genet Genomics 268: 42-48). Therefore, the Nia1 (gene accession number AF203033) promoter can be selected for use to control the expression of the designer genes in an alga according to the concentration levels of nitrate and ammonium in a culture medium. Additional inducible promoters that can also be selected for use in the present invention include, for example, the heat-shock protein promoter HSP70A (accession number: DQ059999, AY456093, M98823; Schroda, Blocker, Beek (2000) The HSP70A promoter as a tool for the improved expression of transgenes in Chlamydomonas. Plant Journal 21:121-131), the promoter of CabII-1 gene (accession number M24072), the promoter of Ca1 gene (accession number P20507), and the promoter of Ca2 gene (accession number P24258).
In the case of blue-green algae (oxyphotobacteria including cyanobacteria and oxychlorobacteria), there are also a number of inducible promoters that can be selected for use in the present invention. For example, the promoters of the anaerobic-responsive bidirectional hydrogenase hox genes of Nostoc sp. PCC 7120 (GenBank: BA000019), Prochlorothrix hollandica (GenBank: U88400; hoxUYH operon promoter), Synechocystis sp. strain PCC 6803 (CyanoBase: s111220 and s111223), Synechococcus elongatus PCC 6301 (CyanoBase: syc1235_c), Arthrospira platensis (GenBank: ABC26906), Cyanothece sp. CCY0110 (GenBank: ZP_01727419) and Synechococcus sp. PCC 7002 (GenBank: AAN03566), which are active under anaerobic conditions but inactive under aerobic conditions (Sjoholm, Oliveira, and Lindblad (2007) “Transcription and regulation of the bidirectional hydrogenase in the Cyanobacterium Nostoc sp. strain PCC 7120,” Applied and Environmental Microbiology, 73(17): 5435-5446), can be used as an effective genetic switch to control the expression of the designer genes in a host oxyphotobacterium, such as Nostoc sp. PCC 7120, Synechocystis sp. strain PCC 6803, Synechococcus elongatus PCC 6301, Cyanothece sp. CCY0110, Arthrospira platensis, or Synechococcus sp. PCC 7002.
In another embodiment in creating switchable butanol-production designer organisms such as switchable designer oxyphotobacteria, the inducible promoter selected for use is a nitrite reductase (nirA) promoter, which is inducible by growth in a medium containing nitrate and repressed in a nitrate-deficient but ammonium-containing medium (Qi, Hao, Ng, Slater, Baszis, Weiss, and Valentin (2005) “Application of the Synechococcus nirA promoter to establish an inducible expression system for engineering the Synechocystis tocopherol pathway,” Applied and Environmental Microbiology, 71(10): 5678-5684; Maeda, Kawaguchi, Ohe, and Omata (1998) “cis-Acting sequences required for NtcB-dependent, nitrite-responsive positive regulation of the nitrate assimilation operon in the Cyanobacterium Synechococcus sp. strain PCC 7942,” Journal of Bacteriology, 180(16):4080-4088). Therefore, the nirA promoter sequences can be selected for use to control the expression of the designer genes in a number of oxyphotobacteria according to the concentration levels of nitrate and ammonium in a culture medium. The nirA promoter sequences that can be selected and modified for use include (but not limited to) the nirA promoters of the following oxyphotobacteria: Synechococcus elongatus PCC 6301 (GenBank: AP008231, region 355890-255950), Synechococcus sp. (GenBank: X67680.1, D16303.1, D12723.1, and D00677), Synechocystis sp. PCC 6803 (GenBank: NP_442378, BA000022, AB001339, D63999-D64006, D90899-D90917), Anabaena sp. (GenBank: X99708.1), Nostoc sp. PCC 7120 (GenBank: BA000019.2 and AJ319648), Plectonema boryanum (GenBank: D31732.1), Synechococcus elongatus PCC 7942 (GenBank: P39661, CP000100.1), Thermosynechococcus elongatus BP-1 (GenBank: BAC08901, NP_682139), Phormidium laminosum (GenBank: CAA79655, Q51879), Mastigocladus laminosus (GenBank: ABD49353, ABD49351, ABD49349, ABD49347), Anabaena variabilis ATCC 29413 (GenBank: YP_325032), Prochlorococcus marinus str. MIT 9303 (GenBank: YP_001018981), Synechococcus sp. WH 8103 (GenBank: AAC17122), Synechococcus sp. WH 7805 (GenBank: ZP_01124915), and Cyanothece sp. CCY0110 (GenBank: ZP_01727861).
In yet another embodiment, an inducible promoter selected for use is the light- and heat-responsive chaperone gene groE promoter, which can be induced by heat and/or light [Kojima and Nakamoto (2007) “A novel light- and heat-responsive regulation of the groE transcription in the absence of HrcA or CIRCE in cyanobacteria,” FEBS Letters 581:1871-1880). A number of groE promoters such as the groES and groEL (chaperones) promoters are available for use as an inducible promoter in controlling the expression of the designer butanol-production-pathway enzymes. The groE promoter sequences that can be selected and modified for use in one of the various embodiments include (but not limited to) the groES and/or groEL promoters of the following oxyphotobacteria: Synechocystis sp. (GenBank: D12677.1), Synechocystis sp. PCC 6803 (GenBank: BA000022.2), Synechococcus elongatus PCC 6301 (GenBank: AP008231.1), Synechococcus sp (GenBank: M58751.1), Synechococcus elongatus PCC 7942 (GenBank: CP000100.1), Nostoc sp. PCC 7120 (GenBank: BA000019.2), Anabaena variabilis ATCC 29413 (GenBank: CP000117.1), Anabaena sp. L-31 (GenBank: AF324500); Thermosynechococcus elongatus BP-1 (CyanoBase: t110185, t110186), Synechococcus vulcanus (GenBank: D78139), Oscillatoria sp. NKBG091600 (GenBank: AF054630), Prochlorococcus marinus MIT9313 (GenBank: BX572099), Prochlorococcus marinus str. MIT 9303 (GenBank: CP000554), Prochlorococcus marinus str. MIT 9211 (GenBank: ZP_01006613), Synechococcus sp. WH8102 (GenBank: BX569690), Synechococcus sp. CC9605 (GenBank: CP000110), Prochlorococcus marinus subsp. marinus str. CCMP1375 (GenBank: AE017126), and Prochlorococcus marinus MED4 (GenBank: BX548174).
Additional inducible promoters that can also be selected for use in the present invention include: for example, the metal (zinc)-inducible smt promoter of Synechococcus PCC 7942 (Erbe, Adams, Taylor and Hall (1996) “Cyanobacteria carrying an smt-lux transcriptional fusion as biosensors for the detection of heavy metal cations,” Journal of Industrial Microbiology, 17:80-83); the iron-responsive idiA promoter of Synechococcus elongatus PCC 7942 (Michel, Pistorius, and Golden (2001) “Unusual regulatory elements for iron deficiency induction of the idiA gene of Synechococcus elongatus PCC 7942” Journal of Bacteriology, 183(17):5015-5024); the redox-responsive cyanobacterial crhR promoter (Patterson-Fortin, Colvin and Owttrim (2006) “A LexA-related protein regulates redox-sensitive expression of the cyanobacterial RNA helicase, crhR”, Nucleic Acids Research, 34(12):3446-3454); the heat-shock gene hsp16.6 promoter of Synechocystis sp. PCC 6803 (Fang and Barnum (2004) “Expression of the heat shock gene hsp16.6 and promoter analysis in the Cyanobacterium, Synechocystis sp. PCC 6803,” Current Microbiology 49:192-198); the small heat-shock protein (Hsp) promoter such as Synechococcus vulcanus gene hspA promoter (Nakamoto, Suzuki, and Roy (2000) “Constitutive expression of a small heat-shock protein confers cellular thermotolerance and thermal protection to the photosynthetic apparatus in cyanobacteria,” FEBS Letters 483:169-174); the CO2-responsive promoters of oxyphotobacterial carbonic-anhydrase genes (GenBank: EAZ90903, EAZ90685, ZP_01624337, EAW33650, ABB17341, AAT41924, CA089711, ZP_00111671, YP_400464, AAC44830; and CyanoBase: a112929, PMT1568 slr0051, s1r1347, and syc0167_c); the nitrate-reductase-gene (narB) promoters (such as GenBank accession numbers: BAC08907, NP_682145, AAO25121; ABI46326, YP_732075, BAB72570, NP_484656); the green/red light-responsive promoters such as the light-regulated cpcB2A2 promoter of Fremyella diplosiphon (Casey and Grossman (1994) “In vivo and in vitro characterization of the light-regulated cpcB2A2 promoter of Fremyella diplosiphont” Journal of Bacteriology, 176(20):6362-6374); and the UV-light responsive promoters of cyanobacterial genes lexA, recA and ruvB (Domain, Houot, Chauvat, and Cassier-Chauvat (2004) “Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation,” Molecular Microbiology, 53(1):65-80).
Furthermore, in one of the various embodiments, certain “semi-inducible” or constitutive promoters can also be selected for use in combination of an inducible promoter(s) for construction of a designer butanol-production pathway(s) as well. For example, the promoters of oxyphotobacterial Rubisco operon such as the rbcL genes (GenBank: X65960, ZP_01728542, Q3M674, BAF48766, NP_895035, 0907262A; CyanoBase: PMT1205, PMM0550, Pro0551, t111506, SYNW1718, g1r2156, a1r1524, slr0009), which have certain light-dependence but could be regarded almost as constitutive promoters, can also be selected for use in combination of an inducible promoter(s) such as the nirA, hox, and/or groE promoters for construction of the designer butanol-production pathway(s) as well.
Throughout this specification, when reference is made to inducible promoter, such as, for example, any of the inducible promoters described above, it includes their analogs, functional derivatives, designer sequences, and combinations thereof. A “functional analog” or “modified designer sequence” in this context refers to a promoter sequence derived or modified (by, e.g., substitution, moderate deletion or addition or modification of nucleotides) based on a native promoter sequence, such as those identified hereinabove, that retains the function of the native promoter sequence.
DNA Constructs and Transformation into Host Organisms
DNA constructs are generated in order to introduce designer butanol-production-pathway genes to a host alga, plant, plant tissue or plant cells. That is, a nucleotide sequence encoding a designer butanol-production-pathway enzyme is placed in a vector, in an operable linkage to a promoter, preferably an inducible promoter, and in an operable linkage to a nucleotide sequence coding for an appropriate chloroplast-targeting transit-peptide sequence. In a preferred embodiment, nucleic acid constructs are made to have the elements placed in the following 5′ (upstream) to 3′ (downstream) orientation: an externally inducible promoter, a transit targeting sequence, and a nucleic acid encoding a designer butanol-production-pathway enzyme, and preferably an appropriate transcription termination sequence. One or more designer genes (DNA constructs) can be placed into one genetic vector. An example of such a construct is depicted in FIG. 2A. As shown in the embodiment illustrated in FIG. 2A, a designer butanol-production-pathway transgene is a nucleic acid construct comprising: a) a PCR forward primer; b) an externally inducible promoter; c) a transit targeting sequence; d) a designer butanol-production-pathway-enzyme-encoding sequence with an appropriate transcription termination sequence; and e) a PCR reverse primer.
In accordance with various embodiments, any of the components a) through e) of this DNA construct are adjusted to suit for certain specific conditions. In practice, any of the components a) through e) of this DNA construct are applied in full or in part, and/or in any adjusted combination to achieve more desirable results. For example, when an algal hydrogenase promoter is used as an inducible promoter in the designer butanol-production-pathway DNA construct, a transgenic designer alga that contains this DNA construct will be able to perform autotrophic photosynthesis using ambient-air CO2 as the carbon source and grows normally under aerobic conditions, such as in an open pond. When the algal culture is grown and ready for butanol production, the designer transgene(s) can then be expressed by induction under anaerobic conditions because of the use of the hydrogenase promoter. The expression of designer gene(s) produces a set of designer butanol-production-pathway enzymes to work with the Calvin cycle for photobiological butanol production (FIG. 1).
The two PCR primers are a PCR forward primer (PCR FD primer) located at the beginning (the 5′ end) of the DNA construct and a PCR reverse primer (PCR RE primer) located at the other end (the 3′ end) as shown in FIG. 2A. This pair of PCR primers is designed to provide certain convenience when needed for relatively easy PCR amplification of the designer DNA construct, which is helpful not only during and after the designer DNA construct is synthesized in preparation for gene transformation, but also after the designer DNA construct is delivered into the genome of a host alga for verification of the designer gene in the transformants. For example, after the transformation of the designer gene is accomplished in a Chlamydomonas reinhardtii-arg7 host cell using the techniques of electroporation and argininosuccinate lyase (arg7) complementation screening, the resulted transformants can be then analyzed by a PCR DNA assay of their nuclear DNA using this pair of PCR primers to verify whether the entire designer butanol-production-pathway gene (the DNA construct) is successfully incorporated into the genome of a given transformant. When the nuclear DNA PCR assay of a transformant can generate a PCR product that matches with the predicted DNA size and sequence according to the designer DNA construct, the successful incorporation of the designer gene(s) into the genome of the transformant is verified.
