Patent Application
20140349348
The present invention relates to mutated and/or transformed microorganisms for the synthesis of various compounds. More specifically, the present invention discloses microorganisms mutated in the genes encoding for the regulators ArcA and IclR. The latter mutations result in a significant upregulation of the genes that are part of the colanic acid operon. Hence, said microorganisms are useful for the synthesis of any compound being part of the colanic acid pathway such as GDP-fucose, GDP-mannose and colanic acid, and/or, can be further used—starting from GDP-fucose as a precursor—to synthesize fucosylated oligosaccharides or—starting from GDP-mannose as a precursor—to synthesize mannosylated oligosaccharides. In addition, mutations in the genes coding for the transcriptional regulators ArcA and IclR lead to an acid resistance phenotype in the exponential growth phase allowing the synthesis of pH sensitive molecules and organic acids.
The genes arcA encoding for the aerobic respiration control protein and iclR encoding the isocitrate lyase regulator are known to regulate the central carbon metabolism. ArcA is a global transcriptional regulator that regulates a wide variety of genes, while IclR is a local transcriptional regulator that regulates the glyoxylate pathway. ArcA is known to regulate the central carbon metabolism in response to oxygen deprivation and has no connection with IclR other than that it also regulates the glyoxylate pathway (24, 28, 29, 37, 38). In an earlier study the combined effect of ΔiclRΔarcA mutant strains on the central carbon metabolism has been observed. Increased fluxes were shown in the tricarboxylic acid (TCA) cycle and glyoxylate pathway and an interesting and surprising phenotype appeared when both genes where knocked out, namely the double mutant strain formed biomass with a yield that approached the maximal theoretical yield (4, 39).
Some compounds, such as GDP-fucose, are in high demand. The latter compound is indeed a precursor of fucosylated oligosaccharides such as fucosyllactose, fucosyllactoNbiose and lewis X oligosaccharides, or, of fucosylated proteins. These sugars are components of human mother milk in which they have anti-inflammatory and prebiotic effects and/or have applications in therapeutics as nutraceutical, anti-inflammatory agent or prebiotic, in addition, fucosylated proteins find applications in the pharmaceutics (5, 8, 27). However, an efficient method to produce the latter high-value compounds is still needed.
In addition GDP-mannose is also an intermediate of the pathway towards GDP-fucose. Interrupting the pathway prematurely leads to the accumulation of this compound, which is a precursor of mannosylated oligosaccharides. These oligosaccharides find for example applications in the treatment of gram-negative bacterial infections, in addition, GDP-mannose is important for the humanization of protein glycosylations, which is essential for the production of certain therapeutic proteins (18, 30). Mannosylated oligosaccharides and mannosylated glycoconjugates are also used for drug targeting, for instance mannosylated antivirals can specifically target the liver and kidneys (7).
The present invention provides microorganisms which are genetically changed in such a manner that they can efficiently produce the latter compounds.
Moreover, the synthesis of pH sensitive molecules, such as—but not limited to—glucosamine, and organic acids, such as—but not limited to—pyruvic acid, succinic acid, adipic, sialic acid, sialylated oligosaccharides . . . are preferably produced at low pH, either to stabilize the product or for downstream processing reasons (4, 12, 40). Therefore, strains that can grow at low pH are beneficial for these production processes. E. coli is an organism that can adapt easily to various conditions, for instance it can easily adapt to the harsh pH conditions in the stomach, which is about pH 2 (14). Nonetheless, E. coli does not seem to grow at these conditions, but induces its acid resistance mechanisms in the stationary phase (40). During this phase the cell does not multiply anymore and therefore hampers productivity. Up to now, no solution was found to this problem. However, in the present invention, a genetically engineered microorganism is provided that can induce acid resistance mechanisms in the exponential growth phase, which is the phase that is mostly used for production of organic acids and pH instable products.
The present invention provides microorganisms such as Enterobacteriaceae which are genetically changed in such a manner that they can efficiently produce compounds which are part of the colanic acid pathway. A particular compound of interest is GDP-fucose which is used as a precursor to synthesize fucosylated oligosaccharides. The latter have health-promoting effects as indicated above but there is no efficient production method available to produce said compounds.
The present invention thus provides for the usage of a mutated and/or transformed microorganism comprising a genetic change leading to a modified expression and/or activity of the transcriptional regulators the aerobic respiration control protein ArcA and the isocitrate lyase regulator IclR to upregulate at least one of the genes of the colanic acid operon, wherein said operon comprises the genes cpsG, cpsB, gmd and fcl that code for a phosphomannomutase, a mannose-1-phosphate guanylyltransferase, GDP-mannose 4,6-dehydratase and GDP-fucose synthase, respectively. The latter operon may also comprise the genes cpsG, cpsB, gmd, fcl and wza. In addition the expression of the gene rcsA is increased. This gene is a transcriptional regulator of the colanic acid operon. Enhanced expression of this gene increases transcription of the colanic acid operon (13, 36).
