Patent Grant
8574875
This application is a National Phase filing under 35 U.S.C. §371 of PCT/EP2008/006714 filed Aug. 14, 2008, which claims priority to Patent Application No. 07114574.2, filed in Europe on Aug. 17, 2008.
The Sequence Listing associated with this application is filed in electronic format via EFS-Web and hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is Revised_Sequence_Listing—60072. The size of the text file is 32 KB, and the text file was created on Jan. 23, 2013.
The present invention relates to a novel bacterial strain designated DD1, which has the ability to produce organic acids, in particular succinic acid (SA), which was originally isolated from bovine rumen, and is capable of utilizing glycerol as a carbon source; and variant strains derived there from retaining said capability; as well as to methods of producing organic acids, in particular succinic acid by making use of said microorganism.
The fermentative production of succinic acid (SA) from biomass has already drawn much attention because said acid represents an important constituent of synthetic resins or is a source of further valuable low-molecular chemical compounds, in particular tetrahydrofuran (THF), 1,4-butanediol (BDO), gamma-butyrolactone (GBL) and pyrrolidones (WO-A-2006/066839).
A SA-producing bacterium isolated from bovine rumen was described by Lee et al (2002a). The bacterium is a non-motile, non-spore-forming, mesophilic and capnophilic gram-negative rod or coccobacillus. Phylogenetic analysis based on the 16S rRNA sequence and physiological analysis indicated that the strain belongs to genus Mannheimia as a novel species, and has been named Mannheimia succiniciproducens MBEL55E. Under 100% CO2 conditions, it grows well in the pH range of 6.0-7.5 and produces succinic acid, acetic acid and formic acid at a constant ratio of 2:1:1. When M. succiniciproducens MBEL55E was cultured anaerobically under CO2-saturation with glucose as carbon source, 19.8 g/L of glucose were consumed and 13.3 g/L of SA were produced in 7.5 h of incubation.
A significant drawback of said organism is, however, its inability to metabolize glycerol, which, as a constituent of triacyl glycerols (TAGS), becomes readily available e.g. as by-product in the transesterification reaction of Biodiesel production (Dharmadi et al., 2006).
The fermentative production of succinic acid from glycerol has been described in the scientific literature (Lee et al., 2001; Dharmadi et al., 2006) and with glycerol higher yields [mass of SA produced/mass of raw material consumed] than with common sugars like glucose were achieved (Lee et al., 2001). However, the space time yield obtained with glycerol was substantially lower than with glucose (0.14 vs. 1.0 g SA/[L h]) and no crude glycerol was used.
Only in a few cases anaerobic metabolisation of glycerol to fermentation products have been described. E. coli is able to ferment glycerol under very specific conditions such as acidic pH, avoiding accumulation of the fermentation gas hydrogen, and appropriate medium composition. (Dharmadi et al 2006, Yazdani and Gonzalez 2007) Many microorganisms are able to metabolize glycerol in the presence of external electron acceptors (respiratory metabolism), few are able to do so fermentatively (i.e. in the absence of electron acceptors). The fermentative metabolism of glycerol has been studied in great detail in several species of the Enterobacteriaceae family, such as Citrobacter freundii and Klebsiella pneumoniae. Dissimilation of glycerol in these organisms is strictly linked to their capacity to synthesize the highly reduced product 1,3-propanediol (1,3-PDO) (Dharmadi et al 2006). The conversion of glycerol into succinic acid using Anaerobiospirillum succiniciproducens has been reported (Lee et al. 2001). This study demonstrated that succinic acid could be produced with little formation of by-product acetic acid by using glycerol as a carbon source, thus facilitating purification of succinic acid. The highest yield was obtained by intermittently feeding glycerol and yeast extract, a strategy that resulted in the production of about 19 g/L of succinic acid. It was noted, however, that unidentified nutritional components present in yeast extract were needed for glycerol fermentation to take place.
Carboxylation reactions of oxaloacetate catalyzed by the enzymes phopshoenolpyruvate carboxylase (PEPC), phopshoenolpyruvate carboxykinase (PEPCK) and pyruvate carboxylase (PycA) are utilizing HCO3− as a source of CO2 (Peters-Wendisch, P G et al). Therefore hydrogencarbonate sources such as NaHCO3, KHCO3, NH4HCO3 and so on can be applied to fermentation and cultivation media to improve the availability of HCO3− in the metabolisations of substrates to succinic acid. The production of succinic acid from glucose has not been found to be dependent on the addition of HCO3− in the prior art so far.
Biomass production by anaerobic organisms is limited by the amount of ATP produced from fermentative pathways. Biomass yield of glycerol in anaerobic organisms is lower than of saccharides, like hexoses such as glucose, fructose, pentoses such as xylose arabinose or disaccharides such as sucrose or maltose (Lee et al. 2001, Dharmadi 2007).
Saccharides, however, theoretically can be converted to succinic acid with a significantly lower yield than glycerol due to the lower reduction state of saccharides compared to the polyol glycerol. The combination of saccharides with glycerol have been found to function in an succinic acid producing anaerobic organisms (Lee et al. 2001), however without reaching succinic acid titers beyond 28 g/l.
There is, therefore, a need for further bacterial strains, which have the ability to produce organic acids, in particular SA, from glycerol. In particular, such strains should produce said acids with high productivity from glycerol, especially if crude glycerol e.g. from bio diesel production can be used without prior purification.
It is an object of the present invention to provide a bacterial strain having the ability to produce succinic acid from glycerol, especially crude glycerol.
Said object was solved by the present inventors who surprisingly isolated a novel bacterial strain, designated DD1, having the desired metabolic characteristic.
Annex 1 shows an alignment of the 23S rDNA sequence (23s_rRNA_seq_rev, SEQ ID NO:2) of DD1 with the corresponding six individual sequences of “M. succiniciproducens” MBEL55E: 23s_rRNA—5 (SEQ ID NO: 7), 23s_rRNA—3 (SEQ ID NO: 5), 23s_rRNA—1 (SEQ ID NO: 3), 23s_rRNA—2 (SEQ ID NO: 4), 23s_rRNA—6 (SEQ ID NO: 8), 23s_rRNA—4 (SEQ ID NO: 6), where differences between the DD1 sequence (bottom) and the MBEL55E sequences are highlighted.
A first embodiment of the invention relates to a bacterial strain, designated DD1, which may be isolated from bovine rumen, and is capable of utilizing glycerol (including crude glycerol) as a carbon source; and variant strains derived there from retaining said capability.
Preferably said strain has the ability to produce succinic acid from glycerol (including crude glycerol), in particular, under anaerobic conditions.
In particular, the novel strain has a 16S rDNA of SEQ ID NO:1 or a sequence which shows a sequence homology of at least 96, 97, 98, 99 or 99.9% and/or a 23S rDNA of SEQ ID NO:2 or a sequence which shows a sequence homology of at least 95, 96, 97, 98, 99 or 99.9%.
“Identity” or “homology” between two nucleotide sequences means identity of the residues over the complete length of the aligned sequences, such as, for example, the identity calculated (for rather similar sequences) with the aid of the program needle from the bioinformatics software package EMBOSS (Version 5.0.0, see webpage at emboss.sourceforge.net/what/) with the default parameters which are:
An alignment of the 23S rDNA sequence of Strain DD1 to the corresponding six individual sequences of “M. succiniciproducens” MBEL55E is shown in Annex 1. Therein, the differences between the DD1 sequence (bottom) and the six 23S rDNA sequences of MBEL55E sequences are highlighted. The DD1 sequence (see also SEQ ID NO:2) represents the sequence information as obtained by sequencing the PCR amplified 23S rDNA of DD1. Sequencing experiments resulted in an unambiguous sequence information indicating that the 23S rDNA information derivable from DD1 may be used as distinguishing feature of the DD1 strain. Said DD1 sequence differs in at least 6 sequence positions from each individual MBEL55E sequence. The most significant difference is an insert of about 133 bp into each of the MBEL55E sequences (near position 1325), which is missing in the DD1 sequence. Further significant, specific sequence differences are at positions 451, 1741, 2040, 2041, 2045 and 2492 (numbering as used in the alignment).
The strain of the present invention also preferably shows at least one of the following additional metabolic characteristics:
a) production of succinic acid from sucrose; in particular, under anaerobic conditions;
b) production of succinic acid from maltose; in particular, under anaerobic conditions;
c) production of succinic acid from D-fructose; in particular, under anaerobic conditions;
d) production of succinic acid from D-galactose; in particular, under anaerobic conditions;
e) production of succinic acid from D-mannose; in particular, under anaerobic conditions;
f) production of succinic acid from D-glucose; in particular, under anaerobic conditions;
g) production of succinic acid from D-xylose; in particular, under anaerobic conditions;
h) production of succinic acid from L-arabinose; in particular, under anaerobic conditions;
i) no utilization of xylitol, inositol and sorbitol;
j) growth both under aerobic and anaerobic conditions;
k) growth at initial glucose concentrations of 75 g/L or more;
l) ammonia tolerance.
In particular, said strain shows at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or all of said additional features.
DD1 was, for example, further analyzed for the capability to co-metabolize a saccharide and the polyol glycerol. It was found that DD1 is capable to co-metabolize maltose and glycerol resulting in biomass formation, succinic acid formation and simultaneous maltose and glycerol utilisation.
The term “acid” (in the context of organic mono or dicarboxylic acids as referred to herein, i.p. acetic, lactic and succinic acid) has to be understood in its broadest sense and also encompasses salts thereof, as for example alkali metal salts, like Na and K salts, or earth alkali salts, like Mg and Ca salts, or ammonium salts; or anhydrides of said acids.
The term “crude glycerol” has to be understood as untreated glycerol-containing stream as it accrues in processes in which glycerol is a by product, as for example the production of bio diesel or bio ethanol. Unless otherwise stated the term “glycerol” as used herein also encompasses “crude glycerol”.
In a preferred embodiment the invention relates to a bacterial strain DD1 as deposited with DSMZ and having the deposit number DSM 18541 and variant or mutant strains derived there from. Said variants and mutants retain at least said ability to produce succinic acid (SA) from glycerol, sucrose, maltose, D-glucose, D-fructose and/or D-xylose. In particular, they may also have a 16S rDNA of SEQ ID NO:1 or a sequence which shows a sequence homology of at least 96, 97, 98, 99 or 99.9% and/or a 23S rDNA of SEQ ID NO:2 or a sequence which shows a sequence homology of at least 95, 96, 97, 98, 99 or 99.9%. Variants or mutants of said DD1 strain may have a 23S rDNA different from that of SEQ ID NO:2, while maintaining at least one of the sequence differences as discussed above which distinguishes the 23S rDNA sequence from that of the MBEL 55E strain. As for example, the 132 bp insert is missing in such variants or mutants as well, optionally combined with one or more of the other specific sequence differences depicted in the alignment of Annex 1.