Therefore, the various embodiments also teach the associated method to effectively create the designer transgenic algae, plants, or plant cells for photobiological butanol production. This method, in one of embodiments, includes the following steps: a) Selecting an appropriate host alga, plant, plant tissue, or plant cells with respect to their genetic backgrounds and special features in relation to butanol production; b) Introducing the nucleic acid constructs of the designer genes into the genome of said host alga, plant, plant tissue, or plant cells; c) Verifying the incorporation of the designer genes in the transformed alga, plant, plant tissue, or plant cells with DNA PCR assays using the said PCR primers of the designer DNA construct; d) Measuring and verifying the designer organism features such as the inducible expression of the designer butanol-pathway genes for photosynthetic butanol production from carbon dioxide and water by assays of mRNA, protein, and butanol-production characteristics according to the specific designer features of the DNA construct(s) (FIG. 2A).
The above embodiment of the method for creating the designer transgenic organism for photobiological butanol production can also be repeatedly applied for a plurality of operational cycles to achieve more desirable results. In various embodiments, any of the steps a) through d) of this method described above are adjusted to suit for certain specific conditions. In various embodiments, any of the steps a) through d) of the method are applied in full or in part, and/or in any adjusted combination.
Examples of designer butanol-production-pathway genes (DNA constructs) are shown in the sequence listings. SEQ ID NO: 1 presents a detailed DNA construct of a designer Butanol Dehydrogenase gene (1809 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase Nia1 promoter (21-282), a 135-bp RbcS2 transit peptide (283-417), an enzyme-encoding sequence (418-1566) selected and modified from a Clostridium saccharoperbutylacetonicum Butanol Dehydrogenase sequence (AB257439), a 223-bp RbcS2 terminator (1567-1789), and a PCR RE primer (1790-1809). The 262-bp Nia1 promoter (DNA sequence 21-282) is used as an example of an inducible promoter to control the expression of a designer butanol-production-pathway Butanol Dehydrogenase gene (DNA sequence 418-1566). The 135-bp RbcS2 transit peptide (DNA sequence 283-417) is used as an example to guide the insertion of the designer enzyme (DNA sequence 418-1566) into the chloroplast of the host organism. The RbcS2 terminator (DNA sequence 1567-1789) is employed so that the transcription and translation of the designer gene is properly terminated to produce the designer apoprotein (RbcS2 transit peptide-Butanol Dehydrogenase) as desired. Because the Nia1 promoter is a nuclear DNA that can control the expression only for nuclear genes, the synthetic butanol-production-pathway gene in this example is designed according to the codon usage of Chlamydomonas nuclear genome. Therefore, in this case, the designer enzyme gene is transcribed in nucleus. Its mRNA is naturally translocated into cytosol, where the mRNA is translated to an apoprotein that consists of the RbcS2 transit peptide (corresponding to DNA sequence 283-417) with its C-terminal end linked together with the N-terminal end of the Butanol Dehydrogenase protein (corresponding to DNA sequence 418-1566). The transit peptide of the apoprotein guides its transportation across the chloroplast membranes and into the stroma area, where the transit peptide is cut off from the apoprotein. The resulting Butanol Dehydrogenase then resumes its function as an enzyme for the designer butanol-production pathway in chloroplast. The two PCR primers (sequences 1-20 and 1790-1809) are selected and modified from the sequence of a Human actin gene and can be paired with each other. Blasting the sequences against Chlamydomonas GenBank found no homologous sequences of them. Therefore, they can be used as appropriate PCR primers in DNA PCR assays for verification of the designer gene in the transformed alga.
SEQ ID NO: 2 presents example 2 for a designer Butyraldehyde Dehydrogenase DNA construct (2067 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase Nia1 promoter (21-282), a 135-bp RbcS2 transit peptide (283-417), a Butyraldehyde Dehydrogenase-encoding sequence (418-1824) selected and modified from a Clostridium saccharoperbutylacetonicum Butyraldehyde Dehydrogenase sequence (AY251646), a 223-bp RbcS2 terminator (1825-2047), and a PCR RE primer (2048-2067). This DNA construct is similar to example 1, SEQ ID NO: 1, except that a Butyraldehyde Dehydrogenase-encoding sequence (418-1824) selected and modified from a Clostridium saccharoperbutylacetonicum Butyraldehyde Dehydrogenase sequence (AY251646) is used.
SEQ ID NO: 3 presents example 3 for a designer Butyryl-CoA Dehydrogenase construct (1815 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase promoter (21-282), a 9-bp Xho I NdeI site (283-291), a 135-bp RbcS2 transit peptide (292-426), a Butyryl-CoA Dehydrogenase encoding sequence (427-1563) selected/modified from the sequences of a Clostridium beijerinckii Butyryl-CoA Dehydrogenase (AF494018), a 9-bp XbaI site (1564-1572), a 223-bp RbcS2 terminator (1573-1795), and a PCR RE primer (1796-1815) at the 3′ end. This DNA construct is similar to example 1, SEQ ID NO: 1, except that a Butyryl-CoA Dehydrogenase encoding sequence (427-1563) selected/modified from the sequences of a Clostridium beijerinckii Butyryl-CoA Dehydrogenase (AF494018) is used and restriction sites of Xho I NdeI and XbaI are added to make the key components such as the targeting sequence (292-426) and the designer enzyme sequence (427-1563) as a modular unit that can be flexible replaced when necessary to save cost of gene synthesis and enhance work productivity. Please note, the enzyme does not have to be Clostridium beijerinckii Butyryl-CoA Dehydrogenase; a number of butyryl-CoA dehydrogenase enzymes (such as those listed in Table 1) including their isozymes, designer modified enzymes, and functional analogs from other sources such as Butyrivibrio fibrisolvens, Butyrate producing bacterium L2-50, Thermoanaerobacterium thermosaccharolyticum, can also be selected for use.
SEQ ID NO: 4 presents example 4 for a designer Crotonase DNA construct (1482 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase promoter (21-282), a 9-bp Xho I NdeI site (283-291) a 135-bp RbcS2 transit peptide (292-426), a Crotonase-encoding sequence (427-1209) selected/modified from the sequences of a Clostridium beijerinckii Crotonase (Genbank: AF494018), a 21-bp Lumio-tag-encoding sequence (1210-1230), a 9-bp XbaI site (1231-1239) containing a stop codon, a 223-bp RbcS2 terminator (1240-1462), and a PCR RE primer (1463-1482) at the 3′ end. This DNA construct is similar to example 3, SEQ ID NO: 3, except that a Crotonase-encoding sequence (427-1209) selected/modified from the sequences of a Clostridium beijerinckii Crotonase (Genbank: AF494018) is used and a 21-bp Lumio-tag-encoding sequence (1210-1230) is added at the C-terminal end of the enolase sequence. The 21-bp Lumio-tag sequence (1210-1230) is employed here to encode a Lumio peptide sequence Gly-Cys-Cys-Pro-Gly-Cys-Cys (SEQ ID NO: 58), which can become fluorescent when treated with a Lumio reagent that is now commercially available from Invitrogen. Lumio molecular tagging technology is based on an EDT (1,2-ethanedithiol) coupled biarsenical derivative (the Lumio reagent) of fluorescein that binds to an engineered tetracysteine sequence (Keppetipola, Coffman, and et al (2003). Rapid detection of in vitro expressed proteins using LumioTM technology, Gene Expression, 25.3: 7-11). The tetracysteine sequence consists of Cys-Cys-Xaa-Xaa-Cys-Cys (SEQ ID NO: 59), where Xaa is any non-cysteine amino acid such as Pro or Gly in this example. The EDT-linked Lumio reagent allows free rotation of the arsenic atoms that quenches the fluorescence of fluorescein. Covalent bond formation between the thiols of the Lumio's arsenic groups and the tetracysteines prevents free rotation of arsenic atoms that releases the fluorescence of fluorescein (Griffin, Adams, and Tsien (1998), “Specific covalent labeling of recombinant protein molecules inside live cells”, Science, 281:269-272). This also permits the visualization of the tetracysteine-tagged proteins by fluorescent molecular imaging. Therefore, use of the Lumio tag in this manner enables monitoring and/or tracking of the designer Crotonase when expressed to verify whether the designer butanol-production pathway enzyme is indeed delivered into the chloroplast of a host organism as designed. The Lumio tag (a short 7 amino acid peptide) that is linked to the C-terminal end of the Crotonase protein in this example should have minimal effect on the function of the designer enzyme, but enable the designer enzyme molecule to be visualized when treated with the Lumio reagent. Use of the Lumio tag is entirely optional. If the Lumio tag somehow affects the designer enzyme function, this tag can be deleted in the DNA sequence design.
SEQ ID NO: 5 presents example 5 for a designer 3-Hydroxybutyryl-CoA Dehydrogenase DNA construct (1367 bp) that includes a PCR FD primer (sequence 1-20), a 84-bp nitrate reductase promoter (21-104), a 9-bp Xho I NdeI site (105-113) a 135-bp RbcS2 transit peptide (114-248), a 3-Hydroxybutyryl-CoA Dehydrogenase-encoding sequence (249-1094) selected/modified from a Clostridium beijerinckii 3-Hydroxybutyryl-CoA Dehydrogenase sequence (Genbank: AF494018), a 21-bp Lumio-tag sequence (1095-1115), a 9-bp XbaI site (1116-1124), a 223-bp RbcS2 terminator (1125-1347), and a PCR RE primer (1348-1367). This DNA construct is similar to example 4, SEQ ID NO: 4, except that an 84-bp nitrate reductase promoter (21-104) and a 3-Hydroxybutyryl-CoA Dehydrogenase-encoding sequence (249-1094) selected/modified from a Clostridium beijerinckii 3-Hydroxybutyryl-CoA Dehydrogenase sequence (Genbank: AF494018) are used. The 84-bp nitrate-reductase promoter is artificially created by joining two partially homologous sequence regions (−231 to −201 and −77 to −25 with respect to the start site of transcription) of the native Chlamydomonas reinhardtii Nia1 promoter. Experimental studies have demonstrated that the 84-bp sequence is more active than the native Nia1 promoter (Loppes and Radoux (2002) “Two short regions of the promoter are essential for activation and repression of the nitrate reductase gene in Chlamydomonas reinhardtii,” Mol Genet Genomics 268: 42-48). Therefore, this is also an example where functional synthetic sequences, analogs, functional derivatives and/or designer modified sequences such as the synthetic 84-bp sequence can be selected for use according to various embodiments in this invention.
SEQ ID NO: 6 presents example 6 for a designer Thiolase DNA construct (1721 bp) that includes a PCR FD primer (sequence 1-20), a 84-bp nitrate reductase promoter (21-104), a 9-bp Xho I NdeI site (105-113) a 135-bp RbcS2 transit peptide (114-248), a Thiolase-encoding sequence (248-1448) selected/modified from a Butyrivibrio fibrisolvens Thiolase sequence (AB190764), a 21-bp Lumio-tag sequence (1449-1469), a 9-bp XbaI site (1470-1478), a 223-bp RbcS2 terminator (1479-1701), and a PCR RE primer (1702-1721). This DNA construct is also similar to example 4, SEQ ID NO: 4, except that a Thiolase-encoding-encoding sequence (249-1448) and an 84-bp synthetic Nia1 promoter (21-104) are used. This is another example that functional synthetic sequences can also be selected for use in designer DNA constructs.
SEQ ID NO: 7 presents example 7 for a designer Pyruvate-Ferredoxin Oxidoreductase DNA construct (4211 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp nitrate reductase promoter (21-188), a 9-bp Xho I NdeI site (189-197) a 135-bp RbcS2 transit peptide (198-332), a Pyruvate-Ferredoxin Oxidoreductase-encoding sequence (333-3938) selected/modified from the sequences of a Mastigamoeba balamuthi Pyruvate-ferredoxin oxidoreductase (GenBank: AY101767), a 21-bp Lumio-tag sequence (3939-3959), a 9-bp XbaI site (3960-3968), a 223-bp RbcS2 terminator (3969-4191), and a PCR RE primer (4192-4211). This DNA construct is also similar to example 4, SEQ ID NO: 4, except a designer 2×84-bp Nia1 promoter and a Pyruvate-Ferredoxin Oxidoreductase-encoding sequence (333-3938) selected/modified from the sequences of a Mastigamoeba balamuthi Pyruvate-ferredoxin oxidoreductase (GenBank: AY101767) are used. The 2×84-bp Nia1 promoter is constructed as a tandem duplication of the 84-bp synthetic Nia1 promoter sequence presented in SEQ ID NO: 6 above. Experimental tests have shown that the 2×84-bp synthetic Nia1 promoter is even more powerful than the 84-bp sequence which is more active than the native Nia1 promoter (Loppes and Radoux (2002) “Two short regions of the promoter are essential for activation and repression of the nitrate reductase gene in Chlamydomonas reinhardtii,” Mol Genet Genomics 268: 42-48). Use of this type of inducible promoter sequences with various promoter strengths can also help in adjusting the expression levels of the designer enzymes for the butanol-production pathway(s).
SEQ ID NO: 8 presents example 8 for a designer Pyruvate Kinase DNA construct (2021 bp) that includes a PCR FD primer (sequence 1-20), a 84-bp nitrate reductase promoter (21-104), a 9-bp Xho I NdeI site (105-113) a 135-bp RbcS2 transit peptide (114-248), a pyruvate kinase-encoding sequence (249-1748) selected/modified from a Saccharomyces cerevisiae Pyruvate Kinase sequence (GenBank: AY949876), a 21-bp Lumio-tag sequence (1749-1769), a 9-bp XbaI site (1770-1778), a 223-bp RbcS2 terminator (1779-2001), and a PCR RE primer (2002-2021). This DNA construct is similar to example 6, SEQ ID NO: 6, except that a pyruvate kinase-encoding sequence (249-1748) is used.