Hence the present invention relates to the usage of a mutated and/or transformed microorganism comprising a genetic change leading to a modified expression and/or activity of the transcriptional regulator, the aerobic respiration control protein, ArcA and the isocitrate lyase regulator IclR to upregulate the transcriptional regulator of the colanic acid operon, rcsA, which in turn upregulates at least one of the genes of the colanic acid operon.
Hence, the present invention relates to a mutated and/or transformed microorganism such as—but not limited to Enterobacteriaceae such as an Escherichia coli (E. coli) strain comprising a genetic change leading to a modified expression of the transcriptional regulators: the aerobic respiration control protein ArcA and the isocitrate lyase regulator IclR.
A mutated and/or transformed microorganism such as E. coli as used here can be obtained by any method known to the person skilled in the art, including but not limited to UV mutagenesis and chemical mutagenesis. A preferred manner to obtain the latter microorganism is by disrupting (knocking-out) the genes (arcA and iclR) encoding for the proteins ArcA and IclR, or, by replacing the endogenous promoters of said genes by artificial promoters or replacing the endogenous ribosome binding site by an artificial ribosome binding site. The term ‘artificial promoters’ relates to heterologous or non-natural or in silico designed promoters with known expression strength, these promoters can be derived from libraries as described by Alper et al. (2005), Hammer et al. (2006), or De Mey et al. (2007) (3, 11, 15). The term heterologous promoter refers to any promoter that does not naturally occur in front of the gene. The term ‘artificial promoter’ may also refer to promoters with DNA sequences that are combinations of the native (autologous) promoter sequence with parts of different (autologous or heterologous) promoter sequences as for example shown further in the examples. Sequences of such ‘artificial promoters’ can be found in databases such as for example partsregistry.org (6). The term ‘artificial ribosome binding site’ relates to heterologous or non-natural or in silico designed ribosome binding sites with known or measurable translation rates, these libraries can be derived from libraries or designed via algorithms as described by Salis et al (2009) (26). Hence, the present invention specifically relates to a mutated and/or transformed microorganism as indicated above wherein said genetic change is disrupting the genes encoding for ArcA and IclR, or, reducing or eliminating the function of ArcA and IclR via mutations in the coding sequence of the genes coding for ArcA and IclR, or, is replacing the endogenous promoters of the genes encoding for ArcA and IclR by artificial promoters; or, is replacing the endogenous ribosome binding site by an artificial ribosome binding site. It is further clear that the mutant and/or transformant according to the present invention may further comprise additional genetic changes in one or more other genes within its genome as is also described further. The term microorganism specifically relates to a bacterium, more specifically a bacterium belonging to the family of Enterobacteriaceae. The latter bacterium preferably relates to any strain belonging to the species Escherichia coli such as but not limited to Escherichia coli B, Escherichia coli C, Escherichia coli W, Escherichia coli K12, Escherichia coli Nissle. More specifically, the latter term relates to cultivated Escherichia coli strains—designated as E. coli K12 strains—which are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Well-known examples of the E. coli K12 strains are K12 Wild type, W3110, MG1655, M182, MC1000, MC1060, MC1061, MC4100, JM101, NZN111 and AA200. Hence, the present invention specifically relates to a mutated and/or transformed Escherichia coli strain as indicated above wherein said E. coli strain is a K12 strain. More specifically, the present invention relates to a mutated and/or transformed Escherichia coli strain as indicated above wherein said K12 strain is E. coli MG1655.
The terms ‘leading to a modified expression or activity’ indicates that the above described mutations/transformations affects the transcription and/or translation and/or post-translational modification of said genes (arcA and iclR) into the transcriptional regulator proteins of the present invention (ArcA and IclR) in such a way that the latter transcription has significantly decreased or has even been completely abolished compared to a wild type strain, which has not been mutated or transformed with regard to both particular genes of the present invention. Hence, the present invention relates to a mutated and/or transformed microorganism such as an Escherichia coli strain as indicated above wherein said modified expression is a decreased expression, and, to a mutated and/or transformed microorganism such as an Escherichia coli strain as indicated above wherein said decreased expression is an abolished expression.