According to another embodiment the bacterial strain of the invention is converting at least one carbon source selected from sucrose, maltose, D-fructose, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and/or glycerol to succinic acid with a yield coefficient YP/S of at least 0.5 g/g up to about 1.28 g/g; as for example a yield coefficient YP/S of at least 0.6 g/g, of at least 0.7 g/g, of at least 0.75 g/g, of at least 0.8 g/g, of at least 0.85 g/g, of at least 0.9 g/g, of at least 0.95 g/g, of at least 1.0 g/g, of at least 1.05 g/g, of at least 1.1 g/g, of at least 1.15 g/g, of at least 1.20 g/g, of at least 1.22 g/g, or of at least 1.24 g/g
According to still another embodiment the bacterial strain of the invention is converting at least 28 g/L of glycerol to at least 28.1 g/L succinic acid, with a yield coefficient YP/S of at least 1.0 g/g, or of >1.0 g/g, or of >1.05 g/g, or of >1.1 g/g, or of >1.15 g/g, or of >1.20 g/g, or of >1.22 g/g, or of >1.24 g/g, up to about 1.28 g/g. For example, 28 g/L of glycerol may be converted to up to about 40 or up to about 35 g/L succinic acid.
According to still another embodiment the bacterial strain of the invention is converting at least one carbon source selected from sucrose, maltose, D-fructose, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and/or glycerol to succinic acid with a specific productivity yield of at least 0.6 g gDCW−1 succinic acid, or of at least of at least 0.65, of at least 0.7 g gDCW−1 h−1, of at least 0.75 g gDCW−1 h−1, or of at least 0.77 g gDCW−1 h−1 succinic acid.
According to still another embodiment the bacterial strain of the invention is converting at least one carbon source selected from sucrose, maltose, D-fructose, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and/or glycerol to succinic acid with a space time yield for succinic acid of at least 2.2 g/(L h) or of at least 2.5, at least 2.75, at least 3, at least 3.25, at least 3.5 or at least 3.7 g/(L*h) succinic acid.
According to still another embodiment the bacterial strain of the invention is converting at least 28 g/L of at least one carbon source selected from sucrose, maltose, D-fructose, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and/or glycerol to succinic acid with a space-time-yield for succinic acid of at least 2.2 g/(L h), or of at least 2.5, at least 2.75, at least 3, at least 3.25, at least 3.5 or at least 3.7 g/(L*h).
According to another embodiment the bacterial strain of the invention is converting at least one carbon source selected from sucrose, maltose, D-fructose, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and/or glycerol to succinic acid with a specific productivity yield of at least 0.6 g gDCW−1 h−1 or of at least of at least 0.65 or of at least 0.7 g gDCW−1 h−1 succinic acid, or of at least 0.77 g gDCW−1 succinic acid, and a space-time-yield for succinic acid of at least 2.2 g/(L h), or of at least 2.5, at least 2.75, at least 3, at least 3.25, at least 3.5 or at least 3.7 g/(L*h).
In another embodiment of the claimed bacterial strains as defined above the carbon source is glycerol or a mixture of glycerol and at least one further carbon source selected from sucrose, maltose, D-fructose, D-galactose, D-mannose, D-glucose, D-xylose, and L-arabinose.
The different yield parameters as described herein (“Yield” or YP/S; “Specific Productivity Yield”; or Space-Time-Yield (STY)) are well known in the art and are determined as described for example by Song and Lee, 2006.
“Yield” and “YP/S” (each expressed in mass of product produced/mass of material consumed) are herein used as synonyms.
The specific productivity yield describes the amount of a product, like succinic acid that is produced per h and L fermentation broth per g of dry biomass. The amount of dry cell weight stated as DCW describes the quantity of biologically active microorganism in a biochemical reaction. The value is given as g product per g DCW per h (i.e. g gDCW−1 h−1).
A further embodiment of the invention relates to a process for the fermentative production of an organic acid or a salt or derivative thereof, which process comprises the steps of:
a) incubating a bacterial strain as defined in one of the preceding claims in a medium containing an assimilable carbon source and cultivating said strain at a temperature in the range of about 10 to 60 or 20 to 50 or 30 to 45° C. at a pH of 5.0 to 9.0 or 5.5 to 8.0 or 6.0 to 7.0 in the presence of carbon dioxide; and
b) obtaining said organic acid or salt or derivative thereof from the medium.
Said process may be performed discontinuously or continuously and the course of the acid production may be monitored by conventional means, as for example HPLC or GC analysis.
Preferably, by said process succinic acid (SA) is produced, preferably under anaerobic conditions. Anaerobic conditions may be established by means of conventional techniques, as for example by degassing the constituents of the reaction medium and maintaining anaerobic conditions by introducing carbon dioxide or nitrogen or mixtures thereof and optionally hydrogen at a flow rate of, for example, 0.1 to 1 or 0.2 to 0.5 vvm.
Aerobic conditions may be established by means of conventional techniques, as for example by introducing air or oxygen at a flow rate of, for example, 0.1 to 1 or 0.2 to 0.5 vvm.
If appropriate a slight over pressure of 0.1 to 1.5 bar may be applied.
In said process said assimilable carbon source is preferably selected from glycerol, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose and mixtures thereof or compositions containing at least one of said compounds, or is selected from decomposition products of starch, cellulose, hemicellulose and/or lignocellulose.
The initial concentration of the assimilable carbon source is preferably adjusted to a value in a range of 5 to 100 g/l and may be maintained in said range during cultivation.
The pH of the reaction medium may be controlled by addition of suitable bases as for example, NH4OH, NH4HCO3, (NH4)2CO3, NaOH, Na2CO3, NaHCO3, KOH, K2CO3, KHCO3, Mg(OH)2, MgCO3, Mg(HCO3)2, Ca(OH)2, CaCO3, Ca(HCO3)2, CaO, CH6N2O2, C2H7N, or other bases and mixtures thereof. The physical condition of the base can either be an aqueous solution, aqueous suspension, gaseous or solid.
Particularly preferred conditions for producing SA are:
Carbon source: Glucose, xylose or maltose and/or glycerol (including crude glycerol)
Temperature: 30 to 45° C.
pH: 6.0 to 7.0, controlled by a base as described above, preferably by a HCO3− source such as Na2CO3, NaHCO3, Mg(HCO3)2, Ca(HCO3)2 or, Mg(OH)2, MgCO3, Ca(OH)2, CaCO3.
supplied gas: CO2
In another embodiment the present invention provides a process for the fermentative production of succinic acid or a salt or derivative thereof, which process comprises the steps of:
In another embodiment the present invention provides a process for the fermentative production of succinic acid or a salt or derivative thereof, which process comprises the steps of:
In another embodiment the present invention provides a process for the fermentative production of succinic acid or a salt or derivative thereof, which process comprises the steps of:
In another embodiment the present invention provides a process for the fermentative production of succinic acid or a salt or derivative thereof, which process comprises the steps of:
In another embodiment the present invention provides a process for the fermentative production of succinic acid or a salt or derivative thereof, which process comprises the steps of:
In another embodiment of the above identified processes of producing succinic acid the carbon source is glycerol or a mixture of glycerol and at least one further carbon source selected from sucrose, maltose, D-fructose, D-galactose, D-mannose, D-glucose, D-xylose, and L-arabinose.
Further preferred conditions will be derivable from the attached examples and figures.
Succinic acid and/or succinic acid salts produced may be isolated in conventional manner by methods known in the art, as for example cristallization, filtration, electrodialysis, chromatography. For example, they may be isolated by precipitating as a calcium succinate product in the fermentor during the fermentation by using calcium hydroxide, -oxide, -carbonate or hydrogencarbonate for neutralization and filtration of the precipitate.
The desired succinic acid product is recovered from the precipitated calcium or succinate by acidification of the succinate with sulfuric acid followed by filtration to remove the calcium sulfate (gypsum) or which precipitates. The resulting solution may be further purified by means of ion exchange chromatography in order to remove undesired residual ions.
Another embodiment of the invention relates to a process for the production of succinic acid and/or succinic acid salts, in particular ammonium salts, which method comprises the fermentative production of succinic acid as defined above and controlling the pH with a suitable base, in particular inorganic base, like ammonia, or an aqueous solution thereof.
Another embodiment of the invention relates to a process for the production of tetrahydrofuran (THF) and/or 1,4-butanediol (BDO) and/or gamma-butyrolactone (GBL) which comprises
a) the fermentative production of succinic acid and/or succinic acid salts, e.g. ammonium salts as defined above, and
b1) either the direct catalytic hydrogenation of the obtained free acid to THF and/or BDO and/or GBL or
b2) the chemical esterification of obtained free succinic acid and/or succinic acid ammonium salts to its corresponding di-loweralkyl ester and subsequent catalytic hydrogenation of said ester to THF and/or BDO and/or GBL.
Lower alkyl preferably represent a straight chain or branched C1-C6-, preferably C1-C4-alkyl residue, in particular methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl, as well as n-pentyl and n-nexyl and branched analogues thereof.
Another embodiment of the invention relates to a process for the production of pyrrolidones which comprises
a) the fermentative production of succinic acid ammonium salts as defined above, and
b) the chemical conversion of succinic acid ammonium salts to pyrrolidones in a manner known per se, for example as described in WO-A-2006/066839 (which document is herewith incorporated by reference).
In a preferred embodiment, said glycerol, which is used as assimilable carbon source, is crude glycerol.
More Details on Direct Hydrogenation of SA:
Suitable experimental conditions for performing direct catalytic hydrogenation are well known, and for example, described in U.S. Pat. No. 4,550,185, incorporated herewith by reference.
The SA is hydrogenated in a manner known per se using processes, apparatus and assistants, such as solvents, familiar to the person skilled in the art. In particular, a continuous or batch wise liquid phase hydrogenation is carried out in the presence of a heterogeneous catalyst suitable for the acid hydrogenation. The optimal process parameters can be established by the person skilled in the art without unacceptable effort. For example, the reaction temperature is in the range from about 100 to about 300° C., preferably in the range from about 130 to 285° C., and the pressure is from about 20 to 350 bar, for example from 100 to 250 bar. Catalysts usable for the hydrogenation reaction are known to the person skilled in the art. For example, various palladium/rhenium/carbon catalysts may be used. Solvents usable for the hydrogenation reaction are known to the person skilled in the art. For example, an aqueous solvent medium may be used.
More Details on Esterification of SA Followed by Hydrogenation:
Suitable experimental conditions for performing the chemical esterification, followed by direct catalytic hydrogenation are well known, and for example, described in European Patent application 06007118.0 incorporated herewith by reference.
a) Esterification Process:
The esterification process which may comprise a reactive distillation can be performed using an apparatus known per se in various designs.
For example an esterification plant which is operated in continuous mode can be used which comprises a rectification column with an appropriate number of theoretical stages achieved by installation of trays or packings. The aqueous charge comprising the ammonium salt of SA is fed into the top of the column from a reservoir vessel as soon as a steady-state temperature profile has formed in the column as a result of feeding-in alkanol that is evaporated in the evaporator loop adherent to the sump of the column. The reaction forms a countercurrent flow of descending, ammonium salt-containing liquid and condensate, and ascending, alkanol-containing vapor phase. To catalyze the esterification reaction, a homogeneous catalyst may be added to the ammonium salt initial charge. Alternatively, heterogeneous catalysts may be provided in the column internals. The carboxylic ester formed is liquid under the process conditions and passes via the lower end of the column into the sump of the distillation column and is continuously withdrawn from the sump. Gaseous components, for example azeotropic mixtures comprising alkanol-water and/or ammonia, are removed from the reaction column and hence from the reaction equilibrium at the top of the column.
Further modifications of the above-described specific embodiments can be implemented by the person skilled in the art without unacceptable effort.
Suitable process parameter ranges for the esterification process according to the invention can be determined easily by the person skilled in the art depending on the configuration of the apparatus used, for example type of column internals used, type and amount of the reactants, type and amount of the catalyst used if appropriate. For instance, without being restrictive thereto, individual parameters may be set within the following parameter ranges:
Column temperature: 0-300° C., in particular 40-250° C., or 70-200° C.
Pressure: from 0.1 to 6 bar, in particular standard pressure
Residence time: a few seconds (for example from 1 to 60) up to days (for example from 1 to 5), in particular from a few minutes (for example from 1 to 60) to a few hours (for example from 1 to 15), more preferably from a few minutes (for example from 5 to 20) to 2 h.
b) Hydrogenation Process
The SA esters prepared in accordance with the invention are hydrogenated in a manner known per se using processes, apparatus and assistants, such as catalysts, familiar to the person skilled in the art.
In particular, a continuous or batchwise gas phase hydrogenation is carried out in the presence of a heterogeneous catalyst suitable for the ester hydrogenation. The optimal process parameters can be established by the person skilled in the art for the particular ester without unacceptable effort. For example, the reaction temperature is in the range from about 100 to about 300° C., preferably in the range from about 200 to 280° C., and the pressure is from about 5 to 100 bar, for example from 10 to 50 bar. The molar ratio of reactant to hydrogen is set within the range from about 1:100 to about 1:2000, for example from 1:800 to 1:1500.
Catalysts usable for the inventive hydrogenation reaction are known to the person skilled in the art. For example, various copper catalysts may be used: The prior art describes, for example, the use of reduced copper chromite catalysts which are obtainable under the name 85/1 from Davy Process Technology Ltd., England. However, catalysts particularly suitable in accordance with the invention are supported copper oxide catalysts, the copper oxide being applied to alumina or silica support materials. The examples of the hydrogenation of succinic esters to BOO (1,4-Butanediol)/GBL (gamma-butyrlactone)/THF with copper catalysts are also described in the following thesis: Schlander, January, February 2000, University of Karlsruhe, “Gasphasenhydrierung von Maleinsäuredimethylester zu 1,4-Butandiol, gamma-Butyrolacton and Tetrahydrofuran an Kupfer-Katalysatoren”.
More Details on Fermentation Steps:
A fermentation as used according to the present invention can be performed in stirred fermenters, bubble columns and loop reactors. A comprehensive overview of the possible method types including stirrer types and geometric designs can be found in “Chmiel: Bioprozesstechnik: Einführung in die Bioverfahrenstechnik, Band 1”. In the process, typical variants available are the following variants known to those skilled in the art or explained, for example, in “Chmiel, Hammes and Bailey: Biochemical Engineering”, such as batch, fed batch, repeated fed batch or else continuous fermentation with and without recycling of the biomass. Depending on the production strain, sparging with air, oxygen, carbon dioxide, hydrogen, nitrogen or appropriate gas mixtures can/must be effected in order to achieve good yields.
Before the chemical conversion in the fermentation broth in the process according to the invention, the fermentation broth can be pretreated; for example, the biomass of the broth can be removed. Processes for removing the biomass are known to those skilled in the art, for example filtration, sedimentation and flotation. Consequently, the biomass can be removed, for example, with centrifuges, separators, decanters, filters or in flotation apparatus. For maximum recovery of the product of value, washing of the biomass is often advisable, for example in the form of a diafiltration. The selection of the method is dependent upon the biomass content in the fermenter broth and the properties of the biomass, and also the interaction of the biomass with the product of value. In one embodiment, the fermentation broth can be sterilized or pasteurized.
In a further embodiment, the fermentation broth is concentrated. Depending on the requirement, this concentration can be done batchwise or continuously. The pressure and temperature range should be selected such that firstly no product damage occurs, and secondly minimal use of apparatus and energy is necessary. The skillful selection of pressure and temperature levels for a multistage evaporation in particular enables saving of energy.
In apparatus terms, stirred tanks, falling-film evaporators, thin-film evaporators, forced-flash circulation evaporators and other evaporator types can be utilized in natural or forced circulation mode.
Consequently, the term “fermentation broth” is understood to mean an aqueous solution which is based on a fermentative process and has not been worked up or has been worked up, for example, as described herein.
The present invention will be described in greater detail by means of the following examples. The following examples are for illustrative purposes and are not intendet to limit the scope of the invention.
For the isolation a four-step approach was used, comprising the steps of sampling, enrichment cultivation, isolation of pure cultures and test of pure cultures for succinic acid (SA) production.
1. Experimental Approach
1.1. Sampling
Samples were taken from bovine rumen, digested sludge from a municipal sewage plant and pomace, the residue from wine making. These habitats are characterized by relatively high concentrations of organic substances and a CO2-rich atmosphere without oxygen. More detailed information on the samples, their origin and handling is given below.
b) Digested sludge was taken from the digestion tower of the municipal sewage plant in Mannheim-Sandhofen. In situ-pH and -temperature were 7.1 and 36.3° C., respectively. The samples were cooled on ice and processed on the same day. The main components of the gas phase in the sludge are methane and carbon dioxide.
Enrichment cultivations were performed on different media containing D-glucose, D-xylose and L-arabinose as sole carbon source. The media composition is described below:
aD-glucose, D-xylose or L-arabinose
bMgCO3 (Riedel-de Haen, product number: 13117 by Sigma-Aldrich Laborchemikalien GmbH, Seelze, Germany).
cStock solution in ethanol.
dStock solution in dimethyl sulfoxide
eRumen liquid was centrifuged. The supernatant was sterile filtered, the sterile filtrate was added to the enrichment trials with rumen content as inoculum.
f10 g digested sludge or pomace were mixed with 25 mL distilled water and stirred intensively for 15 min. Rough particles were separated using a filter fleece. The suspensions were sterile filtered, the sterile filtrates were added to the respective enrichment trials.
MgCO3 and water (0.75 g and 40 mL) were autoclaced in 100 mL-serum bottles (121° C., 20 min). Yeast extract, peptone, C-source, NH4SO4 and K2HPO4 were all separately autoclaved. For Ca-, Mg- and Na-chlorides one stock solution was prepared which was autoclaved. To ensure that no oxygen was present the following standard procedures were used:
Rumen samples and digested sludge were used undiluted as inoculum. 50 g of solid pomace were diluted in 100 mL 0.9% NaCl solution, filtered to remove rough particles and then used as inoculum.
100 mL serum bottles (Zscheile & Klinger, Hamburg, Germany) were filled with 50 mL medium and 2 mL of the respective inoculum, closed with butyl rubber stoppers (Ochs GmbH, Bovenden/Lenglern, Germany) and gassed with CO2. An overpressure of about 0.8 bar was adjusted. The bottles were incubated in a shaking incubator (160 rpm, shaking diameter: 2.5 cm) at 37° C.
Consumption of glucose, xylose and arabinose and formation of succinic acid and by-products were quantified via HPLC analyses of the undiluted cell free supernatants of the cultivation broth using RI-detection. Broth samples were taken with a sterile syringe through the butyl rubber plug, cell separation was performed by filtration (0.22 μm). A 300×7.8 mm I. D. Column Aminex HPX-87H (Biorad) and 5 mm H2SO4 were used as stationary and mobile phase, respectively. The column temperature was 30° C., the flow rate was 0.5 mL min−1.
1.3. Isolation of Pure Cultures
Isolation of pure cultures from the enrichment cultivations was achieved by repeated streaking on agar plates.
1.4. Test of Pure Cultures for Succinic Acid Production
The pure cultures were tested in liquid culture for SA production. Sugar consumption and SA and side product formation were quantified by HPLC. Cultivation and HPLC conditions were the same as those described in the above section ‘Enrichment cultivation’.
2. Results
2.1. Recommended Enrichment Conditions
The following table summarizes those experimental conditions, which are recommendable for the enrichment of succinic acid (SA) producers.
aglucose and xylose were not tested in trials with digested sludge.
For enrichment of SA producers from rumen content the best C-source is arabinose (3/3 enrichment cultures showing SA production, 0/3 with glucose, 2/3 with xylose). The results are summarized in the following table. Addition of the ionophoric antibiotics lasalocid and monensin to the enrichment medium resulted in substantially higher SA production (1.9-5.4 vs. 0.9-1.2 g/L in 17 h) and lower production of lactic and propionic acid. These results therefore confirm that SA producing microorganisms can indeed be favored by adding these compounds to the enrichment medium (Lee et al., 2002a). MgCO3-buffered enrichment cultures showed higher SA production than trials with TRIS (1.9-5.4 vs. 1.2-1.4 g/L in 17 h). Presumably this is caused by i) the higher buffer capacity of MgCO3, ii) its lower osmotic stress due to lower solubility and iii) by liberation of CO2 from the carbonate-ion, which is necessary for the SA biosynthesis.