SEQ ID NO: 9 presents example 9 for a designer Enolase gene (1815 bp) consisting of a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase promoter (21-282), a 9-bp Xho I NdeI site (283-291) a 135-bp RbcS2 transit peptide (292-426), a enolase-encoding sequence (427-1542) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic enolase (Genbank: X66412, P31683), a 21-bp Lumio-tag-encoding sequence (1507-1527), a 9-bp XbaI site (1543-1551) containing a stop codon, a 223-bp RbcS2 terminator (1552-1795), and a PCR RE primer (1796-1815) at the 3′ end. This DNA construct is similar to example 3, SEQ ID NO: 3, except that an enolase-encoding sequence (427-1542) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic enolase is used.
SEQ ID NO: 10 presents example 10 for a designer Phosphoglycerate-Mutase DNA construct (2349 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase promoter (21-282), a 9-bp Xho I NdeI site (283-291), a 135-bp RbcS2 transit peptide (292-426), a phosphoglycerate-mutase encoding sequence (427-2097) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic phosphoglycerate mutase (JGI Chlre2 protein ID 161689, Genbank: AF268078), a 9-bp XbaI site (2098-2106), a 223-bp RbcS2 terminator (2107-2329), and a PCR RE primer (2330-2349) at the 3′ end. This DNA construct is similar to example 3, SEQ ID NO: 3, except that a phosphoglycerate-mutase encoding sequence (427-2097) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic phosphoglycerate mutase is used.
SEQ ID NO: 11 presents example 11 for a designer Phosphoglycerate Kinase DNA construct (1908 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase Nia1 promoter (21-282), a phosphoglycerate-kinase-encoding sequence (283-1665) selected from a Chlamydomonas reinhardtii chloroplast phosphoglycerate-kinase sequence including its chloroplast signal peptide and mature enzyme sequence (GenBank: U14912), a 223-bp RbcS2 terminator (1666-1888), and a PCR RE primer (1889-1908). This DNA construct is similar to example 1, SEQ ID NO: 1, except a phosphoglycerate-kinase-encoding sequence (283-1665) selected from a Chlamydomonas reinhardtii chloroplast phosphoglycerate-kinase sequence including its chloroplast signal peptide and mature enzyme sequence is used. Therefore, this is also an example where the sequence of a nuclear-encoded chloroplast enzyme such as the Chlamydomonas reinhardtii chloroplast phosphoglycerate kinase can also be used in design and construction of a designer butanol-production pathway gene when appropriate with a proper inducible promoter such as the Nia1 promoter (DNA sequence 21-282).
SEQ ID NO: 12 presents example 12 for a designer Glyceraldehyde-3-Phosphate Dehydrogenase gene (1677 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase Nia1 promoter (21-282), a 135-bp RbcS2 transit peptide (283-417), an enzyme-encoding sequence (418-1434) selected and modified from a Mesostigma viride cytosolic glyceraldehyde-3-phosphate dehydrogenase (mRNA) sequence (GenBank accession number DQ873404), a 223-bp RbcS2 terminator (1435-1657), and a PCR RE primer (1658-1677). This DNA construct is similar to example 1, SEQ ID NO: 1, except that an enzyme-encoding sequence (418-1434) selected and modified from a Mesostigma viride cytosolic glyceraldehyde-3-phosphate dehydrogenase (mRNA) sequence (GenBank accession number DQ873404) is used.
SEQ ID NO: 13 presents example 13 for a designer HydA1-promoter-linked Phosphoglycerate Mutase DNA construct (2351 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a phosphoglycerate-mutase encoding sequence (438-2108) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic phosphoglycerate mutase (JGI Chlre2 protein ID 161689, Genbank: AF268078), a 223-bp RbcS2 terminator (2109-2331), and a PCR RE primer (2332-2351). This designer DNA construct is quite similar to example 1, SEQ ID NO:1, except that a 282-bp HydA1 promoter (21-302) and a phosphoglycerate-mutase encoding sequence (438-2108) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic phosphoglycerate mutase are used. The 282-bp HydA1 promoter (21-302) has been proven active by experimental assays at the inventor's laboratory. Use of the HydA1 promoter (21-302) enables activation of designer enzyme expression by using anaerobic culture-medium conditions.
With the same principle of using an inducible anaerobic promoter and a chloroplast-targeting sequence as that shown in SEQ ID NO: 13 (example 13), SEQ ID NOS: 14-23 show designer-gene examples 14-23. Briefly, SEQ ID NO: 14 presents example 14 for a designer HydA1-promoter-linked Enolase DNA construct (1796 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Enolase-encoding sequence (438-1553) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic enolase (Genbank: X66412, P31683), a 223-bp RbcS2 terminator (1554-1776), and a PCR RE primer (1777-1796).
SEQ ID NO: 15 presents example 15 for a designer HydA1-promoter-controlled Pyruvate-Kinase DNA construct that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Pyruvate Kinase-encoding sequence (438-1589) selected/modified from a Chlamydomonas reinhardtii cytosolic pyruvate kinase sequence (JGI Chlre3 protein ID 138105), a 223-bp RbcS2 terminator (1590-1812), and a PCR RE primer (1813-1832).
SEQ ID NO:16 presents example 16 for a designer HydA1-promoter-linked Pyruvate-ferredoxin oxidoreductase DNA construct (4376 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Pyruvate-ferredoxin oxidoreductase-encoding sequence (438-4133) selected/modified from a Desulfovibrio africanus Pyruvate-ferredoxin oxidoreductase sequence (GenBank Accession Number Y09702), a 223-bp RbcS2 terminator (4134-4356), and a PCR RE primer (4357-4376).
SEQ ID NO:17 presents example 17 for a designer HydA1-promoter-linked Pyruvate-NADP+ oxidoreductase DNA construct (6092 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Pyruvate-NADP+ oxidoreductase-encoding sequence (438-5849) selected/modified from a Euglena gracilis Pyruvate-NADP+ oxidoreductase sequence (GenBank Accession Number AB021127), a 223-bp RbcS2 terminator (5850-6072), and a PCR RE primer (6073-6092).
SEQ ID NO:18 presents example 18 for a designer HydA1-promoter-linked Thiolase DNA construct (1856 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Thiolase-encoding sequence (438-1613) selected/modified from the sequences of a Thermoanaerobacterium thermosaccharolyticum Thiolase (GenBank Z92974), a 223-bp RbcS2 terminator (1614-1836), and a PCR RE primer (1837-1856).
SEQ ID NO:19 presents example 19 for a designer HydA1-promoter-linked 3-Hydroxybutyryl-CoA dehydrogenase DNA construct (1550 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a 3-Hydroxybutyryl-CoA dehydrogenase-encoding sequence (438-1307) selected/modified from the sequences of a Thermoanaerobacterium thermosaccharolyticum 3-Hydroxybutyryl-CoA dehydrogenase (GenBank Z92974), a 223-bp RbcS2 terminator (1308-1530), and a PCR RE primer (1531-1550).
SEQ ID NO:20 presents example 20 for a designer HydA1-promoter-linked Crotonase DNA construct (1457 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Crotonase-encoding sequence (438-1214) selected/modified from the sequences of a Thermoanaerobacterium thermosaccharolyticum Crotonase (GenBank Z92974), a 223-bpRbcS2 terminator (1215-1437), and a PCR RE primer (1438-1457).
SEQ ID NO:21 presents example 21 for a designer HydA1-promoter-linked Butyryl-CoA dehydrogenase DNA construct (1817 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Butyryl-CoA dehydrogenase-encoding sequence (438-1574) selected/modified from the sequences of a Thermoanaerobacterium thermosaccharolyticum Butyryl-CoA dehydrogenase (GenBank Z92974), a 223-bp RbcS2 terminator (1575-1797), and a PCR RE primer (1798-1817).
SEQ ID NO: 22 presents example 22 for a designer HydA1-promoter-linked Butyraldehyde dehydrogenase DNA construct (2084 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Butyraldehyde dehydrogenase-encoding sequence (438-1841) selected/modified from the sequences of a Clostridium saccharoperbutylacetonicum Butyraldehyde dehydrogenase (GenBank AY251646), a 223-bp RbcS2 terminator (1842-2064), and a PCR RE primer (2065-2084).
SEQ ID NO: 23 presents example 23 for a designer HydA1-promoter-linked Butanol dehydrogenase DNA construct (1733 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a 135-bp RbcS2 transit peptide (303-437), a Butanol dehydrogenase-encoding sequence (438-1490) selected/modified from the sequences of a Clostridium beijerinckii Butanol dehydrogenase (GenBank AF157307), a 223-bp RbcS2 terminator (1491-1713), and a PCR RE primer (1714-1733).
With the same principle of using a 2×84 synthetic Nia1 promoter and a chloroplast-targeting mechanism as mentioned previously, SEQ ID NOS:24-26 show more examples of designer-enzyme DNA-constructs. Briefly, SEQ ID NO: 24 presents example 24 for a designer Fructose-Diphosphate-Aldolase DNA construct that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a Fructose-Diphosphate Aldolase-encoding sequence (189-1313) selected/modified from a C. reinhardtii chloroplast fructose-1,6-bisphosphate aldolase sequence (GenBank: X69969), a 223-bpRbcS2 terminator (1314-1536), and a PCR RE primer (1537-1556).
SEQ ID NO: 25 presents example 24 for a designer Triose-Phosphate-Isomerase DNA construct that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a Triose-Phosphate Isomerase-encoding sequence (189-1136) selected and modified from a Arabidopsis thaliana chloroplast triosephosphate-isomerase sequence (GenBank: AF247559), a 223-bp RbcS2 terminator (1137-1359), and a PCR RE primer (1360-1379).
SEQ ID NO: 26 presents example 26 for a designer Phosphofructose-Kinase DNA construct that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 135-bp RbcS2 transit peptide (189-323), a Phosphofructose Kinase-encoding sequence (324-1913) selected/modified from Arabidopsis thaliana 6-phosphofructokinase sequence (GenBank: NM_001037043), a 223-bp RbcS2 terminator (1914-2136), and a PCR RE primer (2137-2156).
The nucleic acid constructs, such as those presented in the examples above, may include additional appropriate sequences, for example, a selection marker gene, and an optional biomolecular tag sequence (such as the Lumio tag described in example 4, SEQ ID NO: 4). Selectable markers that can be selected for use in the constructs include markers conferring resistances to kanamycin, hygromycin, spectinomycin, streptomycin, sulfonyl urea, gentamycin, chloramphenicol, among others, all of which have been cloned and are available to those skilled in the art. Alternatively, the selective marker is a nutrition marker gene that can complement a deficiency in the host organism. For example, the gene encoding argininosuccinate lyase (arg7) can be used as a selection marker gene in the designer construct, which permits identification of transformants when Chlamydomonas reinhardtii arg7-(minus) cells are used as host cells.
Nucleic acid constructs carrying designer genes can be delivered into a host alga, blue-green alga, plant, or plant tissue or cells using the available gene-transformation techniques, such as electroporation, PEG induced uptake, and ballistic delivery of DNA, and Agrobacterium-mediated transformation. For the purpose of delivering a designer construct into algal cells, the techniques of electroporation, glass bead, and biolistic genegun can be selected for use as preferred methods; and an alga with single cells or simple thallus structure is preferred for use in transformation. Transformants can be identified and tested based on routine techniques.
The various designer genes can be introduced into host cells sequentially in a step-wise manner, or simultaneously using one construct or in one transformation. For example, the ten DNA constructs shown in SEQ ID NO: 13-16 (or 17) and 18-23 for the ten-enzyme 3-phosphoglycerate-branched butanol-production pathway can be placed into a genetic vector such as p389-Arg7 with a single selection marker (Arg7). Therefore, by use of a plasmid in this manner, it is possible to deliver all the ten DNA constructs (designer genes) into an arginine-requiring Chlamydomonas reinhardtii-arg7 host (CC-48) in one transformation for expression of the 3-phosphoglycerate-branched butanol-production pathway (03-12 in FIG. 1). When necessary, a transformant containing the ten DNA constructs can be further transformed to get more designer genes into its genomic DNA with an additional selection marker such as streptomycin. By using combinations of various designer-enzymes DNA constructs such as those presented in SEQ ID NO: 1-26 in genetic transformation with an appropriate host organism, various butanol-production pathways such as those illustrated in FIG. 1 can be constructed. For example, the designer DNA constructs of SEQ ID NO: 1-12 can be selected for construction of the glyceraldehydes-3-phosphate-branched butanol-production pathway (01-12 in FIG. 1); The designer DNA constructs of SEQ ID NO: 1-12, 24, and 25 can be selected for construction of the fructose-1,6-diphosphate-branched butanol-production pathway (20-33); and the designer DNA constructs of SEQ ID NO: 1-12 and 24-26 can be selected for construction of the fructose-6-phosphate-branched butanol-production pathway (19-33).