The terms ‘upregulating at least one of the genes of the colanic acid operon’ indicates that the expression of at least 1, 2, 3, 4, . . . , or all of the genes belonging to the colanic acid operon are significantly (=P>0.05) upregulated when compared to the expression of said genes within a corresponding wild type microorganism which is cultivated under the same conditions as the mutated and/or transformed microorganism. The genes which belong to the colanic acid operon are wza, wzb, wzc, wcaA, wcaB, wcaC, wcaD, wcaE, wcaF, gmd, fcl, gmm, wcaI, cpsB, cpsG, wcaJ, wzxC, wcaK, wcaL and wcaM as indicated in
The present invention provides for the usage of a mutated and/or transformed microorganism comprising a genetic change leading to a modified expression and/or activity of the transcriptional regulators the aerobic respiration control protein ArcA and the isocitrate lyase regulator IclR to upregulate at least one of the genes of the colanic acid operon, wherein said operon comprises the genes cpsG and cpsB, coding for phosphomannomutase and mannose-1-phosphate guanylyltransferase, which are needed for the biosynthesis of GDP-mannose. As GDP-mannose is a precursor for mannosyllated oligosaccharides and mannosylated glycoconjugates. These oligosaccharides and glycoconjugates find for example applications in the treatment of gram-negative bacterial infections, in addition, GDP-mannose is important for the humanization of protein glycosylations, which is essential for the production of certain therapeutic proteins (18, 30). Mannosylated oligosaccharides and mannosylated glycoconjugates are also used for drug targeting, for instance mannosylated antivirals can specifically target the liver and kidneys (7). In order to efficiently produce mannosylated oligosaccharides (see
The term ‘heterologous expression’ relates to the expression of genes that are not naturally present in the production host, genes which can be synthesized chemically or be picked up from their natural host via PCR, genes which can be codon optimized for the production host or in which point mutation can be added to enhance enzyme activity or expression. Expressing heterologous and/or native genes can either be done on the chromosome, artificial chromosomes or plasmids and transcription can be controlled via inducible, constitutive, native or artificial promoters and translation can be controlled via native or artificial ribosome binding sites.
Consequently, the present invention further relates to mutated and/or transformed organisms in which the regulators ArcA and IclR as describe above, in combination with the genes encoding for the enzymes phosphoglucose isomerase and phosphofructokinase, are knocked out or are rendered less functional. More specifically, the present invention relates to the latter organisms wherein the enzyme phosphoglucose isomerase is encoded by the gene pgi and wherein the enzyme phosphofructokinase is encoded by the gene(s) pfkA and/or pfkB.
The terms ‘genes which are rendered less-functional or non-functional’ refer to the well-known technologies for a skilled person such as the usage of siRNA, RNAi, miRNA, asRNA, mutating genes, knocking-out genes, transposon mutagenesis, etc. . . . which are used to change the genes in such a way that they are less able (i.e. statistically significantly ‘less able’ compared to a functional wild-type gene) or completely unable (such as knocked-out genes) to produce functional final products. The term ‘(gene) knock out’ thus refers to a gene which is rendered non-functional. The term ‘deleted gene’ or ‘gene deletion’ also refers to a gene which is rendered non-functional.
The present invention further relates to a mutated and/or transformed organism as described in the latter paragraph wherein said organism is further transformed with a gene encoding for a sucrose phosphorylase.
The present invention also relates to a mutated and/or transformed organism as described above wherein, in addition, the activity and/or expression of the gene encoding for a lactose permease is made constitutive and/or increased. Said activity can be increased by over-expressing said gene and/or by transforming said organisms with a gene encoding for a lactose permease.
The present invention further relates to any mutated and/or transformed organism as described above wherein at least one of the following genes is knocked out or is rendered less functional:
a gene encoding for a beta-galactosidase, a gene encoding for a glucose-1-phosphate adenylyltransferase, a gene encoding for a glucose-1-phosphatase, a gene encoding for phosphogluconate dehydratase, a gene encoding for 2-keto-3-deoxygluconate-6-phosphate aldolase, a gene encoding for a glucose-1-phosphate uridyltransferase, a gene encoding for an UDP-glucose-4-epimerase, a gene encoding for an UDP-glucose:galactose-1-phosphate uridyltransferase, a gene encoding for an UDP-galactopyranose mutase, a gene encoding for an UDP-galactose:(glucosyl)lipopolysaccharide-1,6-galactosyltransferase, a gene encoding for an UDP-galactosyltransferase, a gene encoding for an UDP-glucosyltransferase, a gene encoding for an UDP-glucuronate transferase, a gene encoding for an UDP-glucose lipid carrier transferase, a gene encoding for a GDP-mannose hydrolase, a gene encoding for an UDP-sugar hydrolase, a gene encoding for a mannose-6-phosphate isomerase, a gene encoding for an UDP-N-acetylglucosamine enoylpyruvoyl transferase, a gene encoding for an UDP-N-acetylglucosamine acetyltransferase, a gene encoding for an UDP-Nacetylglucosamine-2-epimerase, a gene encoding for an undecaprenyl-phosphate alfa-N-acetylglucosaminyl transferase, a gene encoding for a glucose-6-phosphate-1-dehydrogenase, and/or, a gene encoding for a L-glutamine:D-fructose-6-phosphate aminotransferase, a gene encoding for a mannose-6-phosphate isomerase, a gene encoding for a sorbitol-6-phosphate dehydrogenase, a gene encoding for a mannitol-1-phosphate 5-dehydrogenase, a gene encoding for a allulose-6-phosphate 3-epimerase, a gene encoding for an invertase, a gene encoding for a maltase, a gene encoding for a trehalase, a gene encoding for a sugar transporting phosphotransferase, a gene encoding for a protease, or a gene encoding for a hexokinase. The term ‘at least one’ indicated that at least 1, but also 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32 or all 33 genes is (are) knocked out or is (are) rendered less functional.