For enrichment of SA producers from digested sludge the only C-source tested was arabinose.
The results are summarized in the following table. These experiments indicated that short incubation times of 24 h or lower are necessary to prevent substrate depletion and SA consumption, presumably by propionic acid producing bacteria: succinate2−+H2O→propionate−+HCO3− (Janssen, 1991).
Results obtained in enrichment cultures from pomace are summarized in the following table. Enrichment of SA producers from pomace was only successful if pomace from red grapes (Spätburgunder type) were used. It is absolutely necessary to add amphotericin B to the enrichment medium to suppress ethanol production, presumably caused by wine yeasts. Glucose and arabinose were both suitable C-sources but xylose was not. Incubation times that were necessary to unequivocally detect SA production were substantially higher than with sample material from rumen and digested sludge.
ared = pomace from red grapes (Spätburgunder type) as inoculum; white = pomace from white grapes (Müller-Thurgau) as inoculum.
2.2. Best Results from Enrichment Experiments
The best results obtained in enrichment cultures for SA-producers are listed in the following table 6.
aSpace time yield and yield for succinic acid.
Said table indicates that with each of the three sample materials it is possible to receive enrichment cultures producing SA. Enrichment cultures originating from digested sludge showed higher space time yields than those from rumen and pomace (0.4 vs. 0.2 and 0.1 g/[L h]). However, SA-producing isolates were exclusively obtained from SA-producing enrichment cultures with rumen material as inoculum. Apparently isolation of SA producers from digested sludge and pomace requires more sophisticated strategies.
2.3. Succinic Acid Producing Isolates
The best isolates (=pure cultures) showing SA production in pure culture experiments and their characteristics are summarized in the following table. The highest SA concentration (8.8 g/L) and space time yield (0.6 g/[L h]) were achieved with DD1, a rumen isolate.
aIsolate DD1 was tested twice in pure culture. once with glucose and once with arabinose.
bC-source, enr. = C-source during enrichment. C-source, pure = C-source during pure culture experiment.
cspace time yield and yield for succinic acid.
3. Conclusion
The established procedure is suitable for enrichment of SA-producers from rumen, digested sludge and pomace. However, SA-producing isolates were exclusively obtained from SA-producing enrichment cultures with rumen material as inoculum. The most promising isolate is the rumen bacterium DD1. It uses glucose and arabinose for SA production. Under not yet optimized conditions almost 9 g/L of SA are produced from 15 g/L of arabinose.
1. Media Preparation
Composition of the cultivation media is described in table 8.
aGlucose concentrations were 15 g/L (in plates) and 20 or 50 g/L (in liquid media).
bMgCO3 Riedel-de Haen, product number: 13117 by Sigma-Aldrich Laborchemikalien GmbH) concentrations were 5 g/L (in plates) and 0 or 30 g/L (in liquid media).
5 g yeast extract, 5 g peptone, MgCO3 and (for solid media) 12 g Bacto-Agar were mixed in 900 mL distilled water and autoclaved (20 min). After cooling down to about 65° C. the missing components were added as sterile stock solutions. Glucose, ammonium sulfate and K2HPO4 were all separately autoclaved. Ca-, Mg- and Na-chlorides were autoclaved together.
2. MCB Preparation
Two agar plates were freshly inoculated with DD1 and incubated at 37° C. in an anaerobic jar (Anaerocult A, Merck) over night. The biomass was taken off the plates and re-suspended in the MgCO3-free liquid medium with 20 g/L glucose to adjust OD600≈1.0. Inoculation was performed with 0.5 mL of this cell suspension. Cultivations were performed in 100 mL-serum bottles with gas tight butyl rubber stoppers (Ochs GmbH, Bovenden/Lenglern, Germany) containing 50 mL of the liquid medium with 20 g/L glucose and 30 g/L MgCO3 and a CO2-atmosphere with 0.8 bar overpressure. The serum bottles (in total 10) were incubated at 37° C., a rotary speed of 160 rpm and a shaking diameter of 2.5 cm.
To monitor glucose consumption the cultivation of one bottle was stopped and sampling and HPLC analysis were performed after 0, 3, 4, 5, 7, 8 and 8.5 h. After 8.5 h (the glucose concentration was 3.4 g/L) the cultivation was stopped. Aliquots of 0.5 mL cell suspension and 0.5 mL sterile glycerol were filled in cryovials, mixed and stored for 13 h at −20 and afterwards at −80° C. as MCB. The MCB was tested for purity by streaking a loop of the last cryovial on agar plates for contamination control and checking in liquid culture (media as described table 8) the product spectrum and for contamination (by microscopy). HPLC conditions were the same as those described in example 1.
3. WCB Preparation
One vial of the MCB was used to inoculate a 100 mL-serum bottle with gas tight butyl rubber stopper (see above) containing 50 mL of the liquid medium with 50 g/L glucose. Incubation was performed for 10 h at 37° C. in a shaking incubator (rotary speed: 180 rpm, shaking diameter: 2.5 cm). At the end of the cultivation the glucose concentration was 20 g/L and the pH around 6.5. Aliquots of 0.5 mL cell suspension and 0.5 mL sterile glycerol were filled in cryovials, mixed and stored at −80° C. as WCB. Purity checks were the same as for the MCB. HPLC conditions were the same as those described in example 1.
The taxonomic characterization of strain DD1 was performed via 16S- and 23S rDNA analysis which was conducted as described below:
Extraction of genomic DNA, PCR-mediated amplification of the 16S rDNA and purification of PCR products were carried out as described by Rainey et al., 1996. A DNA fragment containing the 23S rDNA was amplified by the same method, using the forward primer 5′-AGTAATAACGAACGACACAG-3′ (SEQ ID NO: 9) and the reverse primer 5′-AGCCGATTCCCTGACTAC-3′ (SEQ ID NO: 10). Purified PCR products were sequenced using the CEQ™DTCS-Quick Start kit (Beckman Coulter) as directed in the manufacturer's protocol. The CEQ™8000 Genetic Analysis System was used for electrophoresis of the sequence reaction products. The ae2 editor (Maidak et al., 1999) was used to align the 16S rDNA sequence of strain DD1 against those of representative members of the γ-subclass of the Proteobacteria available from the EMBL and RDP databases. For the construction of the phylogenetic tree procedures of PHYLIP (Phylogeny Inference Package, version 3.5c., distributed by J. Felsenstein, Department of Genome Sciences, University of Washington, Seattle, USA) were used: Pairwise evolutionary distances were calculated using the method of Jukes and Cantor (1969), the phylogenetic tree was constructed from these distances using the neighbor joining method (Saitou & Nei, 1987).
The 16S rDNA-based phylogenetic tree is depicted in
One vial of the WCB (example 2) was used to inoculate a 100 mL-serum bottle with gas tight butyl rubber stopper (see above) containing 50 mL of the liquid medium with 50 g/L glucose (composition and preparation as described in example 2). Incubation was performed for 15 h at 37° C. and 170 rpm (shaking diameter: 2.5 cm). At the end of the cultivation the glucose concentration had decreased to about 17 g/L (Measurement via HPLC, conditions as described in example 1). To examine the cell morphology of DD1 single cells were observed using light microscopy. To characterize the colony morphology of DD1a loop of the cell suspension was streaked on Brain Heart Infusion plates (Bacto Brain Heart Infusion, product number: 237500 solidified with 12 g/L Bacto Agar, product number: 214010; both by Becton, Dickinson and Company) and incubated aerobically and anaerobically (Anaerocult A, Merck) at 37° C.
Cells of DD1 appear as rods that occur singly, in pairs or short chains (see
Utilization of different C-sources by DD1 was tested under the conditions described by Lee et al., 2002a.
1. Medium Preparation
Composition of the cultivation medium is described in table 9.
Yeast extract, polypeptone and MgCO3 were autoclaved together. After cooling down the missing components were added as sterile stock solutions. Glucose and the other C-sources, ammonium sulfate and K2HPO4 were all separately autoclaved. Ca-, Mg- and Na-chlorides were autoclaved together. Na2S*9H2O was added to a final concentration of 1 mg/L to ensure anaerobic conditions.
2. Cultivations and Analytics
For growing the seed culture one vial of the WCB was used to inoculate a 100 mL-serum bottle with gas tight butyl rubber stopper (see above) containing 50 mL of the liquid medium described in table 9 but with 20 g/L glucose and a CO2-atmosphere with 0.8 bar overpressure. Incubation was performed for 13 h at 37° C. and 160 rpm (shaking diameter: 2.5 cm). The cell suspension was centrifuged (Biofuge primo R, Heraeus,) with 5000 g for 5 minutes and the cell pellet was washed and then resuspended in 50 mL medium without a carbon source and without MgCO3 to generate a glucose-free inoculum (all steps at room temperature and in the anaerobic chamber).
The main cultures were grown in 100 mL-serum bottles containing in 50 mL liquid medium with 10 g/L of the respective C-source (D-mannitol, D-fructose, D-xylose, sucrose, maltose, lactose, xylitol, inositol, D-sorbitol, glycerol, L-arabinose, D-galactose or D-mannose) and a CO2-atmosphere with 0.8 bar overpressure. For the test for glycerol utilization the quality ‘Glycerol 99%, puriss.’ (Riedel-de Haen, product numer: 15523-1 L-R by Sigma-Aldrich Laborchemikalien GmbH, Seelze, Germany) was used. Inoculation was performed with 1.5 mL of the glucose-free inoculum. The bottles were incubated at 37° C., and 160 rpm (shaking diameter: 2.5 cm). Utilization of the respective C-source by DD1 was regarded as positive when at least 3 g/L of the C-source were consumed within 24 h. To verify the results obtained in the main culture 1 mL of the respective main culture was used to inoculate 50 mL of fresh cultivation medium with 10 g/L of the respective C-source. The results were therefore confirmed in two subsequent main cultivations. Consumption of the C-sources was quantified via HPLC as described in example 1. When glycerol was measured the column temperature was adjusted to 50° C. to achieve a sufficient separation of SA, lactic acid and glycerol which have similar retention times.
3. Results
The results are summarized in the following table 10.
aAnalyses for consumption of each C-source after 24 h. Cultivations were conducted as duplicates.
bdata from data from Lee et al., 2002a. ND = not determined.
Said table shows that the C-source utilization pattern of the two strains differs with respect to glycerol. DD1 can metabolize glycerol which is not used by MBEL 55E.
In addition to sucrose, D-glucose and D-fructose DD1 utilizes D-xylose, L-arabinose, D-galactose and D-mannose. Hence all types of monosaccharides in lignoellulose (Kamm et al., 2006; Lee, 1997) are utilized by DD1. Utilization of L-arabinose, D-galactose and D-mannose by MBEL55E was not tested by Lee et al., 2002a.
DD1's succinic acid (SA) productivity on glycerol, D-xylose, L-arabinose, D-galactose and D-mannose was evaluated in serum bottle trials with 10 g/L of the respective C-source (10 g/L glucose as reference).
1. Medium Preparation
Composition and preparation of the cultivation media were the same as in example 2 (seed culture) and example 5 (main cultures).
2. Cultivations and Analytics
Growth of the seed culture in liquid medium with 50 g/L glucose and 30 g/L MgCO3 was done as described in example 2. Preparation of the glucose-free inoculum was performed as described in example 5.
Growth of the main cultures with 10 g/L glycerol, sucrose, D-xylose, D-Fructose, L-arabinose, D-galactose, D-mannose or D-glucose and 10 g/L MgCO3 was done as described in example 5. Consumption of the respective C-source and production of SA and by-products were quantified by HPLC as described in example 5.
3. Results
In the following table 11 the results are summarized.
acultivation time.
bconsumption of carbon source.
cformation of succinic, lactic, formic and acetic acid.
dspace time yield and yield for succinic acid.
Table 11 shows that in all cases substantial SA-amounts are formed. SA production from glycerol (glyc) instead of sucrose (suc), D-glucose (gluc), D-fructose (fruc), D-xylose (xyl), L-arabinose (ara), D-galactose, (gal) or D-mannose (man) by DD1 has two obvious advantages: i) a substantially higher yield, ii) a substantially lower formic and acetic acid formation. On the other hand the SA productivity (space time yield) with glycerol is slightly lower than with the sugars. However, DD1's SA productivity with glycerol is substantially higher than the value obtained with Anaerobiospirillum succiniciproducens by Lee et al., 2001 (0.14 g SA/[L h]).
Especially the substantially higher Yield achieved with glycerol is a very interesting result: It can contribute to a clear reduction of production cost for fermentative succinic acid, succinic acid salts and BDO/GBL/THF or pyrrolidones made from it, respectively—in particular if the cheap crude glycerol from biodiesel plants can be applied.
DD1's SA productivity on different crude glycerols (C1 to C3) was evaluated in serum bottle trials with 10 g/L of the respective glycerol (10 g/L pure glycerol [P1] as reference).
1. Medium Preparation
The medium composition is described in the following table 12.
aConcentrations were 50 g/L of glucose in the seed culture and 10 g/L of the respective glycerol in the main culture.
MgCO3 and water (1.5 g and 40 mL) were sterilized in 100 mL-serum bottles (121° C., 20 min). After cooling down separate sterile solutions of the other compounds were added. Yeast extract, peptone, ammonium sulfate and K2HPO4 were all separately sterilized by filtration of the respective stock solution. For Ca-, Mg- and Na-chlorides one stock solution was prepared which was sterilized by filtration. Glucose and the different glycerols were all separately sterilized (121° C., 20 min). For the reference trial with pure glycerol (P1) the quality ‘Glycerol 99%, puriss.’ (Riedel-de Haen, product numer: 15523-1L-R) by Honeywell Specialty Chemicals Seelze GmbH, Seelze, Germany, was used.
2. Cultivations and Analytics
The seed culture was grown in a 100 mL-serum bottle with gas tight butyl rubber stopper (see above) containing 50 mL of the medium described in table 12 with 50 g/L glucose and a CO2-atmosphere with an overpressure of 0.8 bar. Inoculation was conducted with 1 mL of the WCB (example 2). Incubation was performed for 15 h at 37° C. and 170 rpm (shaking diameter: 2.5 cm). At the end of the cultivation the glucose concentration had decreased to about 17 g/L.
The cell suspension was centrifuged (Biofuge primo R, Heraeus) with 5000 g for 5 minutes and the cell pellet was washed and then resuspended in 50 mL of the medium without glucose and without MgCO3 to generate a glucose-free inoculum.
The main cultures were grown in 100 mL-serum bottles containing in 50 mL of the medium with 10 g/L of the respective glycerol and a CO2-atmosphere with 0.8 bar overpressure. Inoculation was performed with 2.0 mL of the glucose-free inoculum. The bottles were incubated for 9 h at 37° C., and 170 rpm (shaking diameter: 2.5 cm).
Consumption of the respective C-source (glucose in seed culture, glycerol in main culture) and production of SA and by-products was measured by HPLC as described in example 5.
3. Results
In the following table 13 the results are summarized.
aecoMotion GmbH, Stemberg, Germany; Biopetrol Schwarzheide GmbH, Schwarzheide, Germany; Glacon Chemie, Merseburg, Germany: Riedel de Haen (product number: 15523-1L-R) by Sigma-Aldrich Laborchemikalien GmbH, Seeize, Germany.
bProducer's analysis.
ccultivation time.
dconsumption of glycerol.
eformation of succinic, lactic, formic and acetic acid.
fspace time yield and yield for succinic acid.
Table 13 shows that after 9 h the SA concentration and hence the STY obtained with the crude glycerols C1 to C3 (7.4 to 8.4 g SA/L and 0.8 to 0.9 g SA/[L h]) is in all cases higher than the respective values obtained with the pure glycerol P1 (6.2 g SAIL and 0.7 g SA/[L h]). The crude glycerols have therefore in addition to the lower price the advantage of better productivity. The Yields obtained with the crude glycerols C1 to C3 (1.1 to 1.2 g SA/g glycerol) are similar to the respective value obtained with the pure glycerol P1 (1.1 g SA/g glycerol).
A common approach for the fermentative production of succinic acid and/or succinic acid ammonium salts from glucose would be a NH3-controlled fed batch cultivation with a certain initial glucose level. This set-up requires both NH3/NH4OH— and glucose tolerance of the strain. To test DD1 for these properties batch cultivations with NH4OH as pH-control agent and varying glucose levels were performed.
1. Medium Preparation
Composition of the cultivation medium is described in table 14.
aThe initial glucose concentration in the preculture was 50 g/L and in the fermentors 25, 50 or 75, respectively.
Yeast extract, peptone and MgCO3 were autoclaved together in the fermentors and serum bottles. Glucose, ammonium sulfate and K2HPO4 were all separately autoclaved. Ca-, Mg- and Na-chlorides were autoclaved together. After cooling down the fermentors and serum bottles the missing components were added as sterile stock solutions. For the precultures the same medium composition was used but MgCO3 was adjusted to 30 g/L.
2. Cultivations and Analytics
Precultures were grown anaerobically in 100 mL-serum bottles with gas tight butyl rubber stoppers (Ochs GmbH, Bovenden/Lenglern, Germany) containing 50 mL preculture medium at 37° C. in a shaking incubator (rotary speed: 160 rpm, shaking diameter: 2.5 cm). Inoculation of the precultures was performed with 1 mL of a DD1-working cell bank in the anaerobic chamber (MAKS MG 500, meintrup-dws). Immediately after the inoculation the gas atmosphere (80% N2, 15% CO2 and 5% H2) was substituted by pure CO2 with an overpressure of about 0.8 bar. After 16 to 18 h of incubation two bottles were pooled in the anaerobic box and in each case 15 mL were used to inoculate the fermentors (Sixfors, Infors, Switzerland) containing 300 mL cultivation medium which had been gassed over night with CO2 to ensure oxygen-free conditions. Cultivation temperature was 37° C., the pH of 6.5 was maintained with 25% NH4OH. CO2-gas stream and stirrer speed were adjusted to 0.1 L/min and 500 rpm, respectively. Consumption of glucose and production of SA were quantified by HPLC as described in example 1.
3. Results
The results are shown in
In NH4OH-controlled batch cultivations with glucose up to 40 g/L SA are formed within 48 h. DD1 has therefore a strong synthesis potential for succinic acid and/or succinic acid ammonium salts which are favourable for the chemical conversion to THF/BDO/GBL and pyrrolidones (WO-A-2006/066839).
The initial SA production rate in the trials with 75 g/L of glucose is slightly lower than in the trials with 50 and 25 g/L. However, between 6 and 12 h there is no such difference anymore indicating that substrate inhibition is not an issue at glucose levels of up to 75 g/L.
In this experiment cultivation temperature and -pH were varied in NH4OH-controlled batch cultivations with 75 g/L glucose.
1. Medium Preparation
Apart from the constant glucose concentration medium composition and preparation were the same as those in example 8 ‘Ammonia and glucose tolerance of DD1’.
2. Cultivations and Analytics
Apart from the different cultivation temperatures and -pH-values tested the experimental conditions of the cultivations and HPLC analyses were identical to those in example 8 ‘Ammonia and glucose tolerance of DD1’.
3. Results
The results are shown in
Enrichment and isolation of DD1 was performed in a cultivation medium containing 5 g/L yeast extract and 5 g/L peptone. Therefore the first experiments with DD1 were conducted in a medium with these compounds. Since they contribute to cost for raw materials and introduce additional impurities, different media compositions were tested in which yeast extract and peptone are reduced and substituted by the cheaper corn steep liquor (Solulys L48L, Roquette), respectively. The initial media composition of the trials is indicated by figures (representing the concentration, i.e. 2, 5, 15 or 25 g/L) and letters (representing the respective complex compound, i.e. yeast extract, peptone or corn steep liquor).
1. Medium preparation
Apart from the respective modification of the yeast extract—and peptone—concentration and the additional corn steap liquor medium composition and—preparation were the same as those in example 8 ‘Ammonia and glucose tolerance of DD1’. The batch concentration of glucose was 50 g/L in all trials.
2. Cultivations and Analytics
The experimental conditions were identical to those in example 8 ‘Ammonia and glucose tolerance of DD1’. All cultivations were performed at 37° C., the cultivations in fermentors were maintained at pH 6.5 with 25% NH4OH. HPLC analyses were performed as described in example 8.
3. Results
The results are shown in
The by-product spectrum of the trials ‘5Y5P’ and ‘5Y’ is shown in
Since the fermentative SA production is a process that depends on anaerobic conditions, the cultivation of DD1 for SA production has to be performed in the absence of oxygen. However, it is very important to know if DD1 tolerates the presence of oxygen, too. If this is the case the strain can be handled under aerobic conditions which makes the lab work a lot easier and faster. Therefore strain DD1 was tested in shake flask experiments with glucose.
1. Medium Preparation
Medium composition and preparation were the same as described in table 8.
2. Cultivations and Analytics
Anaeorbic seed cultures were grown in 100 mL-serum bottles with gas tight butyl rubber stoppers (see above) containing 50 mL medium with 50 g/L of glucose and 30 g/L of MgCO3 and a CO2-atmosphere with an overpressure of 0.8 bar at 37° C. and 160 rpm (shaking diameter: 2.5 cm) for 16 h. Inoculation was performed with 1 mL of the WCB (example 2). 7.5 mL of these precultures were used to inoculate the aerobic main cultures.
Aerobic main cultures (150 mL medium with 60 g/L of glucose and 80 g/L of MgCO3) were grown at 37° C. and 200 rpm (shaking diameter: 2.5 cm) in 500 mL Erlenmeyer flasks with two baffles and cotton plugs. Substrate consumption and product formation were measured by HPLC as described in example 1.
3. Results
The results are shown in
The closest relative of DD1 is “Mannheimia succiniciproducens” MBEL 55E, a strain isolated by KAIST (see above). To compare DD1 with said strain the cultivation experiment described by KAIST (
1. Medium Preparation
The composition of the cultivation medium was identical to the respective experiment of Lee et al., 2002b and is described in the following table 15.
Yeast extract, peptone and MgCO3 were autoclaved together in the fermentors and serum bottles. Glucose, ammonium sulfate and potassium phosphate were all separately autoclaved. Ca-, Mg- and Na-chlorides were autoclaved together. After cooling down the fermentors and serum bottles the missing components were added as sterile stock solutions. For the seed cultures the same medium was used.
2. Cultivations and Analytics
The seed culture was grown anaerobically in a 100 mL-serum bottle with gas tight butyl rubber stoppers containing 50 mL medium at 39° C. in a shaking incubator (rotary speed: 160 rpm, shaking diameter: 2.5 cm). Inoculation of the seed culture was performed with 1 mL of the WCB (example 2) in the anaerobic chamber (MAKS MG 500, meintrup-dws). Immediately after the inoculation the gas atmosphere (80% N2, 15% CO2 and 5% H2) was substituted by pure CO2 with an overpressure of about 0.8 bar. After 9 h of incubation the fermentor was inoculated with 30 mL to start the cultivation in the fermentor (Sixfors, Infors Switzerland) containing 300 mL cultivation medium which had been gassed over night with CO2 to ensure oxygen-free conditions. The cultivation temperature was maintained at 39° C. and the pH at 6.5 with 5 M NaOH. The CO2-gas stream was adjusted to 0.25 vvm. The stirrer speed was adjusted to 500 rpm.
Glucose consumption and SA and by-product formation were measured by HPLC as described in example 1.
3. Results
The results are summarized in
It is favorable to use a synthetic medium without complex ingredients for the fermentation of DD1 in order to improve downstream processing and design a lean synthetic medium for cost efficient fermentation. Therefore, a synthetic medium was designed for DD1. Meanwhile, a synthetic medium had also been published for the close relative Mannheimia succiniciproducens (Song et al, 2008). Essential and stimulatory compounds had been determined for growth of DD1. Comparing the results with Mannheimia succiniciproducens obvious differences were observed, hinting to a more economic growth medium suitable for the strain DD1.
1. Medium Preparation
The synthetic growth medium for DD1 was developed in relation to other synthetic growth media for rumen bacteria (Nili and Brooker, 1995, McKinlay et al, 2005), previous in house experience with other bacteria and by performing single omission experiments. Finally, the medium contained 50 g/L glucose, 1 g/L (NH4)2SO4, 0.2 g/L CaCl2*2H2O, 0.2 g/L MgCl2*6H2O, 1 g/L NaCl, 3 g/L K2HPO4, 1 mg/L nicotinic acid, 1.5 mg/L pantothenic acid, 5 mg/L pyridoxine, 5 mg/L riboflavin, 5 mg/L biotin, 1.5 mg/L thiamin HCl, 0.26 g/L lysine, 0.15 g/L threonine, 0.05 g/L methionine, 0.71 g/L glutamic acid, 0.06 g/L histidine, 0.07 g/L tryptophane, 0.13 g/L phenylalanine, 0.06 g/L tyrosine, 0.5 g/L serine, 0.5 g/L glycine, 0.5 g/L cysteine, 0.1 g/L β-Alanine, 0.27 g/L alanine, 0.19 g/L valine, 0.23 g/L leucine, 0.16 g/L isoleucine, 0.33 g/L aspartic acid, 0.1 g/L asparagine, 0.13 g/L proline, 0.15 g/L arginine and 0.1 g/L glutamine.
Serum bottles containing 50 mL of complex or synthetic medium were autoclaved with water and 30 g/L MgCO3 as the buffer system. Glucose, ammonium sulfate and potassium phosphate were sterilized, separately. Ca-, Mg- and Na-chlorides were sterilized together. Vitamins and amino acids were assembled in various stock solutions and filter sterilized. After cooling down the serum bottles the components were added as sterile stock solutions.
Standard complex medium was prepared as described in example 12 without using polypeptone and starting at 50 g/L glucose and 30 g/L MgCO3. For seed cultures and some main culture control experiments complex medium was used.
2. Cultivations and Analytics
The seed culture was grown in complex medium anaerobically using a 100 mL-serum bottle with gas tight butyl rubber stoppers containing 50 mL medium at 37° C. in a shaking incubator (rotary speed: 170 rpm, shaking diameter: 2.5 cm). Inoculation of the first seed culture was performed aerobically with 1 mL of the WCB (example 2) under sterile conditions. Immediately after inoculation the aerobic gas atmosphere was substituted by pure CO2 with an overpressure of about 0.8 bar. After 8 h of incubation 2 ml of the first seed culture was centrifuged and washed three times using a sterile wash solution containing 2 g/L (NH4)2SO4, 0.4 g/L CaCl2*2H2O, 0.4 g/L MgCl2*6H2O, 2 g/L NaCl and 6 g/L K2HPO4 before inoculation into the second seed culture 100 mL-serum bottle.
The incubation of the second seed culture occurred for 20 h as described for the first seed culture, before using 2 mL of the second culture again in order to inoculate the main culture, which was incubated for another 20 h. In order to determine essential or stimulatory compounds, the vitamin or amino acid of interest was omitted in the second seed culture and the main culture. Glucose consumption and Succinic acid formation were measured by HPLC as described in example 1.
3. Results
The results are summarized in table 16. It was observed that the medium omitting biotin and thiamin HCl did not sustain growth and succinic acid production. Biotin and thiamin HCl were therefore shown to be essential compounds for growth of DD1. Concentrations of biotin lower than 0.6 mg/L were sufficient for growth of DD1. The amino acid cysteine was found to be not essential for growth off DD1, as the omitting of cysteine lead to similar succinic acid production as in the cysteine containing control.
In contrast to these results, biotin was described as not essential but stimulatory and cysteine as essential for growth of Mannheimia succiniciproducens (Song et al, 2008). Thiamin HCl is essential for both organisms. A strain prototrophic for cysteine is expected to have a leaner and cheaper production medium for succinic acid production.
The productivity of the strain DD1 in the presence of gylcerol as a carbon source was further analyzed utilizing the following optimized medium and incubation conditions:
1. Medium Preparation and Cultivation
DD1 was grown in the following fashion. Cells from a frozen stock solution were streaked on an BHI-Agar plate (Becton Dickinson). Cells were scraped off and suspended in fresh BHI medium and incubated in an anaerobic serum bottle at 37° C. for 5.5 h. Cells were inoculated in the medium containing the compounds described in table 17 using 100 mL serum bottles. The start OD at 600 nm was 0.1 (determined in a 1 mL path). The medium components 1-7 were autoclaved together, compound 8 was autoclaved in the serum bottle, compounds 9 and 10 were autoclaved separately and added to the final medium. Serum bottles were sparged at least three times with CO2 through butyl-rubber stoppers and left with a CO2 overpressure of 0.8 bar. Serum bottles were incubated at 200 rpm and 37° C. After 24 h serum bottles were opened and metabolites were determined by HPLC as described in example 1.
ccultivation time.
dconsumption of glycerol.
eformation of succinic, lactic, formic and acetic acid.
fspace time yield and yield for succinic acid.
gratio g/L succinic acid per g side product formic acid (FA) and acetic acid (AA)
2. Results:
The following results were obtained as described in table 18. DD1 produced 35.3 g/L succinic acid from 28.4 g/L glycerol in 24 h, leading to a space time yield of 1.47 g/L succinic acid per h, which is superior to other documented examples of glycerol metabolisation (Lee et al. 2001). The yield of 1.24 g/g was close to the described theoretical yield of 1.29 g succinic acid per g of glycerol, if the turnover of 1M glycerol and 1M CO2 to 1M succinic acid is achieved (Song and Lee, 2006).
The productivity of DD1 in the presence of two carbon sources was determined. DD1 was grown in the presence of the disaccharide maltose and glycerol simultaneously.
1. Medium Preparation and Cultivation
Cells from a frozen stock solution were streaked on a BHI-Agar plate (Becton Dickinson). Cells were scraped off and suspended in fresh BHI medium and incubated in an anaerobic serum bottle at 37° C. for 5.5 h. The medium is described in table 19. 200 mL serum bottles were used. Cells were inoculated with a start OD of 0.1 (determined in a 1 mL path with a pharmacia photometer at 600 nm). Serum bottles were sparged at least three times with CO2 through butyl-rubber stoppers and left with a CO2 overpressure of 0.8 bar. Serum bottles were incubated at 200 rpm and 37° C.
The seed culture was inoculated with a 2 mL frozen culture grown anaerobically in a 200 mL serum bottle with gas tight butyl rubber stoppers containing 50 mL medium at 37° C. in a shaking incubator (rotary speed: 160 rpm, shaking diameter: 2.5 cm). The bottle was sparged by pure CO2 with an overpressure of about 0.8 bar. After 8 h of incubation the fermentor was inoculated with 50 mL to start the cultivation in the fermentor containing 1 L cultivation medium which had been gassed with CO2 to ensure oxygen-free conditions. The cultivation temperature was maintained at 37° C. and the pH at 6.5 without addition of bases except the buffer MgCO3 in the medium. The CO2-gas stream was adjusted to 0.2 vvm. The stirrer speed was adjusted to 300 rpm. Maltose and glycerol consumption and SA and by-product formation were measured by HPLC as described in example 1. Cells were grown at 37° C. and biomass was determined taking a sample and dissolving the residual MgCO3 by the addition of 1M HCl. After dissolving MgCO3 cells were washed with water and dried by lyophilization. Dry biomass was determined by weighing.
Results:
The results are summarized in table 20. Within 16 h of incubation 36.5 g/L of glycerol and 11.2 g/L maltose are consumed and 57.54 g/L of succinic acid, 3.41 g/L of acetic acid and 3.7 g/L of formic acid are formed by DD1. The space time yield obtained with DD1 for succinic acid is 3.4 g/(L h), which is clearly higher than previously reported for the strain MBEL55E and Anaerobiospirillum succiniciproducens and is superior to other strains described in literature (Lee et al, 2002b, Lee et al, 2001, Song and Lee, 2006).
The succinic acid yield was determined as 1.2 g succinic acid per g of carbon source for the sum of glycerol and maltose. This yield is also superior to strains described in literature (Lee et al, 2002b, Lee et al, 2001, Song and Lee, 2006).
The space time yield of 3.7 g/(L h) succinic acid is superior to strains described in literature (Song et al, 2006)
In addition the specific productivity for succinic acid of 0.77 [g gDCW−1 h−1]h was found to be superior to strains described in literature (Song et al, 2006).
bcultivation time
cdry biomass as determined by solubilisation of MgCO3.
dconsumption of glycerol or maltose
eformation of succinic, formic and acetic acid
fspace time yield g succinic acid per (L *h)
gyield g succinic acid per g substrate (sum of maltose and glycerol)
hSpecific productivity: g succinic acid per g biomass (dry cell weight) per h
In the context of the present invention a bacterial strain DD1 was deposited with Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSMZ, Inhoffenstr. 7B, D-38124 Braunschweig, Germany) on Aug. 11, 2006 having the deposit number DSM 18541. Access to this deposit will be available during the pendency of the application to the Commissioner of Patents and Trademarks and persons determined by the Commissioner to be entitled thereto upon request. Upon granting of any claims in the application, the Applicants will make the deposit available to the public pursuant to 37 CFR §1.808. The deposit will be maintained in the DSMZ Depository, which is a public depository, for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent, whichever is longer, and will be replaced if it becomes nonviable during that period. Applicants have no authority to waive any restrictions imposed by law on the transfer of biological material or its transportation in commerce. Applicants do not wave any infringement of their rights granted under this patent.
| Number | Date | Country | Kind |
|---|---|---|---|
| 07114574 | Aug 2007 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP2008/006714 | 8/14/2008 | WO | 00 | 2/16/2010 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2009/024294 | 2/26/2009 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 4550185 | Mabry et al. | Oct 1985 | A |
| 5504004 | Guettler et al. | Apr 1996 | A |
| 5573931 | Guettler et al. | Nov 1996 | A |
| 5723322 | Guettler et al. | Mar 1998 | A |
| 6596521 | Chang et al. | Jul 2003 | B1 |
| 7063968 | Lee et al. | Jun 2006 | B2 |
| 7192761 | Zeikus et al. | Mar 2007 | B2 |
| 7256016 | San et al. | Aug 2007 | B2 |
| 7262046 | Ka-Yiu et al. | Aug 2007 | B2 |
| 7470531 | Rehberger et al. | Dec 2008 | B2 |
| 20070042481 | Lee et al. | Feb 2007 | A1 |
| 20080293101 | Peters et al. | Nov 2008 | A1 |
| 20090137825 | Bauduin et al. | May 2009 | A1 |
| 20090155869 | Buelter et al. | Jun 2009 | A1 |
| 20100044626 | Fischer et al. | Feb 2010 | A1 |
| 20100159542 | Scholten et al. | Jun 2010 | A1 |
| 20100159543 | Scholten et al. | Jun 2010 | A1 |
| 20100324258 | Zelder et al. | Dec 2010 | A1 |
| 20110300589 | Schroder et al. | Dec 2011 | A1 |
| Number | Date | Country |
|---|---|---|
| 0805208 | May 1997 | EP |
| 1842843 | Oct 2007 | EP |
| 2202294 | Jun 2010 | EP |
| 2204443 | Jul 2010 | EP |
| 2008011714 | Jan 2008 | JP |
| WO-0200846 | Jan 2002 | WO |
| WO-03040690 | May 2003 | WO |
| WO-2005052135 | Jun 2005 | WO |
| WO-2006034156 | Mar 2006 | WO |
| WO-2006066839 | Jun 2006 | WO |
| WO-2008013405 | Jan 2008 | WO |
| WO-2009024294 | Feb 2009 | WO |
| Entry |
|---|
| Guettler et al (Int'l J. of Systematic Bacter., 1999, vol. 49, pp. 207-216). |
| Lee et al. (Applied and Environmental Microbiology, vol. 72, No. 3, Mar. 2006, pp. 1939-1948). |
| Redfield et al. (BMC Evolutionary Biology, 2006, vol. 6 (82), pp. 1-15). |
| Lee et al. (Appl. Microbiol. Biotechnol., 2002, vol. 58, pp. 663-668). |
| Vlysidis et al. ( AlChE100 2008 Annual Meeting). |
| Zeikus (Appl. Microbiol Biotech., 1999, vol. 51, pp. 545-552). |
| Database Em-Pro Mannheimia succiniproducens MBEL55E Sep. 18, 2004, XP002498827 accession No. AE016827 nt 1495543-151059 nt 2233952-2235468 99.7% identity with Seq ID 1 abstract. |
| Dharmadi Y, et al., “Anaerobic Fermentation of Glycerol by Escherichia coli: A New Platform for Metabolic Engineering,” Biotechnology and Bioengineering, vol. 94, No. 5, pp. 821-829 (2006). |
| Hong S.H. et al., “The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens” Nature Biotechnology, vol. 22, No. 10, (Oct. 2004), pp. 1275-1281, XP002498825 ISSN: 1087-0156 table 1. |
| Janssen P.H., “Characterization of a succinate-fermenting anaerobic bacterium isolated from a glycolate-degrading mixed culture,” Arch Microbiol (1991)155: pp. 288-293. |
| Lee J., “Biological conversion of lignocellulosic biomass to ethanol,” Journal of Biotechnology 56: (1997) pp. 1-24. |
| Lee P.C., et al., “Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducens MBEL55E, from bovine rumen,” Appl Microbiol Biotechnol (2002a) 58: pp. 663-668. |
| Lee P.C., et al., Succinic Acid Production with Reduced By-Product Formation in the Fermentation of Anaerobiospirillum succiniciproducens Using Glycerol as a Carbon Source, Biotechnology and Bioengineering, vol. 72, No. 1, pp. 41-48 (2001). |
| Maidak B.L., et al., “A new version of the RDP (Ribosomal Database Project),”. Nucleic Acids Research, 1999, vol. 27, No. 1, pp. 171-173. |
| McKinlay J, Zeikus J, Vieille C (2005) Insights into Actinobacillus succinogenes fermentative metabolism in a chemically defined growth medium. Appl Environ Microbiol 71: 6651-6656. |
| Nili N., et al., “A defined medium for rumen bacteria and identification of strains impaired in de novo biosynthesis of certain amino acids,” Letters in Applied Microbiology 1995, 21d pp. 69-74. |
| Peters-Wendisch, P.G. et al.,C3-Carboxylation as an anaplerotic reaction in phosphoenolpyruvate carboxylase-deficient Corynebacterium glutamicum, Arch Microbiol (1996) 165: pp. 387-396. |
| Rainey F.A., et al., “The genus Nocardiopsis Represents a Phylogenetically Coherent Taxon and a Distinct Actinomycete Lineage: Proposal of Nocardlopsaceae fam. nov.,” International Journal of Systematic Bacteriology, vol. 46, No. 4, 1996, pp. 1088-1092. |
| Saitou N., et al., “The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees,”. Mol. Biol. Evol. 4(4): pp. 406-425 (1987). |
| Schoelten E., et al., “Succinic acid production by a newly isolated bacterium” Biotechnol. Lett., Jul. 24, 2008, XP002498826 [retrieved on Aug. 7, 2008] DOI 10.1007/s10529-008-9806-2. |
| Song H., et al., “Production of succinic acid by bacterial fermentation,” Enzyme and Microbial Technology 39: (2006) pp. 352-361. |
| Song H., et al., “Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence,” Appl Microbiol Biotechnol (2008) 79: pp. 263-272. |
| Yazdani S, et al., “Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry,” Current Opinion Biotechnology 2007,18: pp. 213-219. |
| “SubName: Full-Isocitrate lyase”, EMBL database, Accession No. A1JRX1, Feb. 6, 2007. |
| “RecName: Full-Malate synthase” EMBL database, Accession No. A1JRX8, Feb. 6, 2007. |
| “pflD PflD protein [Mannheimia succiniciproducens MBEL55E]”, Database NCBI, Accession No. 3075405, Dec. 18, 2010. |
| “IdhA D-lactate dehydrogenase [Mannheimia succiniciproducens MBEL55E (strain; MBEL55E”, Database NCBI, Accession No. 3075603, May 21, 2011. |
| “pflA pyruvate formate lyase-activating enzyme 1 [Shigella boydii CDC 3083-94]”, Database NCBI, Accession No. 6268899, Jan. 14, 2011. |
| “ybiW predicted pyruvate formate lyase [Escherichia coli str. K-12 substr. MG1655]”, Database NCBI, Accession No. 945444, Feb. 28, 2011. |
| “pflB pyruvate formate lyase I [Escherichia coli str. K-12 substr. MG1655]”, Database NCBI, Accession No. 945514, Feb. 28, 2011. |
| “IdhA fermentative D-lactate dehydrogenase, NAD-dependent [Escherichia coli str. K-12 substr. MG1655]” Database NCBI, Accession No. 946315, May 21, 2011. |
| “tdcE pyruvate formate-lyase 4/2-ketobutyrate formate-lyase [Escherichia coli str. K-12 substr. MG1655]”, Database NCBI, Accession No. 947623, Feb. 28, 2011. |
| “pflD predicted formate acetyltransferase 2 (pyruvate formate lyase II) [Escherichia coli str. K-12 substr. MG1655]”, Database NCBI Accession No. 948454, Feb. 28, 2011. |
| “pyruvate formate lyase-activating enzyme 1 [Shigella boydii CDC 3083-94]”, Database NCBI, Accession No. YP—001880903.1, Jan. 5, 2011. |
| “Formate acetyltransferase 1”, Database UniProtKB, Accession No. P09373, Feb. 8, 2011. |
| “Formate acetyltransferase 2”, Database UniProtKB, Accession No. P32674, Feb. 8, 2011. |
| “Keto-acid formate acetyltransferase”, Database UniProtKB, Accession No. P42632, Feb. 8, 2011. |
| “Putative formate acetyltransferase”, Database UniProtKB, Accession No. P75793, Feb. 8, 2011. |
| “PflD protein”, Database UniProtKB, Accession No. Q65VK2, Nov. 30, 2010. |
| Berrios-Rivera, S., et al., “The Effect of Increasing NADH Availability on the Redistribution of Metabolic Fluxes in Escherichia coli Chemostat Cultures”, Metabolic Engineering, vol. 4, No. 3, (2002), pp. 230-237. |
| Broun, P., et al., “Catalytic Plasticity of Fatty Acid Modification Enzymes Underlying Chemical Diversity of Plant Lipids”, Science, 1998, vol. 282, pp. 1315-1317. |
| Chica, R.A., et al., “Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design”, Current Opinion Biotechnology, 2005, vol. 16, pp. 378-384. |
| Devos, D., et al., “Practical Limits of Function Prediction”, PROTEINS: Structure, Function and Genetics, 2000, vol. 41, pp. 98-107. |
| Dousse, F., et al., “Routine phenotypic identification of bacterial species of the family Pasteurellaceae isolated from animals,” J. Vet. Diagn. Invest., 2008, vol. 20, pp. 716-724. |
| Durchschlag, H., et al., “Large-Scale Purification and Some Properties of Malate Synthase from Baker's Yeast”, Eur. J. biochem., vol. 114, (1981), pp. 114-255. |
| Eggerer, H., et al., “Über das Katalyseprinzip der Malat-Synthase”, European J. Biochem., vol. 1, (1967), pp. 447-475. |
| European Search Report EP 09 17 8050 dated Feb. 23, 2010. |
| Feng, D.-F., et al., “Progressive Sequence Alignment as a Prerequisite to Correct Phylogenetic Trees”, J. Mol. Evol., vol. 25, (1987), pp. 351-360. |
| Ferry, J. G., “Formate Dehydrogenase”, FEMS Microbiology Reviews, vol. 87, (1990), pp. 377-382. |
| Frey, J., “Construction of a Broad Host Range Shuttle Vector for Gene Cloning and Expression in Actinobacillus pleuropneumoniae and Other Pasteurellaceae”, Res. Microbial, vol. 143, (1992), pp. 263-269. |
| Guo, H.H., et al., “Protein tolerance to random amino acid change”, PNAS, 2004, vol. 101, No. 25, pp. 9205-9210. |
| Higgins, D. G., et al., “Fast and Sensitive Multiple Sequence Alignments on a Microcomputer”, vol. 5, No. 2, (1989), pp. 151-163. |
| Hoyt, J. C., et al., “Escherichia coli Isocitrate Lyase: Properties and Comparisons”, Biochimica et Biophysica Acta, vol. 966, (1988), pp. 30-35. |
| Hong, S. H., et al., “Metabolic Flux Analysis for Succinic Acid Production by Recombinant Escherichia coli with Amplified Malic Enzyme Activity,” Biotechnology and Bioengineering, 2001, vol. 74, No. 2, pp. 89-96. |
| Kim, J. M., et al., “Development of a Markerless Gene Knock-Out System for Mannheimia succiniciproducens Using a Temperature-Sensitive Plasmid”, FEMS Microbiol Lett, vol. 278, (2008), pp. 78-85. |
| Kimchi-Sarfaty, C., et al. “A ‘silent’ polymorphism in the MDR1 gene changes substrate specificity”, Science, 2007, vol. 315, pp. 525-528. |
| Kisselev, L., et al., “Polypeptide release factors in prokaryotes and eukaryotes: same function, different structure”, Structure, 2002, vol. 10, pp. 8-9. |
| Kuhnert, P., et al., “Pasteurellaceae, Biology, Genomics, and Molecular Aspects”, (2008), ISBN 978-1-904455-34-9. |
| Knappe, J., et al., “A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli,” FEMS Microbiology Reviews, 1990, vol. 75, pp. 383-398. |
| Knappe, J., et al., “Pyruvate formate-lyase mechanism involving the protein-based glycyl radical,” Biochemical Society Transactions, 1993, vol. 21, pp. 731-734. |
| Lee, S. Y., et al., “From Genome Sequence to Integrated Bioprocess for Succinic Acid Production by Mannheimia succiniciproducens”, Applied Microbiology Biotechnology, vol. 79, No. 1, (2008), pp. 11-22. |
| Lee, S. Y., “BTEC 18Genome-Scale Metabolic engineering of Mannheimia succiniciproducens for Enhanced Succinic Acid Production”, Genomic and Systems Approaches to Metabolic Engineering, The 229th ACS National Meeting in San Diego, CA., Mar. 13-17, 2005. |
| Leenhouts, K. J., et al., “Campbell-Like Integration of Heterologous Plasmid DNA into the Chromosome of Lactococcus lactis subsp. lactis”, Applied and Environmental Microbiology, vol. 55, (1989), pp. 394-400. |
| Lin, H., et al., “Effect of Sorghum vulgare phosphoenolpyruvate carboxylase and Lactococcus lactis pyruvate carboxylase coexpression on succinate production in mutant strains of Escherichia coli,” Appl. Microbiol. Biotechnol., 2005, vol. 67, pp. 515-523. |
| Mackintosh, C., et al., “Purification and Regulatory Properties of Isocitrate Lyase From Escherichia coli ML308”, Biochem. J., vol. 250, (1988), pp. 25-31. |
| Müller, U., et al., “Formate Dehydrogenase from Pseudomonas oxalaticus”, Eur. J. Biochem, vol. 83, (1978), pp. 485-498. |
| Nackley, A.G., et al. “Human catechol-o-methyltransferase haplotypes modulate protein expression by altering rRNA secondary structure”, Science, 2006, vol. 314, pp. 1930-1933. |
| Needleman, S. B., et al., “A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins”, J. Mol. Biol., vol. 48, (1970), pp. 443-453. |
| Pascal, M. C., et al., “Mutants of Escherichia coli K 12 with Defects in Anaerobic Pyruvate Metabolism,” J. Gen. Microbiol., 1981, vol. 124, pp. 35-42. |
| Robertson, E. F., et al., “Purification and Characterization of Isocitrate Lyase from Escherichia coli”, Current Microbiology, vol. 14, (1987), pp. 347-350. |
| Sanchez, A. M., et al., “Novel pathway engineering design of the anaerobic central metabolic pathway in Escherichia coli to increase succinate yield and productivity,” Metabolic Engineering, 2005, vol. 7, pp. 229-239. |
| Sauna, Z.E., et al., “Silent polymorphisms speak: How they affect pharmacogenomics and the treatment of cancer”, Cancer Research, 2007, vol. 67, No. 2, pp. 9609-9612. |
| Scholten, E., et al., “Continuous Cultivation Approach for Fermentative Succinic Acid Production from Crude Glycerol by Basfia succiniciproducens DD1”, Biotechnol Lett, vol. 31, (2009), pp. 1947-1951. |
| Seffernick, J.L., et al. “Melamine deaminase and atrazine chlorohydrolase; 98 percent identical but functionally different”, J. Bacteriology, 2001, vol. 183, No. 8, pp. 2405-2410. |
| Sen, S., et al, “Developments in directed evolution for improving enzyme functions”, Appl. Biochem. Biotechnol., 2007, vol. 143, pp. 212-223. |
| Smith, T.F., et al., “Identification of Common Molecular Subsequences,” J. Mol. Biol. (1981), vol. 147, pp. 195-197. |
| Sundaram, T. K., et al, “Monomeric Malate Synthase from a Thermophilic Bacillus”, Archives of Biochemistry and Biophysics, vol. 199, No. 2, (1980), pp. 515-525. |
| Thomson, N. R, et al. “The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081”, PLoS Genetics, 2006, vol. 2, No. 12, pp. 2039-2051. |
| Tishkov, V.I, et al., “Catalytic Mechanism and Application of Formate Dehydrogenase”, Biochemistry (Moscow), vol. 69, No. 11, (2004), pp. 1252-1267. |
| Varenne, S., et al., “A Mutant of Escherichia coli Deficient in Pyruvate Formate Lyase,” Molec. Gen. Genet., 1975, vol. 141, pp. 181-184. |
| Watanabe, S., et al., “Purification and Characterization of a Cold-Adapted Isocitrate Lyase and a Malate Synthase from Colwellia maris, a Psychrophilic Bacterium”, Biosci. Biotechnol. Biochem., vol. 65, No. 5, (2001), pp. 1095-1103. |
| Whisstock, J.C.,et al. “Prediction of protein function from protein sequence”, Q. Rev. Biophysics, 2003, vol. 36, No. 3, pp. 307-340. |
| White, W. T., et al., “Species and size compositions and reproductive biology of rays (Chondrichthyes, Batoidea) caught in target and non-target fisheries in eastern Indonesia,” J. Fish Biol., 2007, vol. 70, pp. 1809-1837. |
| Wishart, M.J., et al. “A single mutation converts a novel phosphotyrosine binding domain into a dual-specificity phosphatase”, J. Biol. Chem., 1995, vol. 270, No. 45, pp. 26782-26785. |
| Witkowski, A. et al., Conversion of b-ketoacyl synthase to a malonyl decarboxylase by replacement of the active cysteine with glutamine. Biochemistry, 1999, vol. 38, pp. 11643-11650. |
| Zhang, X., et al., “Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of Escherichia coli,” Applied and Environmental Microbiology, 2010, vol. 76, No. 8, pp. 2397-2401. |
| Zhu, J., et al., “Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition,” Metab. Engineering, 2005, vol. 7, pp. 104-115. |
| International Preliminary Report on Patentability, PCT/EP2010/051798, issued May 12, 2011. |
| International Preliminary Report on Patentability, PCT/EP2008/006714, issued Feb. 24, 2010. |
| European Opinion EP 09 17 8050 dated Feb. 23, 2010. |
| European Search Report EP 09 17 8048 dated Mar. 31, 2010. |
| Patentability Opinion of EP Searching Authority—EP 09 178 048.6, mailed Apr. 13, 2010. |
| Number | Date | Country | |
|---|---|---|---|
| 20110008851 A1 | Jan 2011 | US |