Additional Host Modifications to Enhance Photosynthetic Butanol Production
An NADPH/NADH Conversion Mechanism
According to the photosynthetic butanol production pathway(s), to produce one molecule of butanol from 4CO2 and 5H2O is likely to require 14 ATP and 12 NADPH, both of which are generated by photosynthetic water splitting and photophosphorylation across the thylakoid membrane. In order for the 3-phosphoglycerate-branched butanol-production pathway (03-12 in FIG. 1) to operate, it is a preferred practice to use a butanol-production-pathway enzyme(s) that can use NADPH that is generated by the photo-driven electron transport process. Clostridium saccharoperbutylacetonicum butanol dehydrogenase (GenBank accession number: AB257439) and butyraldehyde dehydrogenase (GenBank: AY251646) are examples of a butanol-production-pathway enzyme that is capable of accepting either NADP(H) or NAD(H). Such a butanol-production-pathway enzyme that can use both NADPH and NADH (i.e., NAD(P)H) can also be selected for use in this 3-phosphoglycerate-branched and any of the other designer butanol-production pathway(s) (FIG. 1) as well. Clostridium beijerinckii Butyryl-CoA dehydrogenase (GenBank: AF494018) and 3-Hydroxybutyryl-CoA dehydrogenase (GenBank: AF494018) are examples of a butanol-production-pathway enzyme that can accept only NAD(H). When a butanol-production-pathway enzyme that can only use NADH is employed, it may require an NADPH/NADH conversion mechanism in order for this 3-phosphoglycerate-branched butanol-production pathway to operate well. However, depending on the genetic backgrounds of a host organism, a conversion mechanism between NADPH and NADH may exist in the host so that NADPH and NADH may be interchangeably used in the organism. In addition, it is known that NADPH could be converted into NADH by a NADPH-phosphatase activity (Pattanayak and Chatterjee (1998) “Nicotinamide adenine dinucleotide phosphate phosphatase facilitates dark reduction of nitrate: regulation by nitrate and ammonia,” Biologia Plantarium 41(1):75-84) and that NAD can be converted to NADP by a NAD kinase activity (Muto, Miyachi, Usuda, Edwards and Bassham (1981) “Light-induced conversion of nicotinamide adenine dinucleotide to nicotinamide adenine dinucleotide phosphate in higher plant leaves,” Plant Physiology 68(2):324-328; Matsumura-Kadota, Muto, Miyachi (1982) “Light-induced conversion of NAD+ to NADP+ in Chlorella cells,” Biochimica Biophysica Acta 679(2):300-300). Therefore, when enhanced NADPH/NADH conversion is desirable, the host may be genetically modified to enhance the NADPH phosphatase and NAD kinase activities. Thus, in one of the various embodiments, the photosynthetic butanol-producing designer plant, designer alga or plant cell further contains additional designer transgenes (FIG. 2B) to inducibly express one or more enzymes to facilitate the NADPH/NADH inter-conversion, such as the NADPH phosphatase and NAD kinase (GenBank: XM_001609395, XM_001324239), in the stroma region of the algal chloroplast.
Another embodiment that can provide an NADPH/NADH conversion mechanism is by properly selecting an appropriate branching point at the Calvin cycle for a designer butanol-production pathway to branch from. To confer this NADPH/NADH conversion mechanism by pathway design according to this embodiment, it is a preferred practice to branch a designer butanol-production pathway at or after the point of glyceraldehydes-3-phosphate of the Calvin cycle as shown in FIG. 1. In these pathway designs, the NADPH/NADH conversion is achieved essentially by a two-step mechanism: 1) Use of the step with the Calvin-cycle's glyceraldehyde-3-phosphate dehydrogenase, which uses NADPH in reducing-1,3-diphosphoglycerate to glyceraldehydes-3-phosphate; and 2) use of the step with the designer pathway's NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase 01, which produces NADH in oxidizing glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate. The net result of the two steps described above is the conversion of NADPH to NADH, which can supply the needed reducing power in the form of NADH for the designer butanol-production pathway(s). For step 1), use of the Calvin-cycle's NADPH-dependent glyceraldehyde-3-phosphate dehydrogenase naturally in the host organism is usually sufficient. Consequently, introduction of a designer NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase 01 to work with the Calvin-cycle's NADPH-dependent glyceraldehyde-3-phosphate dehydrogenase may confer the function of an NADPH/NADH conversion mechanism, which is needed for the 3-phosphoglycerate-branched butanol-production pathway (03-12 in FIG. 1) to operate well. For this reason, the designer NAD−-dependent glyceraldehyde-3-phosphate-dehydrogenase DNA construct (example 12, SEQ ID NO:12) is used also as an NADPH/NADH-conversion designer gene (FIG. 2B) to support the 3-phosphoglycerate-branched butanol-production pathway (03-12 in FIG. 1) in one of the various embodiments. This also explains why it is important to use a NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase 01 to confer this two-step NADPH/NADH conversion mechanism for the designer butanol-production pathway(s). Therefore, in one of the various embodiments, it is also a preferred practice to use a NAD−-dependent glyceraldehyde-3-phosphate dehydrogenase, its isozymes, functional derivatives, analogs, designer modified enzymes and/or combinations thereof in the designer butanol-production pathway(s) as illustrated in FIG. 1.
iRNA Techniques to Further Tame Photosynthesis Regulation Mechanism
In another embodiment of the present invention, the host plant or cell is further modified to tame the Calvin cycle so that the host can directly produce liquid fuel butanol instead of synthesizing starch (glycogen in the case of oxyphotobacteria), celluloses and lignocelluloses that are often inefficient and hard for the biorefinery industry to use. According to the one of the various embodiments, inactivation of starch-synthesis activity is achieved by suppressing the expression of any of the key enzymes, such as, starch synthase (glycogen synthase in the case of oxyphotobacteria) 13, glucose-1-phosphate (G-1-P) adenylyltransferase 14, phosphoglucomutase 15, and hexose-phosphate-isomerase 16 of the starch-synthesis pathway which connects with the Calvin cycle (FIG. 1).
Introduction of a genetically transmittable factor that can inhibit the starch-synthesis activity that is in competition with designer butanol-production pathway(s) for the Calvin-cycle products can further enhance photosynthetic butanol production. In a specific embodiment, a genetically encoded-able inhibitor (FIG. 2C) to the competitive starch-synthesis pathway is an interfering RNA (iRNA) molecule that specifically inhibits the synthesis of a starch-synthesis-pathway enzyme, for example, starch synthase 16, glucose-1-phosphate (G-1-P) adenylyltransferase 15, phosphoglucomutase 14, and/or hexose-phosphate-isomerase 13 as shown with numerical labels 13-16 in FIG. 1. The DNA sequences encoding starch synthase iRNA, glucose-1-phosphate (G-1-P) adenylyltransferase iRNA, a phosphoglucomutase iRNA and/or a G-P-isomerase iRNA, respectively, can be designed and synthesized based on RNA interference techniques known to those skilled in the art (Liszewski (Jun. 1, 2003) Progress in RNA interference, Genetic Engineering News, Vol. 23, number 11, pp. 1-59). Generally speaking, an interfering RNA (iRNA) molecule is anti-sense but complementary to a normal mRNA of a particular protein (gene) so that such iRNA molecule can specifically bind with the normal mRNA of the particular gene, thus inhibiting (blocking) the translation of the gene-specific mRNA to protein (Fire, Xu, Montgomery, Kostas, Driver, Mello (1998) “Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans”. Nature 391(6669):806-11; Dykxhoorn, Novina, Sharp (2003) “Killing the messenger: short RNAs that silence gene expression”, Nat Rev Mol Cell Biol. 4(6):457-67).
Examples of a designer starch-synthesis iRNA DNA construct (FIG. 2C) are shown in SEQ ID NO: 27 and 28 listed. Briefly, SEQ ID NO: 27 presents example 27 for a designer Nia1-promoter-controlled Starch-Synthase-iRNA DNA construct (860 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp Nia1 promoter (21-282), a Starch-Synthase iRNA sequence (283-617) consisting of start codon atg and a reverse complement sequence of two unique sequence fragments of a Chlamydomonas reinhardtii starch-synthase-mRNA sequence (GenBank: AF026422), a 223-bp RbcS2 terminator (618-850), and a PCR RE primer (851-860). Because of the use of a Nia1 promoter (21-282), this designer starch-synthesis iRNA gene is designed to be expressed only when needed to enhance photobiological butanol production in the presence of its specific inducer, nitrate (NO3−), which can be added into the culture medium as a fertilizer for induction of the designer organisms. The Starch-Synthase iRNA sequence (283-617) is designed to bind with the normal mRNA of the starch synthase gene, thus blocking its translation into a functional starch synthase. The inhibition of the starch/glycogen synthase activity at 16 in this manner is to channel more photosynthetic products of the Calvin cycle into the Calvin-cycle-branched butanol-production pathway(s) such as the glyceraldehydes-3-phosphate-branched butanol-production pathway 01-12 as illustrated in FIG. 1.
SEQ ID NO: 28 presents example 28 for a designer HydA1-promoter-controlled Starch-Synthase-iRNA DNA construct (1328 bp) that includes a PCR FD primer (sequence 1-20), a 282-bp HydA1 promoter (21-302), a designer Starch-Synthase iRNA sequence (303-1085), a 223-bp RbcS2 terminator (1086-1308), and a PCR RE primer (1309-1328). The designer Starch-Synthase-iRNA sequence (303-1085) comprises of: a 300-bp sense fragment (303-602) selected from the first 300-bp unique coding sequence of a Chlamydomonas reinhardtii starch synthase mRNA sequence (GenBank: AF026422), a 183-bp designer intron-like loop (603-785), and a 300-bp antisense sequence (786-1085) complement to the first 300-bp coding sequence of a Chlamydomonas reinhardtii starch-synthase-mRNA sequence (GenBank: AF026422). This designer Starch-Synthase-iRNA sequence (303-1085) is designed to inhibit the synthesis of starch synthase by the following two mechanisms. First, the 300-bp antisense complement iRNA sequence (corresponding to DNA sequence 786-1085) binds with the normal mRNA of the starch synthase gene, thus blocking its translation into a functional starch synthase. Second, the 300-bp antisense complement iRNA sequence (corresponding to DNA sequence 786-1085) can also bind with the 300-bp sense counterpart (corresponding to DNA sequence 303-602) in the same designer iRNA molecule, forming a hairpin-like double-stranded RNA structure with the 183-bp designer intron-like sequence (603-785) as a loop. Experimental studies have shown that this type of hairpin-like double-stranded RNA can also trigger post-transcriptional gene silencing (Fuhrmann, Stahlberg, Govorunova, Rank and Hegemann (2001) Journal of Cell Science 114:3857-3863). Because of the use of a HydA1 promoter (21-302), this designer starch-synthesis-iRNA gene is designed to be expressed only under anaerobic conditions when needed to enhance photobiological butanol production by channeling more photosynthetic products of the Calvin cycle into the butanol-production pathway(s) such as 01-12, 03-12, and/or 20-33 as illustrated in FIG. 1.
Designer Starch-Degradation and Glycolysis Genes
In yet another embodiment of the present invention, the photobiological butanol production is enhanced by incorporating an additional set of designer genes (FIG. 2D) that can facilitate starch/glycogen degradation and glycolysis in combination with the designer butanol-production gene(s) (FIG. 2A). Such additional designer genes for starch degradation include, for example, genes coding for 17: amylase, starch phosphorylase, hexokinase, phosphoglucomutase, and for 18: glucose-phosphate-isomerase (G-P-isomerase) as illustrated in FIG. 1. The designer glycolysis genes encode chloroplast-targeted glycolysis enzymes: glucosephosphate isomerase 18, phosphofructose kinase 19, aldolase 20, triose phosphate isomerase 21, glyceraldehyde-3-phosphate dehydrogenase 22, phosphoglycerate kinase 23, phosphoglycerate mutase 24, enolase 25, and pyruvate kinase 26. The designer starch-degradation and glycolysis genes in combination with any of the butanol-production pathways shown in FIG. 1 can form additional pathway(s) from starch/glycogen to butanol (17-33). Consequently, co-expression of the designer starch-degradation and glycolysis genes with the butanol-production-pathway genes can enhance photobiological production of butanol as well. Therefore, this embodiment represents another approach to tame the Calvin cycle for enhanced photobiological production of butanol. In this case, some of the Calvin-cycle products flow through the starch synthesis pathway (13-16) followed by the starch/glycogen-to-butanol pathway (17-33) as shown in FIG. 1. In this case, starch/glycogen acts as a transient storage pool of the Calvin-cycle products before they can be converted to butanol. This mechanism can be quite useful in maximizing the butanol-production yield in certain cases. For example, at high sunlight intensity such as around noon, the rate of Calvin-cycle photosynthetic CO2 fixation can be so high that may exceed the maximal rate capacity of a butanol-production pathway(s); use of the starch-synthesis mechanism allows temporary storage of the excess photosynthetic products to be used later for butanol production as well.