The present invention further relates also to the usage of a mutated and/or transformed microorganism such as an Escherichia coli strain comprising a genetic change leading to a modified expression of the transcriptional regulators the aerobic respiration control protein ArcA and the isocitrate lyase regulator IclR to upregulate at least one of the following acid resistance related genes: ydeP, ydeO, hdeA, hdeD, gadB, gadC, gadE, gadX, gadW and/or slp (17, 22). These genes are normally expressed in stationary phase conditions; however, the present mutated and/or transformed microorganism is able to enhance the expression of these acid resistance related genes in the exponential growth phase. Hence, the present invention relates to the usage as described above for the synthesis of acids or pH sensitive molecules such as but not limited to glucosamine which is pH sensitive and should be produced at low pH (12). Organic acids, such as but not limited to pyruvic acid, succinic acid, adipic, sialic acid, sialylated oligosaccharides (e.g. sialyllactose, sialyl Lewis X sugars, . . . ), acetylated oligosaccharides (chitins, chitosans, . . . ), sulfonated oligosaccharides (heparans and heparosans) . . . are preferably produced at low pH for downstream processing purposes (4). In other words, the present invention relates to a process for the synthesis of acids, sialic acid, sialylated oligosaccharides or glucosamine comprising genetically changing the transcriptional regulators the aerobic respiration control protein ArcA and the isocitrate lyase regulator IclR to upregulate at least one of the following acid resistance related genes: ydeP, ydeO, hdeA, hdeD, gadB, gadC, gadE, gadX, gadW and/or slp.
The present invention will now be illustrated by the following non-limiting examples.
A high throughput RT-qPCR screening of the microorganisms of the present invention has been setup with Biotrove OpenArray® technology. In this experiment the transcription of 1800 genes were measured in 4 strains (wild type, ΔarcA, ΔiclR, ΔarcA ΔiclR) in two conditions (chemostat and batch). The data was processed using a curve fitting toolbox in R (25, 34) and Quantile Normalization, the error on the data was calculated using Bayesian statistics (20, 21, 31).
Escherichia coli MG1655 [−, F−, rph-1] was obtained from the Netherlands Culture Collection of Bacteria (NCCB). Escherichia coli BL21(DE3) was obtained from Novagen. Escherichia coli MG1655 ackA-pta, poxB, pppc ppc-p37 (10), the single knock-outs E. coli MG1655 arcA and E. coli MG1655 iclR and the double knock-out E. coli MG1655 arcA, iclR were constructed in the Laboratory of Genetics and Microbiology (MICR) using the method of Datsenko & Wanner (9).
The Luria Broth (LB) medium consisted of 1% tryptone peptone (Difco, Erembodegem, Belgium), 0.5% yeast extract (Difco) and 0.5% sodium chloride (VWR, Leuven, Belgium). Shake flask medium contained 2 g/l NH4Cl, 5 g/l (NH4)2SO4, 2.993 g/l KH2PO4, 7.315 g/l K2HPO4, 8.372 g/l MOPS, 0.5 g/l NaCl, 0.5 g/l MgSO4.7H2O, 16.5 g/l glucose.H2O, 1 ml/l vitamin solution, 100 μl/l molybdate solution, and 1 ml/l selenium solution. The medium was set to a pH of 7 with 1M KOH.
Vitamin solution consisted of 3.6 g/l FeCl2.4H2O, 5 g/l CaCl2.2H2O, 1.3 g/l MnCl2.2H2O, 0.38 g/l CuCl2.2H2O, 0.5 g/l CoCl2.6H2O, 0.94 g/l ZnCl2, 0.0311 g/l H3BO4, 0.4 g/l Na2EDTA.2H2O and 1.01 g/l thiamine.HCl. The molybdate solution contained 0.967 g/l Na2MoO4.2H2O. The selenium solution contained 42 g/l SeO2.
The minimal medium for fermentations contained 6.75 g/l NH4Cl, 1.25 g/l (NH4)2SO4, 1.15 g/l KH2PO4, 0.5 g/l NaCl, 0.5 g/l MgSO4.7H2O, 16.5 g/l glucose.H2O, 1 ml/l vitamin solution, 100 μl/l molybdate solution, and 1 ml/l selenium solution with the same composition as described above.
A preculture, from a single colony on a LB-plate, in 5 ml LB medium was incubated during 8 hours at 37° C. on an orbital shaker at 200 rpm. From this culture, 2 ml was transferred to 100 ml minimal medium in a 500 ml shake flask and incubated for 16 hours at 37° C. on an orbital shaker at 200 rpm. 4% inoculum was used in a 2 l Biostat B Plus culture vessel with 1.5 l working volume (Sartorius Stedim Biotech, Melsungen, Germany). The culture conditions were: 37° C., stirring at 800 rpm, and a gas flow rate of 1.5 l/min. Aerobic conditions were maintained by sparging with air, anaerobic conditions were obtained by flushing the culture with a mixture of 3% CO2 and 97% of N2. The pH was maintained at 7 with 0.5 M H2504 and 4 M KOH. The exhaust gas was cooled down to 4° C. by an exhaust cooler (Frigomix 1000, Sartorius Stedim Biotech, Melsungen, Germany). 10% solution of silicone antifoaming agent (BDH 331512K, VWR Int Ltd., Poole, England) was added when foaming raised during the fermentation (approximately 10 μl). The off-gas was measured with an EL3020 off-gas analyser (ABB Automation GmbH, 60488 Frankfurt am Main, Germany).
All data was logged with the Sartorius MFCS/win v3.0 system (Sartorius Stedim Biotech, Melsungen, Germany).
All strains were cultivated at least twice and the given standard deviations on yields and rates are based on at least 10 data points taken during the repeated experiments.
The bioreactor contains in its interior a harvest pipe (BD Spinal Needle, 1.2×152 mm (BDMedical Systems, Franklin Lakes, N.J.—USA) connected to a reactor port, linked outside to a Masterflex-14 tubing (Cole-Parmer, Antwerpen, Belgium) followed by a harvest port with a septum for sampling. The other side of this harvest port is connected back to the reactor vessel with a Masterflex-16 tubing. This system is referred to as rapid sampling loop. During sampling, reactor broth is pumped around in the sampling loop. It has been estimated that, at a flow rate of 150 ml/min, the reactor broth needs 0.04 s to reach the harvest port and 3.2 s to re-enter the reactor. At a pO2 level of 50%, there is around 3 mg/l of oxygen in the liquid at 37° C. The pO2 level should never drop below 20% to avoid micro-aerobic conditions. Thus 1.8 mg/l of oxygen may be consumed during transit through the harvesting loop. Assuming an oxygen uptake rate of 0.4 g oxygen/g biomass/h (the maximal oxygen uptake rate found at μmax), this gives for 5 g/l biomass, an oxygen uptake rate of 2 g/l/h or 0.56 mg/l/s, which multiplied by 3.2 s (residence time in the loop) gives 1.8 mg/l oxygen consumption.
In order to quench the metabolism of cells during the sampling, reactor broth was sucked through the harvest port in a syringe filled with 62 g stainless steel beads pre-cooled at −20° C., to cool down 5 ml broth immediately to 4° C. Sampling was immediately followed by cold centrifugation (15000 g, 5 min, 4° C.). During the batch experiments, a sample for OD600nm and RT-qPCR measurements was taken using the rapid sampling loop and the cold stainless bead sampling method.
mRNA was extracted with the RNeasy kit (Qiagen, Venlo, The Netherlands). RNA quality and quantity was checked with a nanodrop ND-1000 spectrophotometer (Nanodrop technologies, Wilmingto, USA). The ratios 260:280 (nm) and 260:230 (nm) were between 1.8 and 2 and at least 100 ng/μl was needed for further analysis. cDNA was synthesised with random primers with the RevertAid™ H minus first strand cDNA synthesis kit (Fermentas, St. Leon-Rot, Germany). Finally, the gene expression of 1800 genes was measured with the Biotrove OpenArray Real time PCR platform. The primers for the RT-PCR assay were designed with Primer design tools from the Primer database (23).
The reaction mixture was composed as described in the Biotrove OpenArray™ Real-Time qPCR system users' manual. In short, a mastermix was made with 26.4 μl LightCycler® DNA Master SYBR® Green I (Roche applied Science), 1.1 μl SYBR GREEN I (100× stock solution, Sigma S9430), 8.8 μl glycerol (Sigma G5150), 5.3 μl Pluronic® F68 (10% stock, Invitrogen), 2.64 μl BSA (Sigma A7906), 26.4 μl magnesium chloride (25 mM stock solution, supplied in the LightCycler® kit of Roche applied Science), 21.1 μl HiDi™ formamide (Applied biosystems), and 94.66 μl RNase free sterile water resulting in a 186.4 μl mastermix, which is enough to load 1 OpenArray™. For 1 SubArray (each OpenArray is subdivided in 48 SubArrays on which 1 sample can be loaded) 1.5 μl sample (with a concentration of 100 ng/μl) was mixed with 3.5 μl of mastermind, as a no template control, water was used as blanc. The sample-mastermix mixture was loaded in a Loader plate (MatriPlate™ 384-well black low volume polypropylene plate, Biotrove) in a RNase free hood. A full loader plate was loaded with an AutoLoader (Biotrove) and loader tips onto the OpenArrays. These OpenArrays were then submerged in OpenArray™ immersion fluid in an OpenArray™ Real-Time qPCR case. The case was sealed with Case sealing glue and incubated in the Case Sealing station, which polymerizes the glue with UV light.
Cell density of the culture was frequently monitored by measuring optical density at 600 nm (Uvikom 922 spectrophotometer, BRS, Brussel, Belgium). Cell dry weight was obtained by centrifugation (15 min, 5000 g, GSA rotor, Sorvall RC-5B, Goffin Meyvis, Kapellen, Belgium) of 20 g reactor broth in pre-dried and weighted falcons. The pellets were subsequently washed once with 20 ml physiological solution (9 g/l NaCl) and dried at 70° C. to a constant weight. To be able to convert OD600nm measurements to biomass concentrations, a correlation curve of the OD600nm to the biomass concentration was made. The concentrations of glucose and organic acids were determined on a Varian Prostar HPLC system (Varian, Sint-Katelijne-Waver, Belgium), using an Aminex HPX-87H column (Bio-Rad, Eke, Belgium) heated at 65° C., equipped with a 1 cm precolumn, using 5 mM H2SO4 (0.6 ml/min) as mobile phase. A dual-wave UV-VIS (210 nm and 265 nm) detector (Varian Prostar 325) and a differential refractive index detector (Merck LaChrom L-7490, Merck, Leuven, Belgium) was used for peak detection. By dividing the absorptions of the peaks in both 265 and 210 nm, the peaks could be identified. The division results in a constant value, typical for a certain compound (formula of Beer-Lambert).
Glucose, fructose, sucrose, fucosyllactose and glucose-1-phosphate were measured by HPLC with a Hypercarb column and were detected with an MSMS detector (Antonio et al., 2007; Nielsen et al., 2006).
All mutant strains were constructed via the methods described below.
Plasmids were maintained in the host E. coli DH5α (F−, φ80dlacZΔM15, Δ(lacZYA-argF)U169, deoR, recA1, endA1, hsdR17(rk−, mk+), phoA, supE44, λ−, thi-1, gyrA96, relA1).
Plasmids.
pKD46 (Red helper plasmid, Ampicillin resistance), pKD3 (contains an FRT-flanked chloramphenicol resistance (cat) gene), pKD4 (contains an FRT-flanked kanamycin resistance (kan) gene), and pCP20 (expresses FLP recombinase activity) plasmids were used for the mutant construction. The plasmid pBluescript (Fermentas, St. Leon-Rot, Germany) was used to construct the derivates of pKD3 and pKD4 with a promoter library, or with alleles carrying a point mutation.
Mutations.
The mutations consisted in gene disruption (knock-out, KO). They were introduced using the concept of Datsenko and Wanner (9). The primers for the mutation strategies are described in Table 1.
Transformants carrying a Red helper plasmid were grown in 10 ml LB media with ampicillin (100 mg/l) and L-arabinose (10 mM) at 30° C. to an OD600nm, of 0.6. The cells were made electrocompetent by washing them with 50 ml of ice-cold water, a first time, and with 1 ml ice-cold water, a second time. Then, the cells were resuspended in 50 μl of ice-cold water. Electroporation was done with 50 μl of cells and 10-100 ng of linear double-stranded-DNA product by using a Gene Pulser™ (BioRad) (600Ω, 25 μFD, and 250 volts).
After electroporation, cells were added to 1 ml LB media incubated 1 h at 37° C., and finally spread onto LB-agar containing 25 mg/l of chloramphenicol or 50 mg/l of kanamycin to select antibiotic resistant transformants. The selected mutants were verified by PCR with primers upstream and downstream of the modified region and were grown in LB-agar at 42° C. for the loss of the helper plasmid. The mutants were tested for ampicillin sensitivity.
Linear Double-Stranded-DNA.
The linear ds-DNA amplicons were obtained by PCR using pKD3, pKD4 and their derivates as template. The primers used had a part of the sequence complementary to the template and another part complementary to the side on the chromosomal DNA where the recombination has to take place (Table 1). For the KO, the region of homology was designed 50-nt upstream and 50-nt downstream of the start and stop codon of the gene of interest. For the KI, the transcriptional starting point (+1) had to be respected. PCR products were PCR-purified, digested with Dpnl, repurified from an agarose gel, and suspended in elution buffer (5 mM Tris, pH 8.0).
Elimination of the Antibiotic Resistance Gene.
The selected mutants (chloramphenicol or kanamycin resistant) were transformed with pCP20 plasmid, which is an ampicillin and chloramphenicol resistant plasmid that shows temperature-sensitive replication and thermal induction of FLP synthesis. The ampicillin-resistant transformants were selected at 30° C., after which a few were colony purified in LB at 42° C. and then tested for loss of all antibiotic resistance and of the FLP helper plasmid. The gene knock outs and knock ins are checked with control primers (Fw/Rv-gene-out). These primers are given in Table 1.
pylori
Transformation.
Plasmids were transformed in CaCl2 competent cells using the simplified procedure of Hanahan (16) or via electroporation as described above.
Different experiments with different strains were performed. In total 8 different conditions were tested. There was variation in the genetic background (WT, iclR knock-out, arcA knock-out, and combined iclR-arcA knock-out) and the mode of fermentation (batch, and chemostat). Each experiment was repeated twice.
When running the samples through the BioTrove apparatus, a qPCR curve (fluorescences in function of cycle number) and a melt curve (fluorescences in function of the temperature) is obtained for each sample. Those data were exported from the BioTrove software and further analysed in R. The analysis was divided in two steps: first the qPCR curves were fitted and Ct values were calculated and in the second step the Ct values were converted to expression data.
Calculating the qPCR Curves
The raw qPCR curve data were extracted from the BioTrove software and imported in R (1). The curves were fitted to a 5 parameter sigmoidal model, with the R package qPCR (25, 34). The maximum of the second derivative of those curves was used as Ct value. No normalisation was applied to the data prior to the curve fitting. However, outliers were removed. The detection of the outliers was done using the following procedure:
Many curves have to be fitted (1800 genes for one experiment). Therefore, it is undoable to manually check each curve and automated methods have to be applied to reject bad curves. For this different parameters are extracted from the curves: the cycle number value at which the maximum of the first derivative occurs (D1), the cycle number value at which the maximum of the second derivative occurs (D2), the minimal fluorescence (Fmin), and the maximal fluorescence (Fmax). Combining the values of those parameters, the validity of the curve and the extent of expression is assessed. How this is done is explained in the next section.
For some gene-experiment combinations, no amplification is detected. This can be due to a variety of reasons:
Some genes are genuinely not expressed and setting their Ct value to something else than infinity is not correct. For genes that are expressed, but for which the expression value, due to technical failures or limitations, are not known, setting the Ct value to infinity is not correct. Furthermore, using arbitrary values that are outside the range of expression complicates the calculation routines and visualisation routines. Therefore it was opted to remove the gene-experiment combinations for which no correct expression data was detected.
An obvious case of gene-experiment pairs for which no expression is detected, are those for which no curve could be fitted to the qPCR data. Less obvious cases are detailed below.
Typically for expressed genes, is that the fluorescence values cover a certain range. Data points for which this range was not high enough, were discarded, as they pointed to very poorly fitted curves and generally bad data. The minimal fluorescence range was set to 400 (thus Fmax−Fmin>400).
In a good amplification curve, the first (D1) and second (D2) derivative are quite close to each other (see the documentation of the SOD function in the qpcR package (25)). Therefore, all data-points for which the difference between D1 and D2 is larger than an arbitrary value (7 was used) were discarded.
For each primer-pair, a qPCR experiment was performed without adding DNA. Only water was added. Normally no expression should be observed in those samples. However, amplification is detected in water for some primer-pairs. Genes for which the Ct value (as mentioned before, D2 was used) is more than the Ct value of water minus 5, are discarded, as it cannot be excluded that the fluorescence comes from the amplification of the primers and not the added DNA.
Prior to calculating the expression differences, the Ct values have to be normalised. As so many genes were measured (1800), quantile normalisation could be used (33). The 1800 genes measured, were divided over 3 types of arrays, each containing 600 genes. Quantile normalisation was done for each type of array separately. A table was constructed where the rows represent the different genes and the columns the different experiments (T1, see Equations 1). Each column was sorted independently (T2) and the original position of the elements was saved. The values in this new table were replaced with the mean value over the different rows (T3). And finally this table was transformed so that the positions of the values corresponded again to the original positions (T4).
Differential expressions were calculated with the normalised data. This was done with the R package limma, which uses a Bayesian approach to calculate the statistical relevances of the differences (31, 32). Limma was adapted to be able to cope with missing data: the original limma package discards all expression values from a gene over the different experiments, when one value in one experiment is not available. This hampers the analysis when one has many different conditions, as for each gene for which one of the experimental conditions produces no expression values, a different contrast matrix has to be generated omitting that experimental condition. Therefore the function for fitting the contrasts was adapted to drop data-points with missing data.
Differential expressions were calculated between Ct values and the mean Ct value for a certain gene. Thus, the higher the value, the lower the expression. For each gene, plots were generated showing those differences. However, in those plots, the Ct values were inversed, so that the higher the value, the higher the expression.
The mutations ΔarcAΔiclR applied in combination with other mutations enhance the production of fucosylated compounds. A first, ‘other’ genetic modification that enhances said production is the deletion of wcaJ from the colanic operon, stopping the initiation of the colanic acid biosynthesis and thus the accumulation of GDP-fucose. Further, a fucosyltransferase has to be introduced to link fucose with different acceptor molecules such as lactose. The metabolism is then engineered further to accumulate the precursor of the GDP-fucose biosynthetic pathway. These modifications are shown in
To accumulate the GDP-fucose precursor fructose and fructose-6-phosphate, a sucrose phosphorylase or invertase is introduced. Because fructose-6-phosphate is easily degraded in the glycolysis, the glycolysis is interrupted in order to steer all fructose-6-phosphate in the direction of GDP-fucose. The genes pgi, pfkA and pfkB are thus knocked out, coding for glucose-6-phosphate isomerase and phosphofructokinase A and B. Finally a fucosyltransferase is introduced to link fucose to an acceptor molecule.
The growth rate of the wild type strain is somewhat affected when grown on sucrose after introduction of a sucrose phosphorylase (BaSP) (plasmid with sequence SEQ ID No 2) (Table 2), however the introduction of pgi mutations and pfkA and pfkB double mutations led to significant reduction of growth rate, the latter was extremely low (0.02 h−1). The combination of all mutations (Apgi and ApfkA and ApfkB) led to the lowest growth rate, however, the growth rate on both sucrose and glucose was surprisingly similar to that of the pgi single mutant.
AATTCGGAGGAAACAAAGATGGGGGGTTCTCATCATCATCATCATCAT
GGTATGGCTAGCATGAAAAACAAGGTGCAGCTCATCACTTACGCCGAC
CGCCTTGGCGACGGCACCATCAAGTCGATGACCGACATTCTGCGCACC
CGCTTCGACGGCGTGTACGACGGCGTTCACATCCTGCCGTTCTTCACC
CCGTTCGACGGCGCCGACGCAGGCTTCGACCCGATCGACCACACCAAG
GTCGACGAACGTCTCGGCAGCTGGGACGACGTCGCCGAACTCTCCAAG
ACCCACAACATCATGGTCGACGCCATCGTCAACCACATGAGTTGGGAA
TCCAAGCAGTTCCAGGACGTGCTGGCCAAGGGCGAGGAGTCCGAATAC
TATCCGATGTTCCTCACCATGAGCTCCGTGTTCCCGAACGGCGCCACC
GAAGAGGACCTGGCCGGCATCTACCGTCCGCGTCCGGGCCTGCCGTTC
ACCCACTACAAGTTCGCCGGCAAGACCCGCCTCGTGTGGGTCAGCTTC
ACCCCGCAGCAGGTGGACATCGACACCGATTCCGACAAGGGTTGGGAA
TACCTCATGTCGATTTTCGACCAGATGGCCGCCTCTCACGTCAGCTAC
ATCCGCCTCGACGCCGTCGGCTATGGCGCCAAGGAAGCCGGCACCAGC
TGCTTCATGACCCCGAAGACCTTCAAGCTGATCTCCCGTCTGCGTGAG
GAAGGCGTCAAGCGCGGTCTGGAAATCCTCATCGAAGTGCACTCCTAC
TACAAGAAGCAGGTCGAAATCGCATCCAAGGTGGACCGCGTCTACGAC
TTCGCCCTGCCTCCGCTGCTGCTGCACGCGCTGAGCACCGGCCACGTC
GAGCCCGTCGCCCACTGGACCGACATACGCCCGAACAACGCCGTCACC
GTGCTCGATACGCACGACGGCATCGGCGTGATCGACATCGGCTCCGAC
CAGCTCGACCGCTCGCTCAAGGGTCTCGTGCCGGATGAGGACGTGGAC
AACCTCGTCAACACCATCCACGCCAACACCCACGGCGAATCCCAGGCA
GCCACTGGCGCCGCCGCATCCAATCTCGACCTCTACCAGGTCAACAGC
ACCTACTATTCGGCGCTCGGGTGCAACGACCAGCACTACATCGCCGCC
CGCGCGGTGCAGTTCTTCCTGCCGGGCGTGCCGCAAGTCTACTACGTC
GGCGCGCTCGCCGGCAAGAACGACATGGAGCTGCTGCGTAAGACGAAT
AACGGCCGCGACATCAATCGCCATTACTACTCCACCGCGGAAATCGAC
GAGAACCTCAAGCGTCCGGTCGTCAAGGCCCTGAACGCGCTCGCCAAG
TTCCGCAACGAGCTCGACGCGTTCGACGGCACGTTCTCGTACACCACC
GATGACGACACGTCCATCAGCTTCACCTGGCGCGGCGAAACCAGCCAG
GCCACGCTGACGTTCGAGCCGAAGCGCGGTCTCGGTGTGGACAACGCT
ACGCCGGTCGCCATGTTGGAATGGGAGGATTCCGCGGGAGACCACCGT
TCGGATGATCTGATCGCCAATCCGCCTGTCGTCGCCTGACTGCAGGTC
GACCATATGGGAGAGCTCCCAACGCGTTGGATGCAGGCATGCAAGCTT
GGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAA
TCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGT
AGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGC
CGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAAC
TGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTT
TCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAA
TCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTG
GCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAA
GGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTTTGT
TTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAA
CCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATT
CAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTT
CCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAA
GATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGC
GGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATG
AGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGAC
GCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGAC
TTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATG
ACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACT
GCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACC
GCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGG
GAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACG
ATGCCTACAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAA
CTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCG
GATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGG
TTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATC
ATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATC
TACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATC
GCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAA
GTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTT
AAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATC
CCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAG
ATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGC
TTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGAT
CAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCG
CAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCAC
TTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTG
TTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTG
GACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACG
GGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAA
CTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAA
GGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGA
GAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGT
CCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGC
TCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTT
TTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCT
GCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGA
GCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTG
AGCGAGGAAGCGGAAGAGCGCCTGATGCGGTATTTTCTCCTTACGCAT
CTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGC
TCTGATGCCGCATAGTTAAGCCAGTATACACTCCGCTATCGCTACGTG
ACTGGGTCATGGCTGCGCCCCGACACCCGCCAACACCCGCTGACGCGC
CCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGA
CCGTCTCCGGGAGAGCTCGATATCCCGGGCGGCCGCTTCATTTATAAA
TTTCTTGACATTTTGGAATAGATGTGATATAATGTGTACATATCCATG
GCGGCCGCTCTAGAAGAAGCTTGGGATCCGTCGