Patent Application
20110097773
The present invention relates to the field of biofuels. More specifically, the invention relates to a method for producing butanol through microbial fermentation, in which the butanol product is removed during the fermentation by extraction into a water-immiscible extractant composition which comprises a first solvent and a second solvent.
Butanol is an important industrial chemical with a variety of applications, such as use as a fuel additive, as a feedstock chemical in the plastics industry, and as a food grade extractant in the food and flavor industry. Each year 10 to 12 billion pounds of butanol are produced by petrochemical means and the need for this chemical will likely increase.
Several chemical synthetic methods are known; however, these methods of producing butanol use starting materials derived from petrochemicals and are generally expensive and are not environmentally friendly. Several methods of producing butanol by fermentation are also known, for example the ABE process which is the fermentive process producing a mixture of acetone, 1-butanol, and ethanol. Acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum is one of the oldest known industrial fermentations; as are also the pathways and genes responsible for the production of these solvents. Production of 1-butanol by the ABE process is limited by the toxic effect of the 1-butanol on Clostridium acetobutylicum. In situ extractive fermentation methods using specific extractants which are nontoxic to the bacterium have been reported to enhance the production of 1-butanol by fermentation using Clostridium acetobutylicum (see for example Roffler et al., Biotechnol. Bioeng. 31:135-143, 1988; Roffler et al., Bioprocess Engineering 2:1-12, 1987, and Evans et al., Appl. Environ. Microbiol. 54:1662-1667, 1988).
In contrast to the native Clostridium acetobutylicum described above, recombinant microbial production hosts expressing 1-butanol, 2-butanol, and isobutanol biosynthetic pathways have also been described. These recombinant hosts have the potential of producing butanol in higher yields compared to the ABE process because they do not produce byproducts such as acetone and ethanol. With these recombinant hosts, the biological production of butanol appears to be limited by the butanol toxicity thresholds of the host microorganism used in the fermentation. U.S. Patent Publication No. 20090305370 discloses a method of making butanol from at least one fermentable carbon source that overcomes the issues of toxicity resulting in an increase in the effective titer, the effective rate, and the effective yield of butanol production by fermentation utilizing a recombinant microbial host wherein the butanol is extracted into specific organic extractants during fermentation.
Improved methods for producing and recovering butanol from a fermentation medium are continually sought. Lower cost processes and improvements to process operability are also desired. Identification of improved extractants for use with fermentation media, such as extractants exhibiting higher partition coefficients, lower viscosity, lower density, commercially useful boiling points, and sufficient microbial biocompatibility, is a continual need.
Provided herein is a method for recovering butanol from a fermentation medium, the method comprising:
a) providing a fermentation medium comprising butanol, water, at least one fermentable carbon source, and a genetically modified microorganism that produces butanol from a fermentation medium comprising at least one fermentable carbon source;
b) contacting the fermentation medium with a water-immiscible extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, C12 to C22 fatty amides and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, and mixtures thereof, to form a two-phase mixture comprising an aqueous phase and a butanol-containing organic phase;
c) separating the butanol-containing organic phase from the aqueous phase; and
d) recovering the butanol from the butanol-containing organic phase to produce recovered butanol.
Also provided is a method for the production of butanol comprising:
a) providing a genetically modified microorganism that produces butanol from a fermentation medium comprising at least one fermentable carbon source;
b) growing the microorganism in a biphasic fermentation medium comprising an aqueous phase and a water-immiscible extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, C12 to C22 fatty amides and mixtures thereof, wherein the biphasic fermentation medium comprises from about 10% to about 90% by volume of the water-immiscible extractant composition, for a time sufficient to allow extraction of the butanol into the extractant composition to form a butanol-containing organic phase;
c) separating the butanol-containing organic phase from the aqueous phase; and
d) recovering the butanol from the butanol-containing organic phase to produce recovered butanol.
Also provided is a method for the production of butanol comprising:
a) providing a genetically modified microorganism that produces butanol from a fermentation medium comprising at least one fermentable carbon source;
b) growing the microorganism in a fermentation medium wherein the microorganism produces the butanol into the fermentation medium to produce a butanol-containing fermentation medium;
c) contacting at least a portion of the butanol-containing fermentation medium with a water immiscible extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, C12 to C22 fatty amides and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, and mixtures thereof, to form a two-phase mixture comprising an aqueous phase and a butanol-containing organic phase;
d) separating the butanol-containing organic phase from the aqueous phase;
e) recovering the butanol from the butanol-containing organic phase; and
f) returning at least a portion of the aqueous phase to the fermentation medium.
In embodiments, the butanol is 1-butanol. In embodiments, the butanol is 2-butanol. In embodiments, the butanol is isobutanol.
In embodiments, the first solvent is selected from the group consisting of oleyl alcohol, behenyl alcohol, cetyl alcohol, lauryl alcohol, myristyl alcohol, stearyl alcohol, oleic acid, lauric acid, myristic acid, stearic acid, methyl myristate, methyl oleate, lauric aldehyde, 1-dodecanol, and a combination of these. In embodiments the first solvent comprises oleyl alcohol.
In embodiments, the second solvent is selected from the group consisting of 1-nonanol, 1-decanol, 1-undecanol, 2-undecanol, 1-nonanal, and a combination of these. In embodiments, the second solvent is selected from the group consisting of 1-nonanol, 1-decanol, 1-nonanal, and a combination of these. In embodiments, the second solvent comprises 1-decanol. In embodiments, the first solvent comprises oleyl alcohol and the second solvent comprises 1-decanol.
In embodiments, the extractant contains about 30 percent to about 90 percent first solvent, based on the total volume of the first and second solvents. In embodiments, the extractant contains about 50 percent to about 70 percent first solvent. In embodiments, the ratio of the extractant to the fermentation medium is from about 1:20 to about 20:1 on a volume:volume basis.
In embodiments, the contacting further comprises contacting the fermentation medium with the first solvent prior to contacting the fermentation medium and the first solvent with the second solvent. In embodiments, the contacting with the second solvent occurs in the same vessel as the contacting with the first solvent. In embodiments, a portion of the butanol is concurrently removed from the fermentation medium by a process comprising the steps of:
a) stripping butanol from the fermentation medium with a gas to form a butanol-containing gas phase; and
b) recovering butanol from the butanol-containing gas phase.
In embodiments, the genetically modified microorganism is selected from the group consisting of bacteria, cyanobacteria, filamentous fungi, and yeasts. In embodiments, bacteria are selected from the group consisting of Zymomonas, Escherichia, Salmonella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Pediococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, and Brevibacterium. In embodiments, the bacteria is an Escherichia coli comprising: a) a set of genes encoding an isobutanol biosynthetic pathway; and b) deletions of the following genes, pflB, LdhA, adhE, and at least one of frdA, frdB, frdC, and FrdD. In embodiments, the set of genes comprises: a) budB as set forth in SEQ ID NO:1; b) ilvC as set forth in SEQ ID NO:3; c) ilvD as set forth in SEQ ID NO:5; d) kivD as set forth in SEQ ID NO:7; and e) sadB as set forth in SEQ ID NO:9. In embodiments, the yeast is selected from the group consisting of Issatchenkia, Pichia, Candida, Hansenula and Saccharomyces.
In embodiments, the genetically modified microorganism contains a butanol biosynthetic pathway. In embodiments, the butanol biosynthetic pathway comprises at least one gene that is heterologous to the microorganism. In embodiments, the butanol biosynthetic pathway comprises at least two genes that are heterologous to the microorganism.
In embodiments, the fermentation medium further comprises ethanol, and the butanol-containing organic phase contains ethanol.
Also provided is a two-phase mixture comprising a fermentation medium comprising butanol, water, at least one fermentable carbon source, and a genetically modified microorganism that produces butanol from a fermentation medium; and a water-immiscible extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, C12 to C22 fatty amides and mixtures thereof.
The following sequences conform with 37 C.F.R. 1.821 1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a bis), and Section 208 and Annex C of the Administrative Instructions).
Klebsiella pneumoniae budB
E. coli ilvC (acetohydroxy
E. coli ilvD (acetohydroxy
Lactococcus lactis kivD
Achromobacter
xylosoxidans.
Bacillus subtilis alsS
S. cerevisiae ILV5
B. subtilis ketoisovalerate
Streptococcus mutans ilvD
SEQ ID NOs:11-22 are the nucleotide sequences of the primers used to construct the recombinant Escherichia coli strain described in the Genetically Modified Microorganisms section herein below.
SEQ ID NO:23 is the nucleotide sequence of the pflB gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:24 is the nucleotide sequence of the IdhA gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:25 is the nucleotide sequence of the adhE gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:26 is the nucleotide sequence of the frdA gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:27 is the nucleotide sequence of the frdB gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:28 is the nucleotide sequence of the frdC gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO:29 is the nucleotide sequence of the frdD gene from Escherichia coli strain K-12 MG1655.
SEQ ID NO: 30 is the nucleotide sequence of pLH475-Z4B8.
SEQ ID NO: 31 is the nucleotide sequence of the CUP1 promoter.
SEQ ID NO: 34 is the nucleotide sequence of the CYC1 terminator.
SEQ ID NO: 35 is the nucleotide sequence of the ILV5 promoter.
SEQ ID NO: 38 is the nucleotide sequence of the ILV5 terminator.
SEQ ID NO: 39 is the nucleotide sequence of the FBA1 promoter.
SEQ ID NO: 42 is the nucleotide sequence of pLH468.
SEQ ID NO: 47 is the nucleotide sequence of pNY8.
SEQ ID NO: 48 is the nucleotide sequence of the GPD1 promoter.
SEQ ID NOs:49, 50, 54, 55, 62-71, 73-83 and 85-86 are the nucleotide sequences of primers used in the examples.
SEQ ID NO: 51 is the nucleotide sequence of pRS425::GPM-sadB.
SEQ ID NO: 52 is the nucleotide sequence of the GPM1 promoter.
SEQ ID NO: 53 is the nucleotide sequence of the ADH1 terminator.
SEQ ID NO: 56 is the nucleotide sequence of pRS423 FBA ilvD(Strep).
SEQ ID NO: 57 is the nucleotide sequence of the FBA terminator.
SEQ ID NO: 60 is the nucleotide sequence of the GPM-sadB-ADHt segment.
SEQ ID NO: 61 is the nucleotide sequence of pUC19-URA3r.
SEQ ID NO: 72 is the nucleotide sequence of the ilvD-FBA1t segment.
SEQ ID NO: 84 is the nucleotide sequence of the URA3r2 template DNA.
The present invention provides methods for recovering butanol from a microbial fermentation medium by extraction into a water-immiscible extractant composition. A method involving contacting the fermentation medium with a water-immiscible extractant composition comprising a first solvent and a second solvent to form a two-phase mixture comprising an aqueous phase and a butanol-containing organic phase is employed. The first and second solvents are chosen to impart a high butanol partition coefficient to the extractant while mitigating any decreased biocompatibility. The butanol-containing organic phase is separated from the aqueous phase and the butanol is recovered. Methods for producing butanol are also provided.
The following definitions are used in this disclosure.
The term “water-immiscible” refers to an extractant or solvent mixture which is incapable of mixing with an aqueous solution such as a fermentation medium to form one liquid phase.
The term “extractant” as used herein refers to a mixture of at least two organic solvents which is used to extract any butanol isomer.
The term “biphasic fermentation medium” refers to a two-phase growth medium comprising a fermentation medium (i.e., an aqueous phase) and a suitable amount of a water-immiscible organic extractant.
The term “organic phase”, as used herein, refers to the phase of a biphasic mixture, obtained by contacting an aqueous fermentation medium with a water-immiscible organic extractant, which comprises the organic extractant.
The term “aqueous phase”, as used herein, refers to the phase of a biphasic mixture, obtained by contacting an aqueous fermentation medium with a water-immiscible organic extractant, which comprises water.
The term “butanol” refers to 1-butanol, 2-butanol, isobutanol, or mixtures thereof. Isobutanol is also known as 2-methyl-1-propanol.
The term “fermentable carbon source” refers to a carbon source capable of being metabolized by the microorganisms such as those disclosed herein. Suitable fermentable carbon sources include, but are not limited to, monosaccharides, such as glucose or fructose; disaccharides, such as lactose or sucrose; oligosaccharides; polysaccharides, such as starch, cellulose, or lignocellulose, hemicellulose; one-carbon substrates; and a combination of these.
The term “fatty acid” as used herein refers to a carboxylic acid having a long, aliphatic chain of C7 to C22 carbon atoms, which is either saturated or unsaturated.
The term “fatty alcohol” as used herein refers to an alcohol having a long, aliphatic chain of C7 to C22 carbon atoms, which is either saturated or unsaturated.
The term “fatty aldehyde” as used herein refers to an aldehyde having a long, aliphatic chain of C7 to C22 carbon atoms, which is either saturated or unsaturated.
The term “fatty amide” as used herein refers to an amide having a long, aliphatic chain of C12 to C22 carbon atoms, which is either saturated or unsaturated.
The term “partition coefficient”, abbreviated herein as Kp, means the ratio of the concentration of a compound in the two phases of a mixture of two immiscible solvents at equilibrium. A partition coefficient is a measure of the differential solubility of a compound between two immiscible solvents. As used herein, the term “partition coefficient for butanol” refers to the ratio of concentrations of butanol between the aqueous phase comprising the fermentation medium and the organic phase comprising the extractant. Partition coefficient, as used herein, is synonymous with the term distribution coefficient.
The term “butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol, 2-butanol, or isobutanol.
The term “1-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol from acetyl-coenzyme A (acetyl-CoA).
The term “2-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 2-butanol from pyruvate.
The term “isobutanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce isobutanol from pyruvate.
The term “gene” refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign gene” or “heterologous gene” refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes.
The term “effective titer” as used herein refers to the total amount of butanol produced by fermentation per liter of fermentation medium. The total amount of butanol includes the amount of butanol in the fermentation medium, and the amount of butanol recovered from the organic extractant composition and from the gas phase, if gas stripping is used.
The term “aerobic conditions” as used herein means growth conditions in the presence of oxygen.
The term “microaerobic conditions” as used herein means growth conditions with low levels of oxygen (i.e., below normal atmospheric oxygen levels).
The term “anaerobic conditions” as used herein means growth conditions in the absence of oxygen.
The term “minimal media” as used herein refers to growth media that contain the minimum nutrients possible for growth, generally without the presence of amino acids. A minimal medium typically contains a fermentable carbon source and various salts, which may vary among microorganisms and growing conditions; these salts generally provide essential elements such as magnesium, nitrogen, phosphorus, and sulfur to allow the microorganism to synthesize proteins and nucleic acids.
The term “defined media” as used herein refers to growth media that have known quantities of all ingredients, e.g., a defined carbon source and nitrogen source, and trace elements and vitamins required by the microorganism.
The term “biocompatibility” as used herein refers to the measure of the ability of a microorganism to utilize glucose in the presence of an extractant. A biocompatible extractant permits the microorganism to utilize glucose. A non-biocompatible (that is, a biotoxic) extractant does not permit the microorganism to utilize glucose, for example at a rate greater than about 25% of the rate when the extractant is not present.
The term, “° C.” means degrees Celsius.
The term “OD” means optical density.
The term “OD600” refers to the optical density at a wavelength of 600 nm.
The term ATCC refers to the American Type Culture Collection, Manassas, Va.
The term “sec” means second(s).
The term “min” means minute(s).
The term “h” means hour(s).
The term “mL” means milliliter(s).
The term “L” means liter.
The term “g” means grams.
The term “mmol” means millimole(s).
The term “M” means molar.
The term “μL” means microliter.
The term “μg” means microgram.
The term “μg/mL” means microgram per liter.
The term “mL/min” means milliliters per minute.
The term “g/L” means grams per liter.
The term “g/L/h” means grams per liter per hour.
The term “mmol/min/mg” means millimole per minute per milligram.
The term “temp” means temperature.
The term “rpm” means revolutions per minute.
The term “HPLC” means high pressure gas chromatography.
The term “GC” means gas chromatography.
Applicants specifically incorporate the entire contents of all cited references in this disclosure. Further, when an amount, concentration, or other value or parameter is given as either a range, preferred range, or a list of upper preferable values and lower preferable values, this is to be understood as specifically disclosing all ranges formed from any pair of any upper range limit or preferred value and any lower range limit or preferred value, regardless of whether ranges are separately disclosed. Where a range of numerical values is recited herein, unless otherwise stated, the range is intended to include the endpoints thereof, and all integers and fractions within the range. It is not intended that the scope of the invention be limited to the specific values recited when defining a range.
Suitable biosynthetic pathways for production of butanol are known in the art, and certain suitable pathways are described herein. In some embodiments, the butanol biosynthetic pathway comprises at least one gene that is heterologous to the host cell. In some embodiments, the butanol biosynthetic pathway comprises more than one gene that is heterologous to the host cell. In some embodiments, the butanol biosynthetic pathway comprises heterologous genes encoding polypeptides corresponding to every step of a biosynthetic pathway.
Likewise, certain suitable proteins having the ability to catalyze indicated substrate to product conversions are described herein and other suitable proteins are provided in the art. For example, US Published Patent Application Nos. US20080261230 and US20090163376, incorporated herein by reference, describe acetohydroxy acid isomeroreductases; U.S. patent application Ser. No. 12/569,636, incorporated by reference, describes dihydroxyacid dehydratases; an alcohol dehydrogenase is described in US Published Patent Application US20090269823, incorporated herein by reference.
A biosynthetic pathway for the production of 1-butanol that may be used is described by Donaldson et al. in U.S. Patent Application Publication No. US20080182308A1, incorporated herein by reference. This biosynthetic pathway comprises the following substrate to product conversions:
In some embodiments, the 1-butanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, at least four genes, or at least five genes that is/are heterologous to the yeast cell.
Biosynthetic pathways for the production of 2-butanol that may be used are described by Donaldson et al. in U.S. Patent Application Publication Nos. US20070259410A1 and US 20070292927A1, and in PCT Publication WO 2007/130521, all of which are incorporated herein by reference. One 2-butanol biosynthetic pathway comprises the following substrate to product conversions:
In some embodiments, the 2-butanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, or at least four genes that is/are heterologous to the yeast cell.
Biosynthetic pathways for the production of isobutanol that may be used are described in U.S. Patent Application Publication No. US20070092957 A1 and PCT Publication WO 2007/050671, incorporated herein by reference. One isobutanol biosynthetic pathway comprises the following substrate to product conversions:
In some embodiments, the isobutanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, or at least four genes that is/are heterologous to the yeast cell.
Microbial hosts for butanol production may be selected from bacteria, cyanobacteria, filamentous fungi and yeasts. The microbial host used should be tolerant to the butanol product produced, so that the yield is not limited by toxicity of the product to the host. The selection of a microbial host for butanol production is described in detail below.
Microbes that are metabolically active at high titer levels of butanol are not well known in the art. Although butanol-tolerant mutants have been isolated from solventogenic Clostridia, little information is available concerning the butanol tolerance of other potentially useful bacterial strains. Most of the studies on the comparison of alcohol tolerance in bacteria suggest that butanol is more toxic than ethanol (de Cavalho et al., Microsc. Res. Tech. 64:215-22 (2004) and Kabelitz et al., FEMS Microbiol. Lett. 220:223-227 (2003)). Tomas et al. (J. Bacteriol. 186:2006-2018 (2004)) report that the yield of 1-butanol during fermentation in Clostridium acetobutylicum may be limited by butanol toxicity. The primary effect of 1-butanol on Clostridium acetobutylicum is disruption of membrane functions (Hermann et al., Appl. Environ. Microbiol. 50:1238-1243 (1985)).
The microbial hosts selected for the production of butanol should be tolerant to butanol and should be able to convert carbohydrates to butanol using the introduced biosynthetic pathway as described below. The criteria for selection of suitable microbial hosts include the following: intrinsic tolerance to butanol, high rate of carbohydrate utilization, availability of genetic tools for gene manipulation, and the ability to generate stable chromosomal alterations.
Suitable host strains with a tolerance for butanol may be identified by screening based on the intrinsic tolerance of the strain. The intrinsic tolerance of microbes to butanol may be measured by determining the concentration of butanol that is responsible for 50% inhibition of the growth rate (IC50) when grown in a minimal medium. The IC50 values may be determined using methods known in the art. For example, the microbes of interest may be grown in the presence of various amounts of butanol and the growth rate monitored by measuring the optical density at 600 nanometers. The doubling time may be calculated from the logarithmic part of the growth curve and used as a measure of the growth rate. The concentration of butanol that produces 50% inhibition of growth may be determined from a graph of the percent inhibition of growth versus the butanol concentration. Preferably, the host strain should have an IC50 for butanol of greater than about 0.5%. More suitable is a host strain with an IC50 for butanol that is greater than about 1.5%. Particularly suitable is a host strain with an IC50 for butanol that is greater than about 2.5%.
The microbial host for butanol production should also utilize glucose and/or other carbohydrates at a high rate. Most microbes are capable of utilizing carbohydrates. However, certain environmental microbes cannot efficiently use carbohydrates, and therefore would not be suitable hosts.
The ability to genetically modify the host is essential for the production of any recombinant microorganism. Modes of gene transfer technology that may be used include by electroporation, conjugation, transduction or natural transformation. A broad range of host conjugative plasmids and drug resistance markers are available. The cloning vectors used with an organism are tailored to the host organism based on the nature of antibiotic resistance markers that can function in that host.
The microbial host also may be manipulated in order to inactivate competing pathways for carbon flow by inactivating various genes. This requires the availability of either transposons or chromosomal integration vectors to direct inactivation. Additionally, production hosts that are amenable to chemical mutagenesis may undergo improvements in intrinsic butanol tolerance through chemical mutagenesis and mutant screening.
Based on the criteria described above, suitable microbial hosts for the production of butanol include, but are not limited to, members of the genera, Zymomonas, Escherichia, Salmonella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Pediococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Pichia, lssatchenkia, Candida, Hansenula and Saccharomyces. Preferred hosts include: Escherichia coli, Alcaligenes eutrophus, Bacillus licheniformis, Paenibacillus macerans, Rhodococcus erythropolis, Pseudomonas putida, Lactobacillus plantarum, Enterococcus faecium, Enterococcus gallinarium, Enterococcus faecalis, Pediococcus pentosaceus, Pediococcus acidilactici, Bacillus subtilis and Saccharomyces cerevisiae.
Microorganisms mentioned above may be genetically modified to convert fermentable carbon sources into butanol, specifically 1-butanol, 2-butanol, or isobutanol, using methods known in the art. Particularly suitable microorganisms include Escherichia, Lactobacillus, and Saccharomyces, where E. coli, L. plantarum and S. cerevisiae are particularly preferred. Additionally, the microorganism may be a butanol-tolerant strain of one of the microorganisms listed above that is isolated using the method described by Bramucci et al. (U.S. patent application Ser. No. 11/761497; and WO 2007/146377). An example of one such strain is Lactobacillus plantarum strain PN0512 (ATCC: PTA-7727, biological deposit made Jul. 12, 2006 for U.S. patent application Ser. No. 11/761497).
The microorganism genetically modified to be capable of converting fermentable carbon sources into butanol may be a recombinant Escherichia coli strain that comprises an isobutanol biosynthetic pathway and deletions of the following genes to eliminate competing pathways that limit isobutanol production, pflB, given as SEQ ID No:23, (encoding for pyruvate formate lyase) IdhA, given as SEQ IS NO:24, (encoding for lactate dehydrogenase), adhE, given as SEQ IS NO:25, (encoding for alcohol dehydrogenase), and at least one gene comprising the frdABCD operon (encoding for fumarate reductase), specifically, frdA, given as SEQ ID NO:26, frdB, given as SEQ ID NO:27, frdC, given as SEQ ID NO:28, and frdD, given as SEQ ID NO:29.
The Escherichia coli strain may comprise: (a) an isobutanol biosynthetic pathway encoded by the following genes: budB (given as SEQ ID NO:1) from Klebsiella pneumoniae encoding acetolactate synthase (given as SEQ ID NO:2), ilvC (given as SEQ ID NO:3) from E. coli encoding acetohydroxy acid reductoisomerase (given as SEQ ID NO:4), ilvD (given as SEQ ID NO:5) from E. coli encoding acetohydroxy acid dehydratase (given as SEQ iD NO:6), kivD (given as SEQ ID NO:7) from Lactococcus lactis encoding the branched-chain keto acid decarboxylase (given as SEQ ID NO:8), and sadB (given as SEQ ID NO:9) from Achromobacter xylosoxidans encoding a butanol dehydrogenase (given as SEQ ID NO:10); and (b) deletions of the following genes: pflB (SEQ ID NO:23), IdhA (SEQ ID NO:24) adhE (SEQ ID NO:25), and frdB (SEQ ID NO:27). The enzymes encoded by the genes of the isobutanol biosynthetic pathway catalyze the substrate to product conversions for converting pyruvate to isobutanol, as described above. Specifically, acetolactate synthase catalyzes the conversion of pyruvate to acetolactate, acetohydroxy acid reductoisomerase catalyzes the conversion of acetolactate to 2,3-dihydroxyisovalerate, acetohydroxy acid dehydratase catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate, branched-chain keto acid decarboxylase catalyzes the conversion of α-ketoisovalerate to isobutyraldehyde, and butanol dehydrogenase catalyzes the conversion of isobutyraldehyde to isobutanol. This recombinant Escherichia coli strain can be constructed using methods known in the art (see US Patent Application Publication Nos. 20090305370 A1 and 20090305369 A1) described herein below.
Construction of Recombinant Escherichia coli Strain NGCI-031
A recombinant Escherichia coli strain comprising an isobutanol biosynthetic pathway and deletions of the following genes, pflB (SEQ ID NO:23, encoding for pyruvate formate lyase), IdhA (SEQ ID NO:24, encoding for lactate dehydrogenase), adhE (SEQ ID NO:25, encoding for alcohol dehydrogenase), and frdB (SEQ ID NO:27, encoding a subunit of fumarate reductase), may be constructed as described below. The genes in the isobutanol biosynthetic pathway are budB from Klebsiella pneumoniae (given as SEQ ID NO:1), ilvC from Escherichia coli (given as SEQ ID NO:3), ilvD from Escherichia coli (given as SEQ ID NO:5), kivD from Lactococcus lactis (given as SEQ ID NO:7), and sadB from Achromobacter xylosoxidans (given as SEQ ID NO:9). The construction of the recombinant strain may be done in two steps. First, an Escherichia coli strain having the aforementioned gene deletions is constructed. Then, the genes encoding the isobutanol biosynthetic pathway are introduced into the strain.
Construction of Recombinant Escherichia coli Strain having Deletions of pflB, IdhA, adhE and frdB Genes
The Keio collection of E. coli strains (Baba et al., Mol. Syst. Biol., 2:1-11, 2006) may be used for the production of the E. coli strain having the intended gene deletions, which is referred to herein as the four-knock out E. coli strain. The Keio collection is a library of single gene knockouts created in strain E. coli BW25113 by the method of Datsenko and Wanner (Datsenko, K. A. & Wanner, B. L., Proc. Natl. Acad. Sci., U.S.A. 97 6640-6645, 2000). In the collection, each deleted gene is replaced with a FRT-flanked kanamycin marker that is removable by Flp recombinase. The four-knock out E. coli strain is constructed by moving the knockout-kanamycin marker from the Keio donor strain by P1 transduction to a recipient strain. After each P1 transduction to produce a knockout, the kanamycin marker is removed by Flp recombinase. This markerless strain acts as the new donor strain for the next P1 transduction.
The four-knock out E. coli strain may be constructed in Keio strain JW0886 by P1vir transductions with P1 phage lysates prepared from three Keio strains in addition to JW0886. The Keio strains to be used are listed below:
P1vir transductions may be carried out as described by Miller with some modifications (Miller, J. H. 1992. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y). Briefly, to prepare a transducing lysate, cells of the donor strain are grown overnight in Luria-Bertani (LB) medium at 37° C. while shaking. An overnight growth of these cells is sub-cultured into LB medium containing 0.005 M CaCl2 and placed in a 37° C. water bath with no aeration. One hour prior to adding phage, the cells are incubated at 37° C. with shaking. After final growth of the cells, a 1.0 mL aliquot of the culture is dispensed into 14-mL tubes and approximately 107 P1vir phage is added. The tubes are incubated in a 37° C. water bath for 20 min, after which 2.5 mL of 0.8% LB top agar is added to each tube. The contents of the tubes are spread on an LB agar plate and are incubated at 37° C. The following day the soft agar layer is scraped into a centrifuge tube. The surface of the plate is washed with LB medium and added to the centrifuge tube, followed by a few drops of CHCl3 and then the tube is vigorously agitated using a vortex mixer. After centrifugation at 4,000 rpm for 10 min, the supernatant containing the P1vir lysate is collected.
For transduction, the recipient strain is grown overnight in 1-2 mL of LB medium at 37° C. with shaking. Cultures are pelleted by centrifugation in a microcentrifuge, for example at 10,000 rpm for 1 min at room temperature. The cell pellet is resuspended in an equal volume of MC buffer (0.1 M MgSO4, 0.005 M CaCl2), dispensed into tubes in 0.1 mL aliquots and 0.1 mL and 0.01 mL of P1vir lysate is added. A control tube containing no P1vir lysate may also be included. The tubes are incubated for 20 min at 37° C. after which time, 0.2 mL of 0.1 M sodium citrate is added to stop the P1 infection. One mL of LB medium is added to each tube before the tubes are incubated at 37° C. for 1 h. After incubation the cells are pelleted as described above, resuspended in 50-200 μL of LB prior to spreading on the LB plates containing 25 μg/mL of kanamycin and incubated overnight at 37° C. Transductants can be screened by colony PCR with chromosome specific primers flanking the region upstream and downstream of the kanamycin marker insertion.
Removal of the kanamycin marker from the chromosome may be obtained by transforming the kanamycin-resistant strain with plasmid pCP20 (Cherepanov, P. P. and Wackernagel, W., Gene, 158: 9-14, 1995) followed by spreading onto LB ampicillin (100 μg/mL) plates and incubating at 30° C. The pCP20 plasmid carries the yeast FLP recombinase under the control of the λPR promoter. Expression from this promoter is controlled by the cl857 temperature-sensitive repressor residing on the plasmid. The origin of replication of pCP20 is also temperature sensitive. Ampicillin resistant colonies are streaked onto LB agar plates and incubated at 42° C. The higher incubation temperature simultaneously induces expression of the FLP recombinase and cures the pCP20 plasmid from the cell. Isolated colonies are patched to grids onto the LB plates containing kanamycin (25 μg/mL), and LB ampicillin (100 μg/mL) plates and LB plates. The resulting kanamycin-sensitive, ampicillin-sensitive colonies may be screened by colony PCR to confirm removal of the kanamycin marker from the chromosome.
For colony PCR amplifications the HotStarTaq Master Mix (Qiagen, Valencia, Calif.; catalog no. 71805-3) may be used according to the manufacturer's protocol. Into a 25 μL Master Mix reaction containing 0.2 μM of each chromosome specific PCR primer, a small amount of a colony is added. Amplification can be carried out in a DNA Thermocycler GeneAmp 9700 (PE Applied Biosystems, Foster City, Calif.). Typical colony PCR conditions are: 15 min at 95° C.; 30 cycles of 95° C. for 30 sec, annealing temperature ranging from 50-58° C. for 30 sec, primers extended at 72° C. with an extension time of approximately 1 min/kb of DNA; then 10 min at 72° C. followed by a hold at 4° C. PCR product sizes can be determined by gel electrophoresis by comparison with known molecular weight standards.
For transformations, electrocompetent cells of E. coli may be prepared as described by Ausubel, F. M., et al., (Current Protocols in Molecular Biology, 1987, Wiley-Interscience,). Cells are grown in 25-50 mL of LB medium at 30-37° C. and may be harvested at an OD600 of 0.5-0.7 by centrifugation at 10,000 rpm for 10 min. These cells are washed twice in sterile ice-cold water in a volume equal to the original starting volume of the culture. After the final wash cells are resuspended in sterile water and the DNA to be transformed is added. The cells and DNA are transferred to chilled cuvettes and electroporated in a Bio-Rad Gene Pulser II according to manufacturer's instructions (Bio-Rad Laboratories, Inc Hercules, Calif.).
Strain JW0886 (ΔpflB::kan) is transformed with plasmid pCP20 and spread on LB plates containing 100 μg/mL of ampicillin at 30° C. Ampicillin resistant transformants are then selected, streaked on LB plates and grown at 42° C. Isolated colonies are patched onto the ampicillin and kanamycin selective medium plates and LB plates. Kanamycin-sensitive and ampicillin-sensitive colonies may be screened by colony PCR with primers pflB CkUp (SEQ ID NO:11) and pflB CkDn (SEQ ID NO:12). A 10 μL aliquot of the PCR reaction mix may be analyzed by gel electrophoresis. The expected approximate 0.4 kb PCR product is observed confirming removal of the marker and creating the “JW0886 markerless” strain. This strain has a deletion of the pflB gene.
The “JW0886 markerless” strain is transduced with a P1vir lysate from JW4114 (frdB::kan) and streaked onto the LB plates containing 25 μg/mL of kanamycin. The kanamycin-resistant transductants are screened by colony PCR with primers frdB CkUp (SEQ ID NO:13) and frdB CkDn (SEQ ID NO: 14). Colonies that produce the expected approximate 1.6 kb PCR product are made electrocompetent, as described above, and transformed with pCP20 for marker removal as described above. Transformants are first spread onto LB plates containing 100 μg/mL of ampicillin at 30° C. and ampicillin resistant transformants are then selected and streaked on LB plates and grown at 42° C. Isolated colonies are patched onto ampicillin and the kanamycin selective medium plates and LB plates. Kanamycin-sensitive, ampicillin-sensitive colonies may be screened by PCR with primers frdB CkUp (SEQ ID NO:13) and frdB CkDn (SEQ ID NO: 14). The expected approximate 0.4 kb PCR product may be observed confirming marker removal and creating the double knockout strain, “ΔpflB frdB”.
The double knockout strain is transduced with a P1vir lysate from JW1375 (ΔIdhA::kan) and spread onto the LB plates containing 25 μg/mL of kanamycin. The kanamycin-resistant transductants are screened by colony PCR with primers IdhA CkUp (SEQ ID NO:15) and IdhA CkDn (SEQ ID NO:16). Clones producing the expected 1.1 kb PCR product are made electrocompetent and transformed with pCP20 for marker removal as described above. Transformants are spread onto LB plates containing 100 μg/mL of ampicillin at 30° C. and ampicillin resistant transformants are streaked on LB plates and grown at 42° C. Isolated colonies are patched onto ampicillin and kanamycin selective medium plates and LB plates. Kanamycin-sensitive, ampicillin-sensitive colonies are screened by PCR with primers IdhA CkUp (SEQ ID NO:15) and IdhA CkDn (SEQ ID NO:16) for a 0.3 kb product. Clones that produce the expected approximate 0.3 kb PCR product confirm marker removal and create the triple knockout strain designated the “three-knock out strain” (ΔpflB frdB IdhA).
The “three-knock out strain” is transduced with a P1vir lysate from JW1228 (ΔadhE::kan) and spread onto the LB plates containing 25 μg/mL kanamycin. The kanamycin-resistant transductants are screened by colony PCR with primers adhE CkUp (SEQ ID NO: 17) and adhE CkDn (SEQ ID NO:18). Clones that produce the expected 1.6 kb PCR product are made electrocompetent and transformed with pCP20 for marker removal. Transformants are spread onto LB plates containing 100 μg/mL of ampicillin at 30° C. Ampicillin resistant transformants are streaked on LB plates and grown at 42° C. Isolated colonies are patched onto ampicillin and kanamycin selective plates and LB plates. Kanamycin-sensitive, ampicillin-sensitive colonies may be screened by PCR with the primers adhE CkUp (SEQ ID NO: 17) and adhE CkDn (SEQ ID NO:18). Clones that produce the expected approximate 0.4 kb PCR product are named the “four-knock out strain” (ΔpflB frdB IdhA adhE).
Introduction of the Set of Genes Encoding an Isobutanol Biosynthetic Pathway into the Four-Knock Out E. coli Strain.
The plasmid pTrc99A::budB-ilvC-ilvD-kivD may be constructed as described in Examples 9-14 of U.S. Patent Application Publication No. 2007/0092957, which are incorporated herein by reference. This plasmid comprises the following genes, budB encoding acetolactate synthase from Klebsiella pneumoniae (SEQ ID NO:1), ilvC gene encoding acetohydroxy acid reductoisomerase from E. coli (SEQ ID NO:3), ilvD encoding acetohydroxy acid dehydratase from E. coli (SEQ ID NO:5), and kivD encoding the branched-chain keto acid decarboxylase from Lactococcus lactis (SEQ ID NO:7). The sadB gene from Achromobacter xylosoxidans encoding a butanol dehydrogenase (SEQ ID NO:9) is subcloned into the pTrc99A::budB-ilvC-ilvD-kivD plasmid as described below.
A DNA fragment encoding a butanol dehydrogenase (DNA: SEQ ID NO:9; protein: SEQ ID NO:10) from Achromobacter xylosoxidans (disclosed in US Patent Application Publication No. 20090269823) is amplified from A. xylosoxidans genomic DNA using standard conditions. The DNA may be prepared using a Gentra Puregene kit (Gentra Systems, Inc., Minneapolis, Minn.; catalog number D-5500A) following the recommended protocol for gram negative organisms. PCR amplification may be done using forward and reverse primers N473 and N469 (SEQ ID NOs:19 and 20, respectively) with Phusion high Fidelity DNA Polymerase (New England Biolabs, Beverly, Mass.). The PCR product may be TOPO-Blunt cloned into pCR4 BLUNT (Invitrogen) to produce pCR4Blunt::sadB, which is transformed into E. coli Mach-1 cells. Plasmid is subsequently isolated from four clones, and the sequence verified.
The sadB coding region is then cloned into the vector pTrc99a (Amann et al., Gene 69: 301-315, 1988). The pCR4Blunt::sadB is digested with EcoRI, releasing the sadB fragment, which is ligated with EcoRI-digested pTrc99a to generate pTrc99a::sadB. This plasmid is transformed into E. coli Mach 1 cells and the resulting transformant is named Mach1/pTrc99a::sadB. The activity of the enzyme expressed from the sadB gene in these cells may be determined to be 3.5 mmol/min/mg protein in cell-free extracts when analyzed using isobutyraldehyde as the standard.
Then, the sadB gene is subcloned into pTrc99A::budB-ilvC-ilvD-kivD as follows. The sadB coding region is amplified from pTrc99a::sadB using primers N695A (SEQ ID NO:21) and N696A (SEQ ID NO:22) with Phusion High Fidelity DNA Polymerase (New England Biolabs, Beverly, Mass.). Amplification is carried out with an initial denaturation at 98° C. for 1 min, followed by 30 cycles of denaturation at 98° C. for 10 sec, annealing at 62° C. for 30 sec, elongation at 72° C. for 20 sec and a final elongation cycle at 72° C. for 5 min, followed by a 4° C. hold. Primer N695A contains an AvrII restriction site for cloning and a RBS (ribosomal binding site) upstream of the ATG start codon of the sadB coding region. The N696A primer includes an XbaI site for cloning. The 1.1 kb PCR product is digested with AvrII and XbaI (New England Biolabs, Beverly, Mass.) and gel purified using a Qiaquick Gel Extraction Kit (Qiagen Inc., Valencia, Calif.)). The purified fragment is ligated with pTrc99A::budB-ilvC-ilvD-kivD, that has been cut with the same restriction enzymes, using T4 DNA ligase (New England Biolabs, Beverly, Mass.). The ligation mixture is incubated at 16° C. overnight and then transformed into E. coli Mach 1™ competent cells (Invitrogen) according to the manufacturer's protocol. Transformants are obtained following growth on LB agar with 100 μg/ml of ampicillin. Plasmid DNA from the transformants is prepared with QIAprep Spin Miniprep Kit (Qiagen Inc., Valencia, Calif.) according to manufacturer's protocols. The resulting plasmid is called pTrc99A::budB-ilvC-ilvD-kivD-sadB. Electrocompetent four-knock out E. coli cells, prepared as described above, are transformed with pTrc99A::budB-ilvC-ilvD-kivD-sadB. Transformants are streaked onto LB agar plates containing 100 μg/mL of ampicillin. The resulting recombinant E. coli strain comprises an isobutanol biosynthetic pathway, encoded by plasmid pTrc99A::budB-ilvC-ilvD-kivD-sadB, and deletions of pflB, frdB, IdhA, and adhE genes and is designated as strain NGCI-031.
The microorganism genetically modified to be capable of converting fermentable carbon sources into butanol may be a recombinant Saccharomyces cerevisiae strain that comprises an isobutanol biosynthetic pathway. A suitable Saccharomyces cerevisiae strain may comprise: an isobutanol biosynthetic pathway encoded by the following genes: alsS coding region from Bacillus subtilis (SEQ ID NO:32) encoding acetolactate synthase (SEQ ID NO:33), ILV5 from S. cerevisiae (SEQ ID NO:40) encoding acetohydroxy acid reductoisomerase (KARI; SEQ ID NO:41) and/or a mutant KARI such as encoded by Pf5.IIvC-Z4B8 (SEQ ID NO:36; protein SEQ ID NO:37), ilvD from Streptococcus mutans (SEQ ID NO:58) encoding acetohydroxy acid dehydratase (SEQ ID NO:59), kivD from Bacillus subtilis (SEQ ID NO:43) encoding the branched-chain keto acid decarboxylase (SEQ ID NO:44), and sadB from Achromobacter xylosoxidans (SEQ ID NO:9) encoding a butanol dehydrogenase (SEQ ID NO:10). The enzymes encoded by the genes of the isobutanol biosynthetic pathway catalyze the substrate to product conversions for converting pyruvate to isobutanol, as described herein.
A recombinant Saccharomyces cerevisiae strain can be constructed using methods known in the art. A suitable yeast strain expressing an isobutanol pathway has acetolactate synthase (ALS) activity in the cytosol and has deletions of the endogenous pyruvate decarboxylase (PDC) genes as described in US Patent Application Publication No. 20090305363, which is herein incorporated by reference.
A suitable strain may be constructed as described herein below.
NGI-049 is a Saccharomyces cerevisiae strain with insertion-inactivation of endogenous PDC1, PDC5, and PDC6 genes, and containing expression vectors pLH475-Z4B8 and pLH468. PDC1, PDC5, and PDC6 genes encode the three major isozymes of pyruvate decarboxylase. The strain expresses genes encoding enzymes for an isobutanol biosynthetic pathway that are integrated or on plasmids.
Expression Vector pLH475-Z4B8
The pLH475-Z4B8 plasmid (SEQ ID NO:30) may be constructed for expression of ALS and KARI in yeast. pLH475-Z4B8 is a pHR81 vector (ATCC #87541) containing the following chimeric genes:
The Pf5.IIvC-Z4B8 coding region is a sequence encoding KARI derived from Pseudomonas fluorescens but containing mutations, that is described in U.S. patent application Ser. No. 12/337,736, which is herein incorporated by reference. The Pf5.IIvC-Z4B8 encoded KARI (SEQ ID NO:37;) has the following amino acid changes as compared to the natural Pseudomonas fluorescens KARI:
The Pf5.IIvC-Z4B8 coding region may be synthesized by DNA 2.0 (Palo Alto, Calif.; SEQ ID NO:6) based on codons that are optimized for expression in Saccharomyces cerevisiae.
Expression Vector pLH468
The pLH468 plasmid (SEQ ID NO:42) is constructed for expression of DHAD, KivD and HADH in yeast.
Coding regions for B. subtilis ketoisovalerate decarboxylase (KivD) and Horse liver alcohol dehydrogenase (HADH) are synthesized by DNA2.0 based on codons that are optimized for expression in Saccharomyces cerevisiae (SEQ ID NO:43 and 45, respectively) and provided in plasmids pKivDy-DNA2.0 and pHadhy-DNA2.0. The encoded proteins are SEQ ID NOs:44 and 46, respectively. Individual expression vectors for KivD and HADH are constructed. To assemble pLH467 (pRS426::PGPD1-kivDy-GPD1t), vector pNY8 (SEQ ID NO:47; also named pRS426.GPD-ald-GPDt, described in US Patent App. Pub. US2008/0182308, Example 17, which is herein incorporated by reference) is digested with AscI and SfiI enzymes, thus excising the GPD1 promoter and the aid coding region. A GPD1 promoter fragment (SEQ ID NO:48) from pNY8 is PCR amplified to add an AscI site at the 5′ end, and an SpeI site at the 3′ end, using 5′ primer OT1068 and 3′ primer OT1067 (SEQ ID NOs:49 and 50). The AscI/SfiI digested pNY8 vector fragment is ligated with the GPD1 promoter PCR product digested with AscI and SpeI, and the SpeI-SfiI fragment containing the codon optimized kivD coding region isolated from the vector pKivD-DNA2.0. The triple ligation generated vector pLH467 (pRS426::PGPD1-kivDy-GPD1t). pLH467 may be verified by restriction mapping and sequencing.
pLH435 (pRS425::PGPM1-Hadhy-ADH1t) is derived from vector pRS425::GPM-sadB (SEQ ID NO:51) which is described in US Patent Application Publication No. 20090305363 A1, Example 3, which is herein incorporated by reference. pRS425::GPM-sadB is the pRS425 vector (ATCC #77106) with a chimeric gene containing the GPM1 promoter (SEQ ID NO:52), coding region from a butanol dehydrogenase of Achromobacter xylosoxidans (sadB; SEQ ID NO:9; protein SEQ ID NO:10: disclosed in US Patent App. Publication #20090269823 A1), and ADH1 terminator (SEQ ID NO:53). pRS425::GPMp-sadB contains BbvI and PacI sites at the 5′ and 3′ ends of the sadB coding region, respectively. A NheI site is added at the 5′ end of the sadB coding region by site-directed mutagenesis using primers OT1074 and OT1075 (SEQ ID NO:54 and 55) to generate vector pRS425-GPMp-sadB-NheI, which may be verified by sequencing. pRS425::PGPM1-sadB-NheI is digested with NheI and PacI to drop out the sadB coding region, and ligated with the NheI-PacI fragment containing the codon optimized HADH coding region from vector pHadhy-DNA2.0 to create pLH435.
To combine KivD and HADH expression cassettes in a single vector, yeast vector pRS411 (ATCC #87474) is digested with SacI and NotI, and ligated with the SacI-SalI fragment from pLH467 that contains the PGPD1-kivDy-GPD1t cassette together with the SalI-NotI fragment from pLH435 that contains the PGPM1-Hadhy-ADH1t cassette in a triple ligation reaction. This yields the vector pRS411::PGPD1-kivDy-PGPM1-Hadhy (pLH441), which may be verified by restriction mapping.
In order to generate a co-expression vector for all three genes in the lower isobutanol pathway: ilvD, kivDy and Hadhy, pRS423 FBA ilvD(Strep) (SEQ ID NO:56), which is described in PCT Publication WO/2010/037112 may be used as the source of the IlvD gene. This shuttle vector contains an F1 origin of replication (nt 1423 to 1879) for maintenance in E. coli and a 2 micron origin (nt 8082 to 9426) for replication in yeast. The vector has an FBA promoter (nt 2111 to 3108; SEQ ID NO:39) and FBA terminator (nt 4861 to 5860; SEQ ID NO:57). In addition, it carries the His marker (nt 504 to 1163) for selection in yeast and ampicillin resistance marker (nt 7092 to 7949) for selection in E. coli. The ilvD coding region (nt 3116 to 4828; SEQ ID NO:58; protein SEQ ID NO:59) from Streptococcus mutans UA159 (ATCC #700610) is between the FBA promoter and FBA terminator forming a chimeric gene for expression. In addition there is a lumio tag fused to the ilvD coding region (nt 4829-4849).
The first step is to linearize pRS423 FBA ilvD(Strep) (also called pRS423-FBA(SpeI)-IlvD(Streptococcus mutans)-Lumio) with SacI and SacII (with SacII site blunt ended using T4 DNA polymerase), to give a vector with total length of 9,482 bp. The second step is to isolate the kivDy-hADHy cassette from pLH441 with SacI and KpnI (with KpnI site blunt ended using T4 DNA polymerase), to give a 6,063 by fragment. This fragment is ligated with the 9,482 by vector fragment from pRS423-FBA(SpeI)-IlvD(Streptococcus mutans)-Lumio. This generates vector pLH468 (pRS423::PFBA1-ilvD(Strep)Lumio-FBA1t-PGPD1-kivDy-GPD1t-PGPM1-hadhy-ADH1t), which may be confirmed by restriction mapping and sequencing.
Construction of pdc6::GPMp1-sadB Integration Cassette and PDC6 Deletion:
A pdc6::GPM1p-sadB-ADH1t-URA3r integration cassette is made by joining the GPM-sadB-ADHt segment (SEQ ID NO:60) from pRS425::GPM-sadB (described above) to the URA3r gene from pUC19-URA3r . pUC19-URA3r (SEQ ID NO:61) contains the URA3 marker from pRS426 (ATCC #77107) flanked by 75 by homologous repeat sequences to allow homologous recombination in vivo and removal of the URA3 marker. The two DNA segments are joined by SOE PCR (as described by Horton et al. (1989) Gene 77:61-68) using as template pRS425::GPM-sadB and pUC19-URA3r plasmid DNAs, with Phusion DNA polymerase (New England Biolabs Inc., Beverly, Mass.; catalog no. F-5405) and primers 114117-11A through 114117-11D (SEQ ID NOs:62, 63, 64 and 65), and 114117-13A and 114117-13B (SEQ ID NOs:66 and 67).
The outer primers for the SOE PCR (114117-13A and 114117-13B) contain 5′ and 3′˜50 by regions homologous to regions upstream and downstream of the PDC6 promoter and terminator, respectively. The completed cassette PCR fragment is transformed into BY4700 (ATCC #200866) and transformants are maintained on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202). Transformants may be screened by PCR using primers 112590-34G and 112590-34H (SEQ ID NOs:68 and 69), and 112590-34F and 112590-49E (SEQ ID NOs:70 and 71) to verify integration at the PDC6 locus with deletion of the PDC6 coding region. The URA3r marker may be recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal may be confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth. The resulting identified strain has the genotype: BY4700 pdc6::PGPM1-sadB-ADH1t.
Construction of pdc1::PDC1-ilvD Integration Cassette and PDC1 Deletion:
A pdc1::PDC1p-ilvD-FBA1t-URA3r integration cassette is made by joining the ilvD-FBA1t segment (SEQ ID NO:72) from pLH468 (described above) to the URA3r gene from pUC19-URA3r by SOE PCR (as described by Horton et al. (1989) Gene 77:61-68) using as template pLH468 and pUC19-URA3r plasmid DNAs, with Phusion DNA polymerase (New England Biolabs Inc., Beverly, Mass.; catalog no. F-5405) and primers 114117-27A through 114117-27D (SEQ ID NOs:73, 74, 75 and 76).
The outer primers for the SOE PCR (114117-27A and 114117-27D) contain 5′ and 3′˜50 by regions homologous to regions downstream of the PDC1 promoter and downstream of the PDC1 coding sequence. The completed cassette PCR fragment is transformed into BY4700 pdc6::PGPM1-sadB-ADH1t and transformants are maintained on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202). Transformants may be screened by PCR using primers 114117-36D and 135 (SEQ ID NOs:77 and 78), and primers 112590-49E and 112590-30F (SEQ ID NOs:70 and 79) to verify integration at the PDC1 locus with deletion of the PDC1 coding sequence. The URA3r marker may be recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal may be confirmed by patching colonies from the 5-FOA plates onto SD—URA media to verify the absence of growth. The resulting identified strain “NYLA67” has the genotype: BY4700 pdc6::GPM1p-sadB-ADH1t pdc1::PDC1p-ilvD-FBA1t.
To delete the endogenous HIS3 coding region, a his3::URA3r2 cassette is PCR-amplified from URA3r2 template DNA (SEQ ID NO:84). URA3r2 contains the URA3 marker from pRS426 (ATCC #77107) flanked by 500 by homologous repeat sequences to allow homologous recombination in vivo and removal of the URA3 marker. PCR is done using Phusion DNA polymerase and primers 114117-45A and 114117-45B (SEQ ID NOs:85 and 86) to generate a ˜2.3 kb PCR product. The HIS3 portion of each primer is derived from the 5′ region upstream of the HIS3 promoter and 3′ region downstream of the coding region such that integration of the URA3r2 marker results in replacement of the HIS3 coding region. The PCR product is transformed into NYLA67 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants are selected on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. Transformants may be screened to verify correct integration by replica plating of transformants onto synthetic complete media lacking histidine and supplemented with 2% glucose at 30° C. The URA3r marker may be recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal may be confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth. The resulting identified strain “NYLA73” has the genotype: BY4700 pdc6::GPM1p-sadB-ADH1t pdc1::PDC1p-ilvD-FBA1t Δhis3.
Construction of pdc5::kanMX Integration Cassette and PDC5 Deletion:
A pdc5::kanMX4 cassette is PCR-amplified from strain YLR134W chromosomal DNA (ATCC No. 4034091) using Phusion DNA polymerase and primers PDC5::KanMXF and PDC5::KanMXR (SEQ ID NOs:80 and 81) which generate a ˜2.2 kb PCR product. The PDC5 portion of each primer is derived from the 5′ region upstream of the PDC5 promoter and 3′ region downstream of the coding region such that integration of the kanMX4 marker results in replacement of the PDC5 coding region. The PCR product is transformed into NYLA73 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants are selected on YP media supplemented with 1% ethanol and geneticin (200 μg/ml) at 30° C. Transformants may be screened by PCR to verify correct integration at the PDC locus with replacement of the PDC5 coding region using primers PDC5kofor and N175 (SEQ ID NOs:82 and 83). The identified correct transformants have the genotype: BY4700 pdc6::GPM1p-sadB-ADH1t pdc1::PDC1p-ilvD-FBA1t Δhis3 pdc5::kanMX4.
Plasmid vectors pLH468 and pLH475-Z4B8 are simultaneously transformed into strain BY4700 pdc6::GPM1p-sadB-ADH1t pdc1::PDC1p-ilvD-FBA1t Δhis3 pdc5::kanMX4 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). and maintained on synthetic complete media lacking histidine and uracil, and supplemented with 1% ethanol at 30° C.
Extractant compositions useful in the methods described herein are water-immiscible and comprise a first solvent and a second solvent, both of which are water-immiscible. A suitable organic extractant composition should meet the criteria for an ideal solvent for a commercial two-phase extractive fermentation for the production or recovery of butanol. Specifically, the extractant composition should (i) be biocompatible with the microorganisms, for example Escherichia coli, Lactobacillus plantarum, and Saccharomyces cerevisiae, (ii) be substantially immiscible with the fermentation medium, (iii) have a high partition coefficient (KP) for the extraction of butanol, (iv) have a low partition coefficient for the extraction of nutrients, (v) have a low tendency to form emulsions with the fermentation medium, and (vi) be low cost and nonhazardous. In addition, for improved process operability and economics, the extractant should (vii) have low viscosity (μ), (viii) have a low density (ρ) relative to the aqueous fermentation medium, and (ix) have a boiling point suitable for downstream separation of the extractant and the butanol. The viscosity of the extractant influences the mass transfer properties of the system, for example the efficiency with which the butanol solute can be extracted from the bulk aqueous phase to the extractant phase. The density of the extractant affects how quickly and cleanly phase separation occurs. The boiling point can affect the cost and method of butanol recovery. For example, in the case where the butanol is recovered from the extractant phase by distillation, the boiling point of the extractant should be sufficiently low as to enable separation of the butanol while minimizing any thermal degradation or side reactions of the extractant, or the need for vacuum in the distillation process.
The extractant should be biocompatible with the microorganism, that is, nontoxic to the microorganism or toxic only to such an extent that the microorganism is impaired to an acceptable level, so that the microorganism continues to produce the butanol product into the fermentation medium. The extent of biocompatibility of an extractant can be determined by the glucose utilization rate of the microorganism in the presence of the extractant and the butanol product, as measured under defined fermentation conditions (see Examples). While a biocompatible extractant permits the microorganism to utilize glucose, a non-biocompatible extractant does not permit the microorganism to utilize glucose at a rate greater than, for example, about 25% of the rate when the extractant is not present. As the presence of the fermentation product butanol can affect the sensitivity of the microorganism to the extractant, the fermentation product should be present during biocompatibility testing of the extractant. The presence of additional fermentation products, for example ethanol, may similarly affect the biocompatibility of the extractant. It would be reasonable to expect that the biocompatibility of an extractant would be improved if fewer additional fermentation products were present during the extraction. By expressing the glucose utilization rates as percentages relative to that of a reference extractant, the biocompatibilities of different extractants in the presence of the butanol product can be compared.
The first and second solvents of which the extractant is comprised should be selected to maximize the desired properties of the extractant, as discussed above, in the presence of the butanol fermentation product. As demonstrated in the Examples, the use of an extractant comprising a longer carbon chain first solvent and a shorter carbon chain second solvent can provide benefits over the use of an extractant comprised of only the first solvent. The longer carbon chain first solvent may have the desirable characteristic of high biocompatibility but also the less desirable characteristics of a relatively low partition coefficient for butanol, a higher viscosity, and/or a higher boiling point. In contrast, the shorter carbon chain second solvent may have the less desirable characteristic of lower biocompatibility but also the more desirable characteristics of a relatively higher partition coefficient for butanol, a lower viscosity, and/or a lower boiling point. In particular, the appropriate combination of a first solvent and a second solvent as described herein may provide an extractant which has a sufficient partition coefficient for butanol and sufficient biocompatibility with the microorganism to enable its economical use for removing butanol from a fermentative process.
The first solvent is selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, C12 to C22 fatty amides, and mixtures thereof. Suitable first solvents are further selected from the group consisting of oleyl alcohol (CAS No. 143-28-2), behenyl alcohol (CAS No. 661-19-8), cetyl alcohol (CAS No. 36653-82-4), lauryl alcohol (CAS No. 112-53-8) also referred to as 1-dodecanol, myristyl alcohol (CAS No. 112-72-1), stearyl alcohol (CAS No. 112-92-5), oleic acid (CAS No. 112-80-1), lauric acid (CAS No. 143-07-7), myristic acid (CAS No. 544-63-8), stearic acid (CAS No. 57-11-4), methyl myristate (CAS No. 124-10-7), methyl oleate (CAS No. 112-62-9), lauric aldehyde (CAS No. 112-54-9), oleamide (CAS No. 301-02-0), linoleamide (CAS No. 3999-01-7), palmitamide (CAS No. 629-54-9) and stearylamide (CAS No. 124-26-5) and mixtures thereof. In one embodiment, the first solvent comprises oleyl alcohol.
The second solvent is selected from the group consisting of C7 to C11 fatty alcohols, C7 to C11 fatty carboxylic acids, esters of C7 to C11 fatty carboxylic acids, C7 to C11 fatty aldehydes, and mixtures thereof. In one embodiment, the second solvent may be selected from the group consisting of C7 to C10 fatty alcohols, C7 to C10 fatty carboxylic acids, esters of C7 to C10 fatty carboxylic acids, C7 to C10 fatty aldehydes, and mixtures thereof. Suitable second solvents are further selected from the group consisting of 1-nonanol (CAS No. 143-08-8), 1-decanol (CAS No. 112-30-1, 1-undecanol (CAS No. 112-42-5), 2-undecanol (CAS No. 1653-30-1), 1-nonanal (CAS No. 124-19-6), and mixtures thereof. In one embodiment, the second solvent is selected from the group consisting of 1-nonanol, 1-decanol, 1-nonanal, and mixtures thereof. In one embodiment, the second solvent comprises 1-decanol.
In one embodiment, the first solvent comprises oleyl alcohol and the second solvent comprises 1-decanol.
As used herein, the term “mixtures thereof” encompasses both mixtures within and mixtures between the group members, for example mixtures within C12 to C22 fatty alcohols, and also mixtures between C12 to C22 fatty alcohols and C12 to C22 fatty acids, for example.
The relative amounts of the first and second solvents which form the extractant can vary within a suitable range. In one embodiment, the extractant may contain about 30 percent to about 90 percent of the first solvent, based on the total volume of the first and second solvents. In one embodiment, the extractant may contain about 40 percent to about 80 percent first solvent. In one embodiment, the extractant may contain about 45 percent to about 75 percent first solvent. In another embodiment, the extractant may contain about 50 percent to about 70 percent first solvent. The optimal range reflects maximization of the extractant characteristics, for example balancing a relatively high partition coefficient for butanol with an acceptable level of biocompatibility. For a two-phase extractive fermentation for the production or recovery of butanol, the temperature, contacting time, butanol concentration in the fermentation medium, relative amounts of extractant and fermentation medium, specific first and second solvents used, relative amounts of the first and second solvents, presence of other organic solutes, and the amount and type of microorganism are related; thus these variables may be adjusted as necessary within appropriate limits to optimize the extraction process as described herein.
The first and second solvents may be available commercially from various sources, such as Sigma-Aldrich (St. Louis, Mo.), in various grades, many of which may be suitable for use in extractive fermentation to produce or recover butanol by the methods disclosed herein. Technical grades of a solvent can contain a mixture of compounds, including the desired component and higher and lower molecular weight components or isomers. For example, one commercially available technical grade oleyl alcohol contains about 65% oleyl alcohol and a mixture of higher and lower fatty alcohols.
The microorganism may be cultured in a suitable fermentation medium in a suitable fermentor to produce butanol. Any suitable fermentor may be used including a stirred tank fermentor, an airlift fermentor, a bubble fermentor, or any combination thereof. Materials and methods for the maintenance and growth of microbial cultures are well known to those skilled in the art of microbiology or fermentation science (see for example, Bailey et al., Biochemical Engineering Fundamentals, second edition, McGraw Hill, New York, 1986). Consideration must be given to appropriate fermentation medium, pH, temperature, and requirements for aerobic, microaerobic, or anaerobic conditions, depending on the specific requirements of the microorganism, the fermentation, and the process. The fermentation medium used is not critical, but it must support growth of the microorganism used and promote the biosynthetic pathway necessary to produce the desired butanol product. A conventional fermentation medium may be used, including, but not limited to, complex media containing organic nitrogen sources such as yeast extract or peptone and at least one fermentable carbon source; minimal media; and defined media. Suitable fermentable carbon sources include, but are not limited to, monosaccharides, such as glucose or fructose; disaccharides, such as lactose or sucrose; oligosaccharides; polysaccharides, such as starch or cellulose; one carbon substrates; and mixtures thereof. In addition to the appropriate carbon source, the fermentation medium may contain a suitable nitrogen source, such as an ammonium salt, yeast extract or peptone, minerals, salts, cofactors, buffers and other components, known to those skilled in the art (Bailey et al., supra). Suitable conditions for the extractive fermentation depend on the particular microorganism used and may be readily determined by one skilled in the art using routine experimentation.
Butanol may be recovered from a fermentation medium containing butanol, water, at least one fermentable carbon source, and a microorganism that has been genetically modified (that is, genetically engineered) to produce butanol via a biosynthetic pathway from at least one carbon source. Such genetically modified microorganisms can be selected from the group consisting of Escherichia coli, Lactobacillus plantarum, and Saccharomyces cerevisiae. The first step in the process is contacting the fermentation medium with a water immiscible organic extractant composition comprising a first solvent and a second solvent, as described above, to form a two-phase mixture comprising an aqueous phase and a butanol-containing organic phase. “Contacting” means the fermentation medium and the organic extractant composition or its solvent components are brought into physical contact at any time during the fermentation process. In one embodiment, the fermentation medium further comprises ethanol, and the butanol-containing organic phase can contain ethanol.
The contacting may be performed with the first and second solvents of the extractant composition having been previously combined. For example, the first and second solvents may be combined in a vessel such as a mixing tank to form the extractant, which is then added to a vessel containing the fermentation medium. Alternatively, the contacting may be performed with the first and second solvents becoming combined during the contacting. For example, the first and second solvents may be added separately to a vessel which contains the fermentation medium. In one embodiment, contacting the fermentation medium with the organic extractant composition further comprises contacting the fermentation medium with the first solvent prior to contacting the fermentation medium and the first solvent with the second solvent. In one embodiment, the contacting with the second solvent occurs in the same vessel as the contacting with the first solvent. In one embodiment, the contacting with the second solvent occurs in a different vessel from the contacting with the first solvent. For example, the first solvent may be contacted with the fermentation medium in one vessel, and the contents transferred to another vessel in which contacting with the second solvent occurs.
The organic extractant composition may contact the fermentation medium at the start of the fermentation forming a biphasic fermentation medium. Alternatively, the organic extractant composition may contact the fermentation medium after the microorganism has achieved a desired amount of growth, which can be determined by measuring the optical density of the culture. In one embodiment, the first solvent of the extractant composition may contact the fermentation medium in one vessel, and the second solvent of the extractant composition may contact the fermentation medium and the first solvent in the same vessel. In another embodiment, the second solvent of the extractant composition may contact the fermentation medium and the first solvent in a different vessel from that in which the first solvent contacts the fermentation medium.
Further, the organic extractant composition may contact the fermentation medium at a time at which the butanol level in the fermentation medium reaches a preselected level, for example, before the butanol concentration reaches a toxic level. The butanol concentration may be monitored during the fermentation using methods known in the art, such as by gas chromatography or high performance liquid chromatography.
Fermentation may be run under aerobic conditions for a time sufficient for the culture to achieve a preselected level of growth, as determined by optical density measurement. An inducer may then be added to induce the expression of the butanol biosynthetic pathway in the modified microorganism, and fermentation conditions are switched to microaerobic or anaerobic conditions to stimulate butanol production, as described in detail in Example 6 of US Patent Application Publication No. 2009-0305370 A1. The extractant is added after the switch to microaerobic or anaerobic conditions. In one embodiment, the first solvent of the extractant may contact the fermentation medium prior to the contacting of the fermentation medium and the first solvent with the second solvent. For example, in a batch fermentation process, a suitable period of time may be allowed to elapse between contacting the fermentation medium with the first and the second solvents. In a continuous fermentation process, contacting the fermentation medium with the first solvent may occur in one vessel, and contacting of that vessel's contents with the second solvent may occur in a second vessel.
Through contacting the fermentation medium with the organic extractant, the butanol product partitions into the organic extractant, decreasing the concentration in the aqueous phase containing the microorganism, thereby limiting the exposure of the production microorganism to the inhibitory butanol product. The volume of the organic extractant to be used depends on a number of factors, including the volume of the fermentation medium, the size of the fermentor, the partition coefficient of the extractant for the butanol product, and the fermentation mode chosen, as described below. The volume of the organic extractant may be about 3% to about 60% of the fermentor working volume. The ratio of the extractant to the fermentation medium is from about 1:20 to about 20:1 on a volume:volume basis, for example from about 1:15 to about 15:1, or from about 1:12 to about 12:1, or from about 1:10 to about 10:1, or from about 1:9 to about 9:1, or from about 1:8 to about 8:1.
The next step is separating the butanol-containing organic phase from the aqueous phase using methods known in the art, including but not limited to, siphoning, decantation, centrifugation, using a gravity settler, membrane-assisted phase splitting, and the like. Recovery of the butanol from the butanol-containing organic phase can be done using methods known in the art, including but not limited to, distillation, adsorption by resins, separation by molecular sieves, pervaporation, and the like. Specifically, distillation may be used to recover the butanol from the butanol-containing organic phase. Optionally, the first and second solvents of the extractant may be separated from each other. The extractant or the solvents may be recycled to the butanol production and/or recovery process.
Gas stripping may be used concurrently with the solvents of the organic extractant composition to remove the butanol product from the fermentation medium. Gas stripping may be done by passing a gas such as air, nitrogen, or carbon dioxide through the fermentation medium, thereby forming a butanol-containing gas phase. The butanol product may be recovered from the butanol-containing gas phase using methods known in the art, such as using a chilled water trap to condense the butanol, or scrubbing the gas phase with a solvent.
Any butanol remaining in the fermentation medium after the fermentation run is completed may be recovered by continued extraction using fresh or recycled organic extractant. Alternatively, the butanol can be recovered from the fermentation medium using methods known in the art, such as distillation, azeotropic distillation, liquid-liquid extraction, adsorption, gas stripping, membrane evaporation, pervaporation, and the like.
The two-phase extractive fermentation method may be carried out in a continuous mode in a stirred tank fermentor. In this mode, the mixture of the fermentation medium and the butanol-containing organic extractant composition is removed from the fermentor. The two phases are separated by means known in the art including, but not limited to, siphoning, decantation, centrifugation, using a gravity settler, membrane-assisted phase splitting, and the like, as described above. After separation, the fermentation medium may be recycled to the fermentor or may be replaced with fresh medium. Then, the extractant is treated to recover the butanol product as described above. The extractant may then be recycled back into the fermentor for further extraction of the product. Alternatively, fresh extractant may be continuously added to the fermentor to replace the removed extractant. This continuous mode of operation offers several advantages. Because the product is continually removed from the reactor, a smaller volume of organic extractant composition is required enabling a larger volume of the fermentation medium to be used. This results in higher production yields. The volume of the organic extractant composition may be about 3% to about 50% of the fermentor working volume; 3% to about 20% of the fermentor working volume; or 3% to about 10% of the fermentor working volume. It is beneficial to use the smallest amount of extractant in the fermentor as possible to maximize the volume of the aqueous phase, and therefore, the amount of cells in the fermentor. The process may be operated in an entirely continuous mode in which the extractant is continuously recycled between the fermentor and a separation apparatus and the fermentation medium is continuously removed from the fermentor and replenished with fresh medium. In this entirely continuous mode, the butanol product is not allowed to reach the critical toxic concentration and fresh nutrients are continuously provided so that the fermentation may be carried out for long periods of time. The apparatus that may be used to carryout these modes of two-phase extractive fermentations are well known in the art. Examples are described, for example, by Kollerup et al. in U.S. Pat. No. 4,865,973.
Batchwise fermentation mode may also be used. Batch fermentation, which is well known in the art, is a closed system in which the composition of the fermentation medium is set at the beginning of the fermentation and is not subjected to artificial alterations during the process. In this mode, a volume of organic extractant composition is added to the fermentor and the extractant is not removed during the process. The organic extractant composition may be formed in the fermentor by separate addition of the first and the second solvents, or the solvents may be combined to form the extractant composition prior to the addition of the extractant composition to the fermentor. Although this mode is simpler than the continuous or the entirely continuous modes described above, it requires a larger volume of organic extractant composition to minimize the concentration of the inhibitory butanol product in the fermentation medium. Consequently, the volume of the fermentation medium is less and the amount of product produced is less than that obtained using the continuous mode. The volume of the organic extractant composition in the batchwise mode may be 20% to about 60% of the fermentor working volume; or 30% to about 60% of the fermentor working volume. It is beneficial to use the smallest volume of extractant in the fermentor as possible, for the reason described above.
Fed-batch fermentation mode may also be used. Fed-batch fermentation is a variation of the standard batch system, in which the nutrients, for example glucose, are added in increments during the fermentation. The amount and the rate of addition of the nutrient may be determined by routine experimentation. For example, the concentration of critical nutrients in the fermentation medium may be monitored during the fermentation. Alternatively, more easily measured factors such as pH, dissolved oxygen, and the partial pressure of waste gases, such as carbon dioxide, may be monitored. From these measured parameters, the rate of nutrient addition may be determined. The amount of organic extractant composition used and its methods of addition in this mode is the same as that used in the batchwise mode, described above.
Extraction of the product may be done downstream of the fermentor, rather than in situ. In this external mode, the extraction of the butanol product into the organic extractant composition is carried out on the fermentation medium removed from the fermentor. The amount of organic solvent used is about 20% to about 60% of the fermentor working volume; or 30% to about 60% of the fermentor working volume. The fermentation medium may be removed from the fermentor continuously or periodically, and the extraction of the butanol product by the organic extractant composition may be done with or without the removal of the cells from the fermentation medium. The cells may be removed from the fermentation medium by means known in the art including, but not limited to, filtration or centrifugation. After separation of the fermentation medium from the extractant by means described above, the fermentation medium may be recycled into the fermentor, discarded, or treated for the removal of any remaining butanol product. Similarly, the isolated cells may also be recycled into the fermentor. After treatment to recover the butanol product, the extractant, the first solvent, and/or the second solvent may be recycled for use in the extraction process. Alternatively, fresh extractant may be used. In this mode the extractant is not present in the fermentor, so the toxicity of the extractant is much less of a problem. If the cells are separated from the fermentation medium before contacting with the extractant, the problem of extractant toxicity is further reduced. Furthermore, using this external mode there is less chance of forming an emulsion and evaporation of the extractant is minimized, alleviating environmental concerns.
Methods for Production of Butanol Using Extractive Fermentation with an Extractant Comprising a First Solvent and a Second Solvent
An improved method for the production of butanol is provided, wherein a microorganism that has been genetically modified to produce butanol via a biosynthetic pathway from at least one carbon source, is grown in a biphasic fermentation medium. Such genetically modified microorganisms can be selected from the group consisting of Escherichia coli, Lactobacillus plantarum, and Saccharomyces cerevisiae. The biphasic fermentation medium comprises an aqueous phase and a water immiscible organic extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, C12 to C22 fatty amides and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, and mixtures thereof, wherein the biphasic fermentation medium comprises from about 10% to about 90% by volume of the organic extractant composition. Alternatively, the biphasic fermentation medium may comprise from about 3% to about 60% by volume of the organic extractant composition, or from about 15% to about 50%. The microorganism is grown in the biphasic fermentation medium for a time sufficient to extract butanol into the extractant to form a butanol-containing organic phase. In one embodiment, the fermentation medium further comprises ethanol, and the butanol-containing organic phase can contain ethanol. The butanol-containing organic phase is then separated from the aqueous phase, as described above. Subsequently, the butanol is recovered from the butanol-containing organic phase, as described above.
Also provided is an improved method for the production of butanol wherein a microorganism that has been genetically modified to produce butanol via a biosynthetic pathway from at least one carbon source, is grown in a fermentation medium wherein the microorganism produces the butanol into the fermentation medium to produce a butanol-containing fermentation medium. Such genetically modified microorganisms can be selected from the group consisting of Escherichia coli, Lactobacillus plantarum, and Saccharomyces cerevisiae. At least a portion of the butanol-containing fermentation medium is contacted with a water immiscible organic extractant composition comprising a first solvent and a second solvent, the first solvent being selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, C12 to C22 fatty amides, and mixtures thereof, and the second solvent being selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, and mixtures thereof, to form a two-phase mixture comprising an aqueous phase and a butanol-containing organic phase. In one embodiment, the fermentation medium further comprises ethanol, and the butanol-containing organic phase can contain ethanol. The butanol-containing organic phase is then separated from the aqueous phase, as described above. Subsequently, the butanol is recovered from the butanol-containing organic phase, as described above. At least a portion of the aqueous phase is returned to the fermentation medium.
Isobutanol may be produced by extractive fermentation with the use of a modified Escherichia coli strain in combination with an oleyl alcohol as the organic extractant, as disclosed in US Patent Application Publication No. 2009-0305370 A1. The method yields a higher effective titer for isobutanol (i.e., 37 g/L) compared to using conventional fermentation techniques (see Example 6 of US Patent Application Publication No. 2009-0305370 A1). For example, Atsumi et al. (Nature 451(3):86-90, 2008) report isobutanol titers up to 22 g/L using fermentation with an Escherichia coli that was genetically modified to contain an isobutanol biosynthetic pathway. The higher butanol titer obtained with the extractive fermentation method disclosed in US Patent Application Publication No. 2009-0305370 A1 results, in part, from the removal of the toxic butanol product from the fermentation medium, thereby keeping the level below that which is toxic to the microorganism. It is reasonable to assume that the present extractive fermentation method employing a water-immiscible organic extractant composition comprising a first solvent and a second solvent as defined herein would be used in a similar way and provide similar results.
Butanol produced by the method disclosed herein may have an effective titer of greater than 22 g per liter of the fermentation medium. Alternatively, the butanol produced by methods disclosed may have an effective titer of at least 25 g per liter of the fermentation medium. Alternatively, the butanol produced by methods described herein may have an effective titer of at least 30 g per liter of the fermentation medium. Alternatively, the butanol produced by methods described herein may have an effective titer of at least 37 g per liter of the fermentation medium.
The present methods are generally described below with reference to a
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The extractive processes described herein can be run as batch processes or can be run in a continuous mode where fresh extractant is added and used extractant is pumped out such that the amount of extractant in the fermentor remains constant during the entire fermentation process. Such continuous extraction of products and byproducts from the fermentation can increase effective rate, titer and yield.
In yet another embodiment, it is also possible to operate the liquid-liquid extraction in a flexible co-current or, alternatively, counter-current way that accounts for the difference in batch operating profiles when a series of batch fermentors are used. In this scenario the fermentors are filled with fermentable mash which provides at least one fermentable carbon source and microorganism in a continuous fashion one after another for as long as the plant is operating. Referring to
Adaptive co-current extraction follows the fermentation profile assuming the fermentor operating at the higher broth phase titer can utilize the extracting solvent stream richest in butanol concentration and the fermentor operating at the lowest broth phase titer will benefit from the extracting solvent stream leanest in butanol concentration. For example, referring again to
As the fermentations proceed in an orderly fashion the valves in the extracting solvent manifold can be repositioned to feed the leanest extracting solvent to the fermentor operating at the lowest butanol broth phase titer. For example, assume (a) Fermentor F102 completes its fermentation and has been reloaded and fermentation begins anew, (b) Fermentor F100 is in the middle of its fermentation operating at moderate butanol broth phase titer and (c) Fermentor F101 is near the end of its fermentation operating at relatively higher butanol broth phase titer. In this scenario the leanest extracting solvent would feed F102, the extracting solvent leaving F102 would feed Fermentor F100 and the extracting solvent leaving Fermentor F100 would feed Fermentor F101. The advantage of operating this way can be to maintain the broth phase butanol titer as low as possible for as long as possible to realize improvements in productivity. Additionally, it can be possible to drop the temperature in the other fermentors that have progressed further into fermentation that are operating at higher butanol broth phase titers. The drop in temperature can allow for improved tolerance to the higher butanol broth phase titers.
The present extractive fermentation methods provide butanol known to have an energy content similar to that of gasoline and which can be blended with any fossil fuel. Butanol is favored as a fuel or fuel additive as it yields only CO2 and little or no SOx or NOx when burned in the standard internal combustion engine. Additionally, butanol is less corrosive than ethanol, the most preferred fuel additive to date.
In addition to its utility as a biofuel or fuel additive, the butanol produced according to the present methods has the potential of impacting hydrogen distribution problems in the emerging fuel cell industry. Fuel cells today are plagued by safety concerns associated with hydrogen transport and distribution. Butanol can be easily reformed for its hydrogen content and can be distributed through existing gas stations in the purity required for either fuel cells or vehicles. Furthermore, the present methods produce butanol from plant derived carbon sources, avoiding the negative environmental impact associated with standard petrochemical processes for butanol production.
One of the advantages of the present methods is the higher butanol partition coefficient which may be obtained by the appropriate combination of a first and a second solvent as described herein. Extractants having higher partition coefficients may provide more effective extraction of butanol from the fermentation medium. Another advantage of the present method is the ability to use an extractant comprising a shorter carbon chain solvent—a solvent which has a desirably higher partition coefficient but undesirably lower biocompatibility—and to mitigate the lower biocompatibility by the combination with a longer carbon chain solvent. As a result, a more effective extractant is obtained, an extractant which can be used in the presence of the microorganism with continued viability of the microorganism.
Further advantages of the present methods include the improved process operability characteristics of the extractant relative to those characteristics of a longer carbon chain extractant such as oleyl alcohol. The extractant of the present methods has lower viscosity, lower density, and lower boiling point than oleyl alcohol, which provides improvements to the extraction process using such an extractant. Improved viscosity and density of the extractant may lead to improved efficiency of extraction and ease of phase separation. A lower boiling point may reduce the energy required for distillative separations and may lower the bottoms temperatures in a distillation column separating the butanol from the extractant. Together these characteristics may provide an economic advantage for extractive fermentation using an extractant as disclosed herein.
The present invention is further defined in the following examples. It should be understood that these examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions.
The following materials were used in the examples. All commercial reagents were used as received.
All solvents were obtained from Sigma-Aldrich (St. Louis, Mo.) and were used without further purification. The oleyl alcohol used was technical grade, which contained a mixture of oleyl alcohol (65%) and higher and lower fatty alcohols. The purity of the other solvents used was as follows: 1-nonanol, 98%; 1-decanol, 98%; 1-undecanol, 98%; 2-undecanol, 98%; dodecanol, 98%; 1-nonanal, 98%. Isobutanol (purity 99.5%) was obtained from Sigma-Aldrich and was used without further purification.
Wild-type Saccharomyces cerevisiae BY4741 strain was obtained from ATCC.
Optical density reading for measuring microorganism cell concentration was done using a Thermo Electron Corporation Helios Alpha spectrophotometer. Measurements were typically done using a wavelength of 600 nanometers.
Glucose concentration in the culture broth was measured rapidly using a 2700 Select Biochemistry Analyzer (YSI Life Sciences, Yellow Springs, Ohio). Culture broth samples were centrifuged at room temperature for 2 minutes at 13,200 rpm in 1.8 mL Eppendorf tubes, and the aqueous supernatant analyzed for glucose concentration. The analyzer performed a self-calibration with a known glucose standard before assaying each set of fermentor samples; an external standard was also assayed periodically to ensure the integrity of the culture broth assays. The analyzer specifications for the analysis were as follows:
Sample size: 15 μL
Black probe chemistry: dextrose
White probe chemistry: dextrose
Isobutanol and glucose concentrations in the aqueous phase were measured by HPLC (Waters Alliance Model, Milford, Mass. or Agilent 1200 Series, Santa Clara, Calif.) using a BioRad Aminex HPX-87H column, 7.8 mm×300 mm, (Bio-Rad laboratories, Hercules, Calif.) with appropriate guard columns, using 0.01 N aqueous sulfuric acid, isocratic, as the eluant. The sample was passed through a 0.2 μm centrifuge filter (Nanosep MF modified nylon) into an HPLC vial. The HPLC run conditions were as follows:
Injection volume: 10 μL
Flow rate: 0.60 mL/minute
Run time: 40 minutes
Column Temperature: 40° C.
Detector: refractive index
Detector temperature: 35° C.
UV detection: 210 nm, 8 nm bandwidth
After the run, concentrations in the sample were determined from standard curves for each of the compounds. The retention times were 32.6 and 9.1 minutes for isobutanol and glucose, respectively.
A series of Comparative Examples were performed using the water-immiscible organic extractants listed in Table 1. Each extractant was contacted with a fermentation medium and isobutanol as described below to determine the partition coefficient of the extractant. The biocompatibility of the extractant was also assessed by determining the glucose utilization rate of the microorganism during the extraction.
The following experimental procedure was used. In these experiments the amount of ethanol depended on the amount of glucose consumption but typical ethanol values were in the range of 10-15 g/L. The presence of ethanol in these concentrations is not expected to impact glucose consumption and the partitioning of butanol into the extractant. Seed shake flasks containing 250 mL of yeast extract/peptone/dextrose (YPD) medium were inoculated with 150 μL of S. cerevisiae BY4741 inoculum and incubated for about 14 hours at 30° C. with shaking at 250 rpm in a table top shaker (Innova 4230, New Brunswick scientific, Edison, N.J.). When the OD600 reached about 0.4, the glucose concentration in the culture broth was analyzed rapidly by a Select Biochemistry Analyzer and extra glucose was added to reach a final concentration of about 25 g/L. The culture broth was divided into 125 mL flasks, each containing 75 mL of the culture broth. The extractant (25 mL) was added to the appropriate flask, as shown in Table 1. After one hour of incubation at 30° C. with shaking at 200 rpm, 3.75 mL of isobutanol was added to each flask in order to bring the initial isobutanol concentration in the aqueous phase to 40 g/L. The incubation of the biphasic fermentation medium comprising an aqueous phase and a butanol-containing organic phase was continued at 30° C. with shaking at 100 rpm for 8 hours. The aqueous and organic phases in each flask were separated by decantation. The aqueous phase was centrifuged (2 minutes on 13,000 rpm with an Eppendorf centrifuge model 5415R) to remove cells and the supernatant analyzed for glucose, ethanol, and isobutanol by HPLC.
Glucose utilization rates were calculated by noting the difference in glucose concentrations between samples and the time between samples and computing a rate accordingly, for example ([glucose]t2−[glucose]t1)/(t2−t1) where t1 refers to a time earlier than t2 and [glucose] means the concentration of glucose.
Partition coefficients for the isobutanol distribution between the organic and aqueous phases were calculated from the known amount of isobutanol added to the flask and the isobutanol concentration data measured for the aqueous phase. The concentration of isobutanol in the extractant phase was determined by the mass balance. The partition coefficient was determined as the ratio of the isobutanol concentrations in the organic and the aqueous phases, i.e., Kp=[Isobutanol]Organic phase/[isobutanol]Aqueous phase.
Comparative Example A was repeated three times and the results averaged. For the extractants of Comparative Examples A-G, the partition coefficient for isobutanol and the glucose utilization rate are expressed below in Table 3 as percentages of the average values determined for oleyl alcohol (Comparative Example A). A value greater than 100% indicates a result which is numerically larger than that for oleyl alcohol. A value less than 100% indicates a result which is numerically smaller than that for oleyl alcohol. A value of 100% indicates a result which is the same as that for oleyl alcohol. As disclosed in US Patent Application Publication No. 2009-0305370 A1, oleyl alcohol performed well in single solvent extractive fermentations for isobutanol production.
The extractants listed in Table 2 were evaluated using the procedure described above, but with the following modifications. After the culture broth was divided into 125 mL flasks, each containing 75 mL of the culture broth, oleyl alcohol was added as the first solvent to each flask in the amount shown in Table 2. After one hour of incubation at 30° C. with shaking at 200 rpm, the corresponding second solvent, as indicated in Table 2, was added to each flask to complete formation of the extractant, followed by addition of 3.75 mL of isobutanol in order to bring the initial isobutanol concentration in the aqueous phase to 40 g/L. From this point on, the additional incubation, work-up, and measurements were done as described above.
For the extractants of Examples 1-15, the partition coefficients for isobutanol and the glucose utilization rate are expressed below in Table 3, together with the results for Comparative examples A-G, as percentages of the average values determined for oleyl alcohol (Comparative Example A). A value greater than 100% indicates a result which is numerically larger than that for oleyl alcohol. A value less than 100% indicates a result which is numerically smaller than that for oleyl alcohol. A value of 100% indicates a result which is the same as that for oleyl alcohol.
The data in Table 3 show that all the extractants comprising the indicated single solvent (Comparative Examples A-G) have higher isobutanol partition coefficients than that for oleyl alcohol, indicating these extractants would be advantageous to use in an extractive fermentation process. However, with the exception of oleyl alcohol and 1-dodecanol, the single solvent extractants have a percent glucose utilization rate of zero, which indicates a severe lack of biocompatibility with the microorganism. The extent of the lack of biocompatibility would negate the potential advantage of the partition coefficient if the extractant were used for in situ product removal in a fermentation process.
The data in Table 3 also show that the biotoxic effect of the extractants of Comparative Examples B, C, D, E, and F to the strain of Saccharomyces cerevisiae studied can be mitigated by combining these shorter carbon chain solvents selected from the group consisting of C7 to C11 alcohols, C7 to C11 carboxylic acids, esters of C7 to C11 carboxylic acids, C7 to C11 aldehydes, and mixtures thereof with a longer carbon chain solvent selected from the group consisting of C12 to C22 fatty alcohols, C12 to C22 fatty acids, esters of C12 to C22 fatty acids, C12 to C22 fatty aldehydes, and mixtures thereof to form an extractant comprising a first solvent and a second solvent as described above. The solvent combination also provides a generally improved partition coefficient for isobutanol. It would be reasonable to expect that the extractants disclosed herein could be used to mitigate the toxicity of isobutanol, as well as other butanols, to other strains of Saccharomyces cerevisiae, including recombinant strains, while also providing an improved partition coefficient for butanol. It would also be reasonable to expect that the mitigating effect could be extended to Escherichia coli and Lactobacillus plantarum which have been genetically modified of being capable of converting at least one fermentable carbon source into butanol.
Data from Examples 1 and 2 show that extractants comprising 70/30 oleyl alcohol/1-nonanol (volume/volume basis) or 50/50 oleyl alcohol/1-nonanol, while having lower percent glucose utilization rates than oleyl alcohol, are still biocompatible with the microorganism, allowing it to produce butanol in the presence of the extractant. The oleyl alcohol/1-nonanol extractants also have improved isobutanol partition coefficients, which are advantageous for an in situ product removal process.
Similarly, data from Examples 3-5 show that extractants comprising 70/30, 50/50, or 30/70 oleyl alcohol/1-undecanol have significantly better biocompatibility with the microorganism than 1-undecanol and higher isobutanol partition coefficients than oleyl alcohol.
Data from Examples 6 and 7 show that extractants comprising 70/30 or 50/50 oleyl alcohol/2-undecanol have significantly better biocompatibility with the microorganism than 2-undecanol and the same or higher isobutanol partition coefficients than oleyl alcohol.
Data from Examples 8 and 9 show that extractants comprising 70/30 or 50/50 oleyl alcohol/1-nonanal have better biocompatibility than 1-nonanal and about the same or higher isobutanol partition coefficients than oleyl alcohol.
Data from Examples 10-12 show that extractants comprising 70/30, 50/50, or 30/70 oleyl alcohol/decanol have higher biocompatibility than decanol and higher isobutanol partition coefficients than oleyl alcohol.
Similarly, data from Examples 13-15 show that extractants comprising 70/30, 50/50, or 30/70 oleyl alcohol/1-dodecanol have higher biocompatibility than 1-dodecanol and higher isobutanol partition coefficients than oleyl alcohol.
Table 4 presents calculated viscosity, density, and boiling point data for the extractants of Examples 1-15 and Comparative Examples A-G, relative to the values for oleyl alcohol. Physical property calculations were performed according to standard methods as described, for example, in Properties of Gases and Liquids (Reid, Prausnitz, and Poling, McGraw-hill, 1987). Data for pure components may be obtained, for example, from physical property databases or from the open literature.
The data in Table 4 show that extractants of the Examples can have significantly reduced boiling point and viscosity and slightly reduced density, relative to the base case of oleyl alcohol. Thus, from the perspective of process operability, the extractants of the Examples may provide advantages over extractants which comprise only single solvents.
Although particular embodiments of the present invention have been described in the foregoing description, it will be understood by those skilled in the art that the invention is capable of numerous modifications, substitutions, and rearrangements without departing from the spirit or essential attributes of the invention. Reference should be made to the appended claims, rather than to the foregoing specification, as indicating the scope of the invention.
This application claims the benefit of priority of U.S. Provisional Application Nos. 61/168640, 61/168642, and 61/168645, all of which were filed on Apr. 13, 2009, and U.S. Provisional Application Nos. 61/231,697, 61/231698, and 61/231699, all of which were filed on Aug. 6, 2009. Each of the referenced applications is herein incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 61168640 | Apr 2009 | US | |
| 61168642 | Apr 2009 | US | |
| 61168645 | Apr 2009 | US | |
| 61231697 | Aug 2009 | US | |
| 61231698 | Aug 2009 | US | |
| 61231699 | Aug 2009 | US |