FIG. 1 also illustrates the use of a designer starch/glycogen-to-butanol pathway with designer enzymes (as labeled from 17 to 33) in combination with a Calvin-cycle-branched designer butanol-production pathway(s) such as the glyceraldehydes-3-phosphate-branched butanol-production pathway 01-12 for enhanced photobiological butanol production. Similar to the benefits of using the Calvin-cycle-branched designer butanol-production pathways, the use of the designer starch/glycogen-to-butanol pathway (17-33) can also help to convert the photosynthetic products to butanol before the sugars could be converted into other complicated biomolecules such as lignocellulosic biomasses which cannot be readily used by the biorefinery industries. Therefore, appropriate use of the Calvin-cycle-branched designer butanol-production pathway(s) (such as 01-12, 03-12, and/or 20-33) and/or the designer starch/glycogen-to-butanol pathway (17-33) may represent revolutionary inter alia technologies that can effectively bypass the bottleneck problems of the current biomass technology including the “lignocellulosic recalcitrance” problem.
Another feature is that a Calvin-cycle-branched designer butanol-production pathway activity (such as 01-12, 03-12, and/or 20-33) can occur predominantly during the days when there is light because it uses an intermediate product of the Calvin cycle which requires supplies of reducing power (NADPH) and energy (ATP) generated by the photosynthetic water splitting and the light-driven proton-translocation-coupled electron transport process through the thylakoid membrane system. The designer starch/glycogen-to-butanol pathway (17-33) which can use the surplus sugar that has been stored as starch/glycogen during photosynthesis can operate not only during the days, but also at nights. Consequently, the use of a Calvin-cycle-branched designer butanol-production pathway (such as 01-12, 03-12, and/or 20-33) together with a designer starch/glycogen-to-butanol pathway(s) (17-33) as illustrated in FIG. 1 enables production of butanol both during the days and at nights.
Because the expression for both the designer starch/glycogen-to-butanol pathway(s) and the Calvin-cycle-branched designer butanol-production pathway(s) is controlled by the use of an inducible promoter such as an anaerobic hydrogenase promoter, this type of designer organisms is also able to grow photoautotrophically under aerobic (normal) conditions. When the designer photosynthetic organisms are grown and ready for photobiological butanol production, the cells are then placed under the specific inducing conditions such as under anaerobic conditions [or an ammonium-to-nitrate fertilizer use shift, if designer Nia1/nirA promoter-controlled butanol-production pathway(s) is used] for enhanced butanol production, as shown in FIGS. 1 and 3.
Examples of designer starch (glycogen)-degradation genes are shown in SEQ ID NO: 29-33 listed. Briefly, SEQ ID NO:29 presents example 29 for a designer Amylase DNA construct (1889 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 9-bp Xho I NdeI site (189-197), a 135-bp RbcS2 transit peptide (198-332), an Amylase-encoding sequence (333-1616) selected and modified from a Barley alpha-amylase (GenBank: J04202A my46 expression tested in aleurone cells), a 21-bp Lumio-tag sequence (1617-1637), a 9-bp XbaI site (1638-1646), a 223-bp RbcS2 terminator (1647-1869), and a PCR RE primer (1870-1889).
SEQ ID NO: 30 presents example 30 for a designer Starch-Phosphorylase DNA construct (3089 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 135-bp RbcS2 transit peptide (189-323), a Starch Phosphorylase-encoding sequence (324-2846) selected and modified from a Citrus root starch-phosphorylase sequence (GenBank: AY098895, expression tested in citrus root), a 223-bp RbcS2 terminator (2847-3069), and a PCR RE primer (3070-3089).
SEQ ID NO: 31 presents example 31 for a designer Hexose-Kinase DNA construct (1949 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 135-bp RbcS2 transit peptide (189-323), a Hexose Kinase-encoding sequence (324-1706) selected and modified from Ajellomyces capsulatus hexokinase mRNA sequence (Genbank: XM_001541513), a 223-bp RbcS2 terminator (1707-1929), and a PCR RE primer (1930-1949).
SEQ ID NO: 32 presents example 32 for a designer Phosphoglucomutase DNA construct (2249 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 135-bp RbcS2 transit peptide (189-323), a Phosphoglucomutase-encoding sequence (324-2006) selected and modified from Pichia stipitis phosphoglucomutase sequence (GenBank: XM_001383281), a 223-bp RbcS2 terminator (2007-2229), and a PCR RE primer (2230-2249).
SEQ ID NO: 33 presents example 33 for a designer Glucosephosphate-Isomerase DNA construct (2231 bp) that includes a PCR FD primer (sequence 1-20), a 2×84-bp NR promoter (21-188), a 135-bp RbcS2 transit peptide (189-323), a Glucosephosphate Isomerase-encoding sequence (324-1988) selected and modified from a S. cerevisiae phosphoglucoisomerase sequence (GenBank: M21696), a 223-bp RbcS2 terminator (1989-2211), and a PCR RE primer (2212-2231).
The designer starch-degradation genes such as those shown in SEQ ID NO: 29-33 can be selected for use in combination with various designer butanol-production-pathway genes for construction of various designer starch-degradation butanol-production pathways such as the pathways shown in FIG. 1. For example, the designer genes shown in SEQ ID NOS: 1-12, 24-26, and 29-33 can be selected for construction of a Nia1 promoter-controlled starch-to-butanol production pathway that comprises of the following designer enzymes: amylase, starch phosphorylase, hexokinase, phosphoglucomutase, glucosephosphate isomerase, phosphofructose kinase, fructose diphosphate aldolase, triose phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, pyruvate kinase, pyruvate-NADP+ oxidoreductase (or pyruvate-ferredoxin oxidoreductase), thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and butanol dehydrogenase. This starch/glycogen-to-butanol pathway 17-33 may be used alone and/or in combinations with other butanol-production pathway(s) such as the 3-phosphoglycerate-branched butanol-production pathway 03-12 as illustrated in FIG. 1.
Distribution of Designer Butanol-Production Pathways Between Chloroplast and Cytoplasm
In yet another embodiment of the present invention, photobiological butanol productivity is enhanced by a selected distribution of the designer butanol-production pathway(s) between chloroplast and cytoplasm in a eukaryotic plant cell. That is, not all the designer butanol-production pathway(s) (FIG. 1) have to operate in the chloroplast; when needed, part of the designer butanol-production pathway(s) can operate in cytoplasm as well. For example, in one of the various embodiments, a significant part of the designer starch-to-butanol pathway activity from dihydroxyacetone phosphate to butanol (21-33) is designed to occur at the cytoplasm while the steps from starch to dihydroxyacetone phosphate (17-20) are in the chloroplast. In this example, the linkage between the chloroplast and cytoplasm parts of the designer pathway is accomplished by use of the triose phosphate-phosphate translocator, which facilitates translocation of dihydroxyacetone across the chloroplast membrane. By use of the triose phosphate-phosphate translocator, it also enables the glyceraldehyde-3-phosphate-branched designer butanol-production pathway to operate not only in chloroplast, but also in cytoplasm as well. The cytoplasm part of the designer butanol-production pathway can be constructed by use of designer butanol-production pathway genes (DNA constructs of FIG. 2A) with their chloroplast-targeting sequence omitted as shown in FIG. 2E.
Designer Oxyphotobacteria with Designer Butanol-Production Pathways in Cytoplasm
In prokaryotic photosynthetic organisms such as blue-green algae (oxyphotobacteria including cyanobacteria and oxychlorobacteria), which typically contain photosynthetic thylakoid membrane but no chloroplast structure, the Calvin cycle is located in the cytoplasm. In this special case, the entire designer butanol-production pathway(s) (FIG. 1) including (but not limited to) the glyceraldehyde-3-phosphate branched butanol-production pathway (01-12), the 3-phosphoglycerate-branched butanol-production pathway (03-12), the fructose-1,6-diphosphate-branched pathway (20-33), the fructose-6-phosphate-branched pathway (19-33), and the starch (or glycogen)-to-butanol pathways (17-33) are adjusted in design to operate with the Calvin cycle in the cytoplasm of a blue-green alga. The construction of the cytoplasm designer butanol-production pathways can be accomplished by use of designer butanol-production pathway genes (DNA construct of FIG. 2A) with their chloroplast-targeting sequence all omitted. When the chloroplast-targeting sequence is omitted in the designer DNA construct(s) as illustrated in FIG. 2E, the designer gene(s) is transcribed and translated into designer enzymes in the cytoplasm whereby conferring the designer butanol-production pathway(s). The designer gene(s) can be incorporated into the chromosomal and/or plasmid DNA in host blue-green algae (oxyphotobacteria including cyanobacteria and oxychlorobacteria) by using the techniques of gene transformation known to those skilled in the art. It is a preferred practice to integrate the designer genes through an integrative transformation into the chromosomal DNA that can usually provide better genetic stability for the designer genes. In oxyphotobacteria such as cyanobacteria, integrative transformation can be achieved through a process of homologous DNA double recombination into the host's chromosomal DNA using a designer DNA construct as illustrated in FIG. 2F, which typically, from the 5′ upstream to the 3′ downstream, consists of: recombination site 1, a designer butanol-production-pathway gene(s), and recombination site 2. This type of DNA constructs (FIG. 2F) can be delivered into oxyphotobacteria (blue-green algae) with a number of available genetic transformation techniques including electroporation, natural transformation, and/or conjugation. The transgenic designer organisms created from blue-green algae are also called designer blue-green algae (designer oxyphotobacteria including designer cyanobacteria and designer oxychlorobacteria).
Examples of designer oxyphotobacterial butanol-production-pathway genes are shown in SEQ ID NO: 34-45 listed. Briefly, SEQ ID NO:34 presents example 34 for a designer oxyphotobacterial Butanol Dehydrogenase DNA construct (1709 bp) that includes a PCR FD primer (sequence 1-20), a 400-bp nitrite reductase (nirA) promoter from Thermosynechococcus elongatus BP-1 (21-420), an enzyme-encoding sequence (421-1569) selected and modified from a Clostridium saccharoperbutylacetonicum Butanol Dehydrogenase sequence (AB257439), a 120-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (1570-1689), and a PCR RE primer (1690-1709) at the 3′ end.
SEQ ID NO:35 presents example 35 for a designer oxyphotobacterial Butyraldehyde Dehydrogenase DNA construct (1967 bp) that includes a PCR FD primer (sequence 1-20), a 400-bp Thermosynechococcus elongatus BP-1 nitrite reductase nirA promoter (21-420), an enzyme-encoding sequence (421-1827) selected and modified from a Clostridium saccharoperbutylacetonicum Butyraldehyde Dehydrogenase sequence (AY251646), a 120-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (1828-1947), and a PCR RE primer (1948-1967) at the 3′ end.
SEQ ID NO:36 presents example 36 for a designer oxyphotobacterial Butyryl-CoA Dehydrogenase DNA construct (1602 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp Thermosynechococcus elongatus BP-1 nitrate reductase promoter (21-325), a Butyryl-CoA Dehydrogenase encoding sequence (326-1422) selected/modified from the sequences of a Clostridium beijerinckii Butyryl-CoA Dehydrogenase (AF494018), a 120-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1423-1582), and a PCR RE primer (1583-1602) at the 3′ end.
SEQ ID NO:37 presents example 37 for a designer oxyphotobacterial Crotonase DNA construct (1248 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp Thermosynechococcus elongatus BP-1 nitrate reductase promoter (21-325), a Crotonase-encoding sequence (326-1108) selected/modified from the sequences of a Clostridium beijerinckii Crotonase (GenBank: AF494018), 120-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1109-1228), and a PCR RE primer (1229-1248).
SEQ ID NO:38 presents example 38 for a designer oxyphotobacterial 3-Hydroxybutyryl-CoA Dehydrogenase DNA construct (1311 bp) that include of a PCR FD primer (sequence 1-20), a 305-bp nirA promoter from (21-325), a 3-Hydroxybutyryl-CoA Dehydrogenase-encoding sequence (326-1171) selected/modified from a Clostridium beijerinckii 3-Hydroxybutyryl-CoA Dehydrogenase sequence Crotonase (GenBank: AF494018), a 120-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1172-1291), and a PCR RE primer (1292-1311).
SEQ ID NO:39 presents example 39 for a designer oxyphotobacterial Thiolase DNA construct (1665 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-325), a Thiolase-encoding sequence (326-1525) selected/modified from a Butyrivibrio fibrisolvens Thiolase sequence (AB190764), a 120-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (1526-1645), and a PCR RE primer (1646-1665).
SEQ ID NO:40 presents example 40 for a designer oxyphotobacterial Pyruvate-Ferredoxin Oxidoreductase DNA construct (4071 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-325), a Pyruvate-Ferredoxin Oxidoreductase-encoding sequence (326-3931) selected/modified from the sequences of a Mastigamoeba balamuthi Pyruvate-ferredoxin oxidoreductase (GenBank: AY101767), a 120-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (3932-4051), and a PCR RE primer (4052-4071).
SEQ ID NO:41 presents example 41 for a designer oxyphotobacterial Pyruvate Kinase DNA construct (1806 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-325), a pyruvate kinase-encoding sequence (326-1666) selected/modified from a Thermoproteus tenax pyruvate kinase (GenBank: AF065890), a 120-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1667-1786), and a PCR RE primer (1787-1806) at the 3′ end.
SEQ ID NO:42 presents example 42 for a designer oxyphotobacterial Enolase DNA construct (1696 bp) that includes a PCR FD primer (sequence 1-20), a 231-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-251), a enolase-encoding sequence (252-1556) selected/modified from the sequences of a Chlamydomonas reinhardtii cytosolic enolase (GenBank: X66412, P31683), a 120-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (1557-1676), and a PCR RE primer (1677-1696) at the 3′ end.
SEQ ID NO:43 presents example 43 for a designer oxyphotobacterial Phosphoglycerate-Mutase DNA construct (2029 bp) that includes a PCR FD primer (sequence 1-20), a 231-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-251), a phosphoglycerate-mutase encoding sequence (252-1889) selected/modified from the sequences of a Pelotomaculum thermopropionicum SI phosphoglycerate mutase (GenBank: YP_001213270), a 120-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1890-2009), and a PCR RE primer (2010-2029) at the 3′ end.
SEQ ID NO:44 presents example 44 for a designer oxyphotobacterial Phosphoglycerate Kinase DNA construct (1687 bp) that includes a PCR FD primer (sequence 1-20), a 231-bp nirA promoter from Thermosynechococcus elongatus BP-1 (21-251), a phosphoglycerate-kinase-encoding sequence (252-1433) selected from Pelotomaculum thermopropionicum SI phosphoglycerate kinase (BAF60903), a 234-bp Thermosynechococcus elongatus BP-1 rbcS terminator (1434-1667), and a PCR RE primer (1668-1687).
SEQ ID NO:45 presents example 45 for a designer oxyphotobacterial Glyceraldehyde-3-Phosphate Dehydrogenase DNA construct (1514 bp) that includes a PCR FD primer (sequence 1-20), a 305-bp Thermosynechococcus elongatus BP-1 nirA promoter (21-325), an enzyme-encoding sequence (326-1260) selected and modified from Blastochloris viridis NAD-dependent Glyceraldehyde-3-phosphate dehydrogenase (CAC80993), a 234-bp rbcS terminator from Thermosynechococcus elongatus BP-1 (1261-1494), and a PCR RE primer (1495-1514).
The designer oxyphotobacterial genes such as those shown in SEQ ID NO: 34-45 can be selected for use in full or in part, and/or in combination with various other designer butanol-production-pathway genes for construction of various designer oxyphotobacterial butanol-production pathways such as the pathways shown in FIG. 1. For example, the designer genes shown in SEQ ID NOS: 34-45 can be selected for construction of an oxyphotobacterial nirA promoter-controlled and glyceraldehyde-3-phosphate-branched butanol-production pathway (01-12) that comprises of the following designer enzymes: NAD-dependent glyceraldehyde-3-phosphate dehydrogenase 01, phosphoglycerate kinase O2, phosphoglycerate mutase 03, enolase 04, pyruvate kinase 05, pyruvate-ferredoxin oxidoreductase (or pyruvate-NADP+ oxidoreductase) 06, thiolase 07, 3-hydroxybutyryl-CoA dehydrogenase 08, crotonase 09, butyryl-CoA dehydrogenase 10, butyraldehyde dehydrogenase 11, and butanol dehydrogenase 12. Use of these designer oxyphotobacterial butanol-production-pathway genes (SEQ ID NOS: 34-45) in a thermophilic and/or thermotolerant cyanobacterium may represent a thermophilic and/or thermotolerant butanol-producing oxyphotobacterium. Fox example, use of these designer genes (SEQ ID NOS: 34-45) in a thermophilic/thermotolerant cyanobacterium such as Thermosynechococcus elongatus BP-1 may represent a designer thermophilic/thermotolerant butanol-producing cyanobacterium such as a designer butanol-producing Thermosynechococcus. 
Further Host Modifications to Help Ensure Biosafety
The present invention also provides biosafety-guarded photosynthetic biofuel production methods based on cell-division-controllable designer transgenic plants (such as algae and oxyphotobacteria) or plant cells. The cell-division-controllable designer photosynthetic organism (FIG. 3) are created through use of a designer biosafety-control gene(s) (FIG. 2G) in conjunction with the designer butanol-production-pathway gene(s) (FIGS. 2A-2F) such that its cell division and mating function can be controllably stopped to provide better biosafety features.
In one of the various embodiments, a fundamental feature is that a designer cell-division-controllable photosynthetic organism (such as an alga, plant cell, or oxyphotobacterium) contains two key functions (FIG. 3A): a designer biosafety mechanism(s) and a designer biofuel-production pathway(s). As shown in FIG. 3B, the designer biosafety feature(s) is conferred by a number of mechanisms including: (1) the inducible insertion of designer proton-channels into cytoplasm membrane to permanently disable any cell division and mating capability, (2) the selective application of designer cell-division-cycle regulatory protein or interference RNA (iRNA) to permanently inhibit the cell division cycle and preferably keep the cell at the G1 phase or G0 state, and (3) the innovative use of a high-CO2-requiring host photosynthetic organism for expression of the designer biofuel-production pathway(s). Examples of the designer biofuel-production pathway(s) include the designer butanol-production pathway(s), which work with the Calvin cycle to synthesize biofuel such as butanol directly from carbon dioxide (CO2) and water (H2O). The designer cell-division-control technology can help ensure biosafety in using the designer organisms for photosynthetic biofuel production. Accordingly, this embodiment provides, inter alia, biosafety-guarded methods for producing biofuel based on a cell-division-controllable designer biofuel-producing alga, cyanobacterium, oxychlorobacterium, plant or plant cells.
In one of the various embodiments, a cell-division-controllable designer butanol-producing eukaryotic alga or plant cell is created by introducing a designer proton-channel gene (FIG. 2H) into a host alga or plant cell (FIG. 3B). SEQ ID NO: 46 presents example 46 for a detailed DNA construct of a designer Nia1-promoter-controlled proton-channel gene (609 bp) that includes a PCR FD primer (sequence 1-20), a 262-bp nitrate reductase Nia1 promoter (21-282), a Melittin proton-channel encoding sequence (283-366), a 223-bp RbcS2 terminator (367-589), and a PCR RE primer (590-609).
The expression of the designer proton-channel gene (FIG. 2H) is controlled by an inducible promoter such as the nitrate reductase (Nia1) promoter, which can also be used to control the expression of a designer biofuel-production-pathway gene(s). Therefore, before the expression of the designer gene(s) is induced, the designer organism can grow photoautotrophically using CO2 as the carbon source and H2O as the source of electrons just like wild-type organism. When the designer organism culture is grown and ready for photobiological production of biofuels, the cell culture is then placed under a specific inducing condition (such as by adding nitrate into the culture medium if the nitrate reductase (Nia1) promoter is used as an inducible promoter) to induce the expression of both the designer proton-channel gene and the designer biofuel-production-pathway gene(s). The expression of the proton-channel gene is designed to occur through its transcription in the nucleus and its translation in the cytosol. Because of the specific molecular design, the expressed proton channels are automatically inserted into the cytoplasm membrane, but leave the photosynthetic thylakoid membrane intact. The insertion of the designer proton channels into cytoplasm membrane collapses the proton gradient across the cytoplasm membrane so that the cell division and mating function are permanently disabled. However, the photosynthetic thylakoid membrane inside the chloroplast is kept intact (functional) so that the designer biofuel-production-pathway enzymes expressed into the stroma region can work with the Calvin cycle for photobiological production of biofuels from CO2 and H2O. That is, when both the designer proton-channel gene and the designer biofuel-production-pathway gene(s) are turned on, the designer organism becomes a non-reproducible cell for dedicated photosynthetic production of biofuels. Because the cell division and mating function are permanently disabled (killed) at this stage, the designer-organism culture is no longer a living matter except its catalytic function for photochemical conversion of CO2 and H2O into a biofuel. It will no longer be able to mate or exchange any genetic materials with any other cells, even if it somehow comes in contact with a wild-type cell as it would be the case of an accidental release into the environments.
According to one of the various embodiments, the nitrate reductase (Nia1) promoter or nitrite reductase (nirA) promoter is a preferred inducible promoter for use to control the expression of the designer genes. In the presence of ammonium (but not nitrate) in culture medium, for example, a designer organism with Nia1-promoter-controlled designer proton-channel gene and biofuel-production-pathway gene(s) can grow photoauotrophically using CO2 as the carbon source and H2O as the source of electrons just like a wild-type organism. When the designer organism culture is grown and ready for photobiological production of biofuels, the expression of both the designer proton-channel gene and the designer biofuel-production-pathway gene(s) can then be induced by adding some nitrate fertilizer into the culture medium. Nitrate is widely present in soils and nearly all surface water on Earth. Therefore, even if a Nia1-promoter-controlled designer organism is accidentally released into the natural environment, it will soon die since the nitrate in the environment will trig the expression of a Nia1-promoter-controlled designer proton-channel gene which inserts proton-channels into the cytoplasm membrane thereby killing the cell. That is, a designer photosynthetic organism with Nia1-promoter-controlled proton-channel gene is programmed to die as soon as it sees nitrate in the environment. This characteristic of cell-division-controllable designer organisms with Nia1-promoter-controlled proton-channel gene provides an added biosafety feature.
The art in constructing proton-channel gene (FIG. 2H) with a thylakoid-membrane targeting sequence has recently been disclosed [James W. Lee (2007). Designer proton-channel transgenic algae for photobiological hydrogen production, PCT International Publication Number: WO 2007/134340 A2]. In the present invention of creating a cell-division-controllable designer organism, the thylakoid-membrane-targeting sequence must be omitted in the proton-channel gene design. For example, the essential components of a Nia1-promoter-controlled designer proton-channel gene can simply be a Nia1 promoter linked with a proton-channel-encoding sequence (without any thylakoid-membrane-targeting sequence) so that the proton channel will insert into the cytoplasm membrane but not into the photosynthetic thylakoid membrane.
According to one of the various embodiments, it is a preferred practice to use the same inducible promoter such as the Nia1 promoter to control the expression of both the designer proton-channel gene and the designer biofuel-production pathway genes. In this way, the designer biofuel-production pathway(s) can be inducibly expressed simultaneously with the expression of the designer proton-channel gene that terminates certain cellular functions including cell division and mating.
In one of the various embodiments, an inducible promoter that can be used in this designer biosafety embodiment is selected from the group consisting of the hydrogenase promoters [HydA1 (Hyd1) and HydA2, accession number: AJ308413, AF289201, AY090770], the Cyc6 gene promoter, the Cpx1 gene promoter, the heat-shock protein promoter HSP70A, the CabII-1 gene (accession number M24072) promoter, the Ca1 gene (accession number P20507) promoter, the a2 gene (accession number P24258) promoter, the nitrate reductase (Nia1) promoter, the nitrite-reductase-gene (nirA) promoters, the bidirectional-hydrogenase-gene hox promoters, the light- and heat-responsive groE promoters, the Rubisco-operon rbcL promoters, the metal (zinc)-inducible smt promoter, the iron-responsive idiA promoter, the redox-responsive crhR promoter, the heat-shock-gene hsp16.6 promoter, the small heat-shock protein (Hsp) promoter, the CO2-responsive carbonic-anhydrase-gene promoters, the green/red light responsive cpcB2 A2 promoter, the UV-light responsive lexA, recA and ruvB promoters, the nitrate-reductase-gene (narB) promoters, and combinations thereof.
In another embodiment, a cell-division-controllable designer photosynthetic organism is created by use of a carbonic anhydrase deficient mutant or a high-CO2-requiring mutant as a host organism to create the designer biofuel-production organism. High-CO2-requiring mutants that can be selected for use in this invention include (but not limited to): Chlamydomonas reinhardtii carbonic-anhydrase-deficient mutant12-1C(CC-1219 cal mt-), Chlamydomonas reinhardtii cia3 mutant (Plant Physiology 2003, 132:2267-2275), the high-CO2-requiring mutant M3 of Synechococcus sp. Strain PCC 7942, or the carboxysome-deficient cells of Synechocystis sp. PCC 6803 (Plant biol (Stuttg) 2005, 7:342-347) that lacks the CO2-concentrating mechanism can grow photoautotrophically only under elevated CO2 concentration level such as 0.2-3% CO2.
Under atmospheric CO2 concentration level (380 ppm), the carbonic anhydrase deficient or high-CO2-requiring mutants commonly can not survive. Therefore, the key concept here is that a high-CO2-requiring designer biofuel-production organism that lacks the CO2 concentrating mechanism will be grown and used for photobiological production of biofuels always under an elevated CO2 concentration level (0.2-5% CO2) in a sealed bioreactor with CO2 feeding. Such a designer transgenic organism can not survive when it is exposed to an atmospheric CO2 concentration level (380 ppm=0.038% CO2) because its CO2-concentrating mechanism (CCM) for effective photosynthetic CO2 fixation has been impaired by the mutation. Even if such a designer organism is accidentally released into the natural environment, its cell will soon not be able to divide or mate, but die quickly of carbon starvation since it can not effectively perform photosynthetic CO2 fixation at the atmospheric CO2 concentration (380 ppm). Therefore, use of such a high-CO2-requiring mutant as a host organism for the gene transformation of the designer biofuel-production-pathway gene(s) represents another way in creating the envisioned cell-division-controllable designer organisms for biosafety-guarded photobiological production of biofuels from CO2 and H2O, No designer proton-channel gene is required here.
In another embodiment, a cell-division-controllable designer organism (FIG. 3B) is created by use of a designer cell-division-cycle regulatory gene as a biosafety-control gene (FIG. 2G) that can control the expression of the cell-division-cycle (cdc) genes in the host organism so that it can inducibly turn off its reproductive functions such as permanently shutting off the cell division and mating capability upon specific induction of the designer gene.
Biologically, it is the expression of the natural cdc genes that controls the cell growth and cell division cycle in cyanobacteria, algae, and higher plant cells. The most basic function of the cell cycle is to duplicate accurately the vast amount of DNA in the chromosomes during the S phase (S for synthesis) and then segregate the copies precisely into two genetically identical daughter cells during the M phase (M for mitosis). Mitosis begins typically with chromosome condensation: the duplicated DNA strands, packaged into elongated chromosomes, condense into the much-more compact chromosomes required for their segregation. The nuclear envelope then breaks down, and the replicated chromosomes, each consisting of a pair of sister chromatids, become attached to the microtubules of the mitotic spindle. As mitosis proceeds, the cell pauses briefly in a state called metaphase, when the chromosomes are aligned at the equator of the mitotic spindle, poised for segregation. The sudden segregation of sister chromatids marks the beginning of anaphase during which the chromosomes move to opposite poles of the spindle, where they decondense and reform intact nuclei. The cell is then pinched into two by cytoplasmic division (cytokinesis) and the cell division is then complete. Note, most cells require much more time to grow and double their mass of proteins and organelles than they require to replicate their DNA (the S phase) and divide (the M phase). Therefore, there are two gap phases: a G1 phase between M phase and S phase, and a G2 phase between S phase and mitosis. As a result, the eukaryotic cell cycle is traditionally divided into four sequential phases: G1, S, G2, and M. Physiologically, the two gap phases also provide time for the cell to monitor the internal and external environment to ensure that conditions are suitable and preparation are complete before the cell commits itself to the major upheavals of S phase and mitosis. The G1 phase is especially important in this aspect. Its length can vary greatly depending on external conditions and extracellular signals from other cells. If extracellular conditions are unfavorable, for example, cells delay progress through G1 and may even enter a specialized resting state known as G0 (G zero), in which they remain for days, weeks, or even for years before resuming proliferation. Indeed, many cells remain permanently in G0 state until they die.
In one of the various embodiments, a designer gene(s) that encodes a designer cdc-regulatory protein or a specific cdc-iRNA is used to inducibly inhibit the expression of certain cdc gene(s) to stop cell division and disable the mating capability when the designer gene(s) is trigged by a specific inducing condition. When the cell-division-controllable designer culture is grown and ready for photosynthetic production of biofuels, for example, it is a preferred practice to induce the expression of a specific designer cdc-iRNA gene(s) along with induction of the designer biofuel-production-pathway gene(s) so that the cells will permanently halt at the G1 phase or G0 state. In this way, the grown designer-organism cells become perfect catalysts for photosynthetic production of biofuels from CO2 and H2O while their functions of cell division and mating are permanently shut off at the G1 phase or G0 state to help ensure biosafety.
Use of the biosafety embodiments with various designer biofuel-production-pathways genes listed in SEQ ID: 1-45 can create various biosafety-guarded photobiological biofuel producers (FIGS. 3A, 3B, and 3C). Note, SEQ ID NO: 46 and 1-12 (examples 1-12) represent an example for a cell-division-controllable designer eukaryotic organism such as a cell-division-controllable designer alga (e.g., Chlamydomonas) that contains a designer Nia1-promoter-controlled proton-channel gene (SEQ ID NO: 46) and a set of designer Nia1-promoter-controlled butanol-production-pathway genes (SEQ ID NO: 1-12). Because the designer proton-channel gene and the designer biofuel-production-pathway gene(s) are all controlled by the same Nia1-promoter sequences, they can be simultaneously expressed upon induction by adding nitrate fertilizer into the culture medium to provide the biosafety-guarded photosynthetic biofuel-producing capability as illustrated in FIG. 3B. Use of the designer Nia1-promoter-controlled butanol-production-pathway genes (SEQ ID NO: 1-12) in a high CO2-requiring host photosynthetic organism, such as Chlamydomonas reinhardtii carbonic-anhydrase-deficient mutant12-1C(CC-1219 cal mt-) or Chlamydomonas reinhardtii cia3 mutant, represents another example in creating a designer cell-division-controllable photosynthetic organism to help ensure biosafety.
This designer biosafety feature may be useful to the production of other biofuels such as biooils, biohydrogen, ethanol, and intermediate products as well. For example, this biosafety embodiment in combination with a set of designer ethanol-production-pathway genes such as those shown SEQ ID NO: 47-53 can represent a cell-division-controllable ethanol producer (FIG. 3C). Briefly, SEQ ID NO: 47 presents example 47 for a detailed DNA construct (1360 base pairs (bp)) of a nirA-promoter-controlled designer NAD-dependent Glyceraldehyde-3-Phosphate-Dehydrogenase gene including: a PCR FD primer (sequence 1-20), a 88-bp nirA promoter (21-108) selected from the Synechococcus sp. strain PCC 7942 (freshwater cyanobacterium) nitrite-reductase-gene promoter sequence, an enzyme-encoding sequence (109-1032) selected and modified from a Cyanidium caldarium cytosolic NAD-dependent glyceraldehyde-3-phosphate-dehydrogenase sequence (GenBank accession number: CAC85917), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1033-1340), and a PCR RE primer (1341-1360) at the 3′ end.
SEQ ID NO: 48 presents example 48 for a designer nirA-promoter-controlled Phosphoglycerate Kinase DNA construct (1621 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite-reductase nirA promoter (21-108), a phosphoglycerate-kinase-encoding sequence (109-1293) selected from a Geobacillus kaustophilus HTA426 phosphoglycerate-kinase sequence (GenBank: BAD77342), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1294-1601), and a PCR RE primer (1602-1621).
SEQ ID NO: 49 presents example 49 for a designer nirA-promoter-controlled Phosphoglycerate-Mutase DNA construct (1990 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite-reductase nirA promoter (21-108), a 9-bp Xho I NdeI site (109-117), a phosphoglycerate-mutase encoding sequence (118-1653) selected from the sequences of a Caldicellulosiruptor saccharolyticus DSM 8903 phosphoglycerate mutase (GenBank: ABP67536), a 9-bp XbaI site (1654-1662), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1663-1970), and a PCR RE primer (1971-1990).
SEQ ID NO: 50 presents example 50 for a designer nirA-promoter-controlled Enolase DNA construct (1765 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite reductase nirA promoter (21-108), a 9-bp Xho I NdeI site (109-117), an enolase-encoding sequence (118-1407) selected from the sequence of a Cyanothece sp. CCY0110 enolase (GenBank: ZP_01727912), a 21-bp Lumio-tag-encoding sequence (1408-1428), a 9-bp XbaI site (1429-1437) containing a stop codon, a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1438-1745), and a PCR RE primer (1746-1765) at the 3′ end.
SEQ ID NO: 51 presents example 51 for a designer nirA-promoter-controlled Pyruvate Kinase DNA construct (1888 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite reductase nirA promoter (21-108), a 9-bp Xho I NdeI site (109-117), a Pyruvate-Kinase-encoding sequence (118-1530) selected from a Selenomonas ruminantium Pyruvate Kinase sequence (GenBank: AB037182), a 21-bp Lumio-tag sequence (1531-1551), a 9-bp XbaI site (1552-1560), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1561-1868), and a PCR RE primer (1869-1888).
SEQ ID NO: 52 presents example 52 for a designer nirA-promoter-controlled Pyruvate Decarboxylase DNA construct (2188 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite reductase nirA promoter (21-108), a 9-bp Xho I NdeI site (109-117), a Pyruvate-Decarboxylase-encoding sequence (118-1830) selected from the sequences of a Pichia stipitis pyruvate-decarboxylase sequence (GenBank: XM_001387668), a 21-bp Lumio-tag sequence (1831-1851), a 9-bp XbaI site (1852-1860), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1861-2168), and a PCR RE primer (2169-2188) at the 3′ end.
SEQ ID NO: 53 presents example 53 for a nirA-promoter-controlled designer NAD(P)H-dependent Alcohol Dehydrogenase DNA construct (1510 bp) that includes a PCR FD primer (sequence 1-20), a 88-bp Synechococcus sp. strain PCC 7942 nitrite-reductase nirA promoter (21-108), a NAD(P)H dependent Alcohol-Dehydrogenase-encoding sequence (109-1161) selected/modified (its mitochondrial signal peptide sequence removed) from the sequence of a Kluyveromyces lactis alcohol dehydrogenase (ADH3) gene (GenBank: X62766), a 21-bp Lumio-tag sequence (1162-1182), a 308-bp Synechococcus sp. strain PCC 7942 rbcS terminator (1183-1490), and a PCR RE primer (1491-1510) at the 3′ end.
Note, SEQ ID NO: 47-53 (DNA-construct examples 47-53) represent a set of designer nirA-promoter-controlled ethanol-production-pathway genes that can be used in oxyphotobacteria such as Synechococcus sp. strain PCC 7942. Use of this set of designer ethanol-production-pathway genes in a high-CO2-requiring cyanobacterium such as the Synechococcus sp. Strain PCC 7942 mutant M3 represents another example of cell-division-controllable designer cyanobacterium for biosafety-guarded photosynthetic production of biofuels from CO2 and H2O.
Use of Designer Butanol-Producing Organisms with Photobioreactor-Butanol-Harvesting Processes
The various embodiments further teach how the designer organisms including the designer cell-division-controllable organisms (FIG. 3) may be used with a photobioreactor and a butanol-separation-harvesting process for photosynthetic production of butanol (CH3CH2CH2CH2OH) and O2 directly from CO2 and H2O using sunlight. There are a number of embodiments on how the designer organisms may be used for photobiological butanol production. One of the preferred embodiments is to use the designer organisms for direct photosynthetic butanol production from CO2 and H2O with a photobiological reactor and butanol-harvesting (filtration and distillation/evaporation) system, which includes a specific operational process described as a series of the following steps: a) Growing a designer transgenic organism photoautotrophically in minimal culture medium using air CO2 as the carbon source under aerobic (normal) conditions before inducing the expression of the designer butanol-production-pathway genes; b) When the designer organism culture is grown and ready for butanol production, sealing or placing the culture into a specific condition, such as an anaerobic condition that can be generated by removal of O2 from the photobiological reactor, to induce the expression of designer butanol-production genes; c) When the designer butanol-production-pathway enzymes are expressed, supplying visible light energy such as sunlight for the designer-genes-expressed cells to work as the catalysts for photosynthetic butanol production from CO2 and H2O; d) Harvesting the product butanol by any method known to those skilled in the art. For example, harvesting the butanol product from the photobiological reactor by a combination of membrane filtration and distillation/evaporation butanol-harvesting techniques and flexibly collecting the O2 gas product from the reactor.
The above process to use the designer organisms for photosynthetic CH3CH2CH2CH2OH and O2 production from CO2 and H2O with a biological reactor and butanol-harvesting and gas product separation and collection system can be repeated for a plurality of operational cycles to achieve more desirable results. Any of the steps a) through d) of this process described above can also be adjusted in accordance of the invention to suit for certain specific conditions. In practice, any of the steps a) through d) of the process can be applied in full or in part, and/or in any adjusted combination as well for enhanced photobiological butanol production in accordance of this invention.
The sources of CO2 that can be used in this process include, but not limited to, industrial CO2, (bi)carbonates, and atmospheric CO2. For an example, flue-gas CO2 from fossil fuel-fired and/or biomass-fired industrial facilities can be fed through a pipeline into a photobiological reactor in this process. The industrial facilities that can generate CO2 supplies for the designer photosynthetic butanol-production process include (but not limited to): coal-fired power plants, iron and steelmaking industries, cement-manufacturing plants, petroleum refinery facilities, chemical fertilizer production factories, biomass-fired and/or fossil fuel-fired biofuels (or intermediate products) distillation/separation facilities, biomass-pyrolysis processes, smokestacks, fermentation bioreactors, biofuel-refinery facilities, and combinations thereof.
Alternatively, this designer photobiological butanol-production process can also use the CO2 in the environment and from the atmosphere as well. Gaseous CO2, dissolved CO2, bicarbonate, and carbonates can all be used by the designer-organism photobiological butanol-production technology.
This embodiment is illustrated in more details here using designer algae as an example. As described above, designer algae of the present invention, such as the one that contains a set of designer HydA1 promoter-controlled designer butanol-production-pathway genes (for examples, the DNA constructs of SEQ ID NO: 13-16 (or 17) and 18-23), can grow normally under aerobic conditions by autotrophic photosynthesis using air CO2 in a manner similar to that of a wild-type alga. The designer algae can grow also photoheterotrophically using an organic substrate as well.
In a preferred embodiment, a designer alga is grown photoautotrophically using air CO2 as the carbon source under the aerobic conditions in a minimal medium that contains the essential mineral (inorganic) nutrients. No organic substrate such as acetate is required to grow a designer alga under the normal conditions before the designer photosynthetic butanol-production-pathway genes are expressed. Most of the algae can grow rapidly in water through autotrophic photosynthesis using air CO2 as long as there are sufficient mineral nutrients. The nutrient elements that are commonly required for algal growth are: N, P, and K at the concentrations of about 1-10 mM, and Mg, Ca, S, and Cl at the concentrations of about 0.5 to 1.0 mM, plus some trace elements Mn, Fe, Cu, Zn, B, Co, Mo among others at μM concentration levels. All of the mineral nutrients can be supplied in an aqueous minimal medium that can be made with well-established recipes of algal culture media using water (freshwater for the designer freshwater algae; seawater for the salt-tolerant designer marine algae) and relatively small of inexpensive fertilizers and mineral salts such as ammonium bicarbonate (NH4HCO3) (or ammonium nitrate, urea, ammonium chloride), potassium phosphates (K2HPO4 and KH2PO4), magnesium sulfate heptahydrate (MgSO4.7H2O), calcium chloride (CaCl2), zinc sulfate heptahydrate (ZnSO4.7H2O), iron (II) sulfate heptahydrate (FeSO4.7H2O), and boric acid (H3BO3), among others. That is, large amounts of designer algae cells can be inexpensively grown in a short period of time because, under aerobic conditions such as in an open pond, the designer algae can photoautotrophically grow by themselves using air CO2 as rapidly as their wild-type parental strains. This is a significant feature (benefit) of the invention that could provide a cost-effective solution in generation of photoactive biocatalysts (the designer photosynthetic butanol-producing algae) for renewable solar energy production.
When the algal culture is grown and ready for butanol production, the grown algal culture is sealed or placed into certain specific conditions, such as anaerobic conditions that can be generated by removal of O2 from the sealed photobiological reactor, to induce the expression of the designer HydA1-promoter-controlled butanol-production-pathway genes. When the designer butanol-production-pathway enzymes are expressed, visible light energy such as sunlight is supplied for the designer-genes-expressing algal cells to work as the catalysts for photosynthetic butanol production from CO2 and H2O. When the designer genes are expressed, the algal cells can essentially become efficient and robust “green machines” that are perfect for photosynthetic production of butanol (CH3CH2CH2CH2OH) and O2 from CO2 and H2O. The product butanol from the algal photobiological rector can be harvested by a combination of membrane filtration and distillation/evaporation butanol-harvesting techniques including (but not limited to) liquid/liquid extraction, gas stripping, membrane evaporation, pervaporation, and adsorption techniques (Durre, P. 1998 Appl Microbiol Biotechnol 49: 639-648; Qureshi, Hughes, Maddox, and Cotta 2005 Bioprocess Biosyst Eng 27: 215-222).
Photosynthetic production of CH3CH2CH2CH2OH and O2 directly from CO2 and H2O in accordance with the present invention can, in principle, have high quantum yield. Theoretically, it requires only 48 photons to produce a CH3CH2CH2CH2OH and 6O2 from water and carbon dioxide by this mechanism. The maximal theoretical sunlight-to-butanol energy efficiency by the process of direct photosynthetic butanol production from CO2 and H2O is about 10%, which is the highest possible among all the biological approaches. Consequently, this approach has great potential when implemented properly with an algal reactor and butanol-oxygen-harvesting process.
The above process to use the designer algae for photosynthetic production of CH3CH2CH2CH2OH and O2 from CO2 and H2O with an algal reactor and a butanol-harvesting and gas product separation and collection system can be repeated for a plurality of operational cycles to achieve more desirable results.
Another feature is that the designer switchable butanol-production organism provides the capability for repeated cycles of photoautotrophic culture growth under normal aerobic conditions with a manner similar to that of a wild type and efficient photobiological production of butanol (FIGS. 1 and 3) when the designer butanol-production pathway is switched on by an inducible promoter (such as hydrogenase promoter) at certain specific inducing conditions (such as under anaerobic conditions) in a bioreactor. For example, the switchable designer alga with designer hydrogenase promoter-controlled butanol-production genes contains normal mitochondria, which uses the reducing power (NADH) from organic reserves (and/or exogenous substrates, such as acetate) to power the cell immediately after its return to aerobic conditions. Therefore, when the algal cell is returned to aerobic conditions after its use under anaerobic conditions for production of butanol, the cell will stop producing butanol-production-pathway enzymes and start to restore its normal photoautotrophic capability by synthesizing normal functional chloroplast. Consequently, it is possible to use this type of genetically transformed organism for repeated cycles of photoautotrophic culture growth under normal aerobic conditions and efficient production of butanol under anaerobic conditions in an anaerobic reactor. That is, this photobiological butanol-production technology can be operated for a plurality of operational cycles by rejuvenating the used culture under aerobic conditions and recyclably using the rejuvenated algal culture under butanol-producing conditions to achieve more desirable results. Optionally, this photobiological butanol-production technology is operated continuously by circulating rejuvenated algal culture from an aerobic reactor into the anaerobic reactor while circulating the used algal culture from the anaerobic reactor (after its use for butanol production) into the aerobic reactor for rejuvenation by synthesizing normal functional chloroplasts through photosynthetic CO2 fixation and photoautotrophic growth.
Some of the designer organisms could grow photoautotrophically even with the butanol-production pathway(s) switched on. Whether or how fast a designer organism could grow under the butanol-producing conditions may depend on its genetic background and how much of the Calvin cycle products are still available for cell growth after use by the designer butanol-production pathway(s). Designer organisms that can, under the butanol-producing conditions, maintain essential cellular functions with an appropriate growth rate can also be used for continuous photobiological production of CH3CH2CH2CH2OH and O2 from CO2 and H2O with a bioreactor and butanol-harvesting process.
There are additional ways that the switchable designer organisms including the cell-division-controllable designer organisms (FIG. 3) can be used for biosafety-guarded photobiological production of biofuels. With use of the designer biosafety features described previously, for example, the used designer algal culture from a photobiological butanol-production reactor does not have to be circulated back to a culture-growth reactor. Instead, the used algal culture is taken out to be used as fertilizers or biomass feed stocks for other processing because the photoautotrophic growth of the switchable designer alga in a culture-growth reactor is capable of continuously supplying algal cells to a photobiological butanol-production reactor for the biofuel production. This embodiment is, especially, helpful to using some of the designer organisms that can grow photoautotrophically only before but not after the butanol-production-pathway(s) is switched on. For example, by keeping a continuously growing culture of a designer alga (that can grow photoautotrophically only before the butanol-production-pathway(s) is switched on) in a culture-growth reactor, it can provide continuous supplies of grown algal cells for use in a photobiological butanol-production reactor. This approach makes it possible to use those designer organisms that can grow only before the butanol-production-pathway(s) is switched on for photobiological butanol production as well.
Because of various reasons, some of the designer butanol-production organisms could grow only photohetrotrophically or photomixotrophically but not photoautotrophically. Use of a culture-growth reactor can also grow this type of designer butanol-production organisms photohetrotrophically or photomixotrophically using organic substrates including, but not limited to, sucrose, glucose, acetate, ethanol, methanol, propanol, butanol, acetone, starch, hemicellulose, cellulose, lipids, proteins, organic acids, biomass materials and combination thereof. The so-grown culture can also be supplied to a photobiological butanol-production reactor for induction of the designer pathways for butanol production. This modified embodiment on culture growth makes it possible to use those designer organisms that can grow only photohetrotrophically, or photomixotrophically also for photobiological butanol production as well.
For certain specific designer organisms with designer nitrate reductase (Nia1) promoter-controlled butanol-production-pathway genes, the above photobiological reactor process may be further adjusted to achieve more beneficial results. For example, both a designer alga that contains Nia1 (or nirA) promoter-controlled butanol-production-pathway genes such as the ones shown in DNA sequence design examples 1-12 (SEQ ID NO: 1-12) and a designer oxyphotobacterium that carries designer nirA promoter-controlled butanol-production-pathway genes shown in SEQ ID NO: 34-45, can grow normally in a culture medium with ammonium (but no nitrate) by autotrophic photosynthesis using air CO2 in a manner similar to that of a wild-type alga. This is because the expression of the butanol-production-pathway genes in the designer organism will be turned on only in the presence of nitrate as desired owning to the use of a nitrate reductase (Nia1) promoter or a nitrite reductase (nirA) promoter in controlling the designer pathway(s) expression. A significant feature of the designer organisms with nirA or Nia1 promoter-controlled butanol-production-pathway genes is that the expression of the designer butanol-production pathways can be induced by manipulating the concentration levels of nitrate (NO3−) relative to that of ammonium (NH4+) in the culture medium without requiring any anaerobic conditions. That is, the expression of the designer butanol-production pathway(s) can be induced under both aerobic and anaerobic conditions. This enables the designer photobiological butanol-production process to operate even under aerobic conditions using atmospheric CO2. Likewise, this type of designer organisms with Nia1 promoter-controlled butanol-production-pathway genes can grow photoautotrophically both under aerobic and anaerobic conditions as well. Therefore, as a further embodiment, the operational process of using designer organism with nitrate reductase (Nia1) promoter-controlled butanol-production-pathway genes is adjusted to the following: a) Growing a designer transgenic organism photoautotrophically in minimal culture medium in the presence of ammonium (NH4+) but no nitrate (NO3−) before inducing the expression of the designer butanol-production-pathway genes; b) When the designer organism culture is grown and ready for butanol production, adding nitrate (NO3−) fertilizer into the culture medium to raise the concentration of nitrate (NO3−) relative to that of ammonium (NH4+) to induce the expression of designer butanol-production-pathway genes; c) When the designer butanol-production-pathway enzymes are expressed, supplying visible light energy such as sunlight for the designer-genes-expressed cells to work as the catalysts for photosynthetic butanol production from CO2 and H2O; d) Harvesting the butanol product from the photobiological reactor by a combination of membrane filtration and butanol-harvesting techniques.
In addition to butanol production, it is also possible to use a designer organism or part of its designer butanol-production pathway(s) to produce certain intermediate products including: butyraldehyde, butyryl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA, acetoacetyl-CoA, acetyl-CoA, pyruvate, phosphoenolpyruvate, 2-phosphoglycerate, 1,3-diphosphoglycerate, glyceraldehyde-3-phosphate, dihydroxyacetone phosphate, fructose-1,6-diphosphate, fructose-6-phosphate, glucose-6-phosphate, glucose, and glucose-1-phosphate. Therefore, a further embodiment comprises an additional step of harvesting the intermediate products that can be produced also from an induced transgenic designer organism. The production of an intermediate product can be selectively enhanced by switching off a designer-enzyme activity that catalyzes its consumption in the designer pathways. The production of a said intermediate product can be enhanced also by using a designer organism with one or some of designer enzymes omitted from the designer butanol-production pathways. For example, a designer organism with the butanol dehydrogenase or butyraldehyde dehydrogenase omitted from the designer pathway(s) of FIG. 1 may be used to produce butyraldehyde or butyryl-CoA, respectively.
While the present invention has been illustrated by description of several embodiments and while the illustrative embodiments have been described in considerable detail, it is not the intention of the applicant to restrict or in any way limit the scope of the appended claims to such detail. Additional advantages and modifications will readily appear to those skilled in the art. The invention in its broader aspects is therefore not limited to the specific details, representative apparatus and methods, and illustrative examples shown and described. Accordingly, departures may be made from such details without departing from the spirit or scope of applicant's general inventive concept.

## Claims

1. A method for photosynthetic production of butanol, the method comprising:
introducing into a carbonic anhydrase deficient mutant plant or plants cells nucleic acid molecules encoding for a set of enzymes that interact with at least one intermediate product of the Calvin cycle for photobiological butanol production selected from glyceraldehyde-3-phosphate, 3-phosphoglycerate, fructose-1,6-diphosphate and fructose-6-phosphate, each enzyme in the set of enzymes comprising a butanol-production-pathway enzyme that serves as a catalyst for at least one of the steps in a butanol-production pathway, the carbonic anhydrase deficient mutant lacking a carbonic anhydrase catalyzed CO2 concentrating mechanism for achieving effective photosynthetic CO2 fixation;
growing the carbonic anhydrase deficient mutant plant or plant cells containing the nucleic acid molecules photoautotrophically in a liquid medium using CO2 as a carbon source and H2O as a source of electrons in an elevated CO2 concentration level greater than about 0.2% CO2 in a sealed bioreactor so that the expressed designer biofuel-production-pathway enzymes interact with the Calvin cycle for photobiological production of butanol; and
recovering butanol from the liquid medium.

2. The method of claim 1, wherein the elevated CO2 concentration level is from about 0.2% CO2 to about 5% CO2.

3. The method of claim 2, wherein the carbonic anhydrase deficient mutant comprises Chlamydomonas reinhardtii carbonic-anhydrase-deficient mutant12-1C, Chlamydomonas reinhardtii cia3 mutant, a high-CO2-requiring mutant M3 of Synechococcus sp. Strain PCC 7942, or a carboxysome-deficient cells of Synechocystis sp. PCC 6803.

4. The method of claim 1, wherein the method comprises introducing into the plant or plant cells a functional chloroplast-targeting sequence functionally linked with the nucleic acid molecules to insert the set of enzymes into a chloroplast of the plant or plant cells.

5. The method of claim 4, wherein the functional chloroplast-targeting sequence comprises a transit peptide sequence that encodes for a signal peptide that is synthesized as part of a apoprotein of an enzyme in the cytosol and that guides insertion of each butanol-production-pathway enzyme apoprotein from cytosol into the chloroplast.

6. The method of claim 1, wherein the set of enzymes comprises phosphoglycerate kinase, phosphoglycerate mutase, enolase, pyruvate kinase, pyruvate-ferredoxin oxidoreductase, thiolase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, butanol dehydrogenase, aldolase, triose phosphate isomerase, phosphofructose kinase or combinations thereof.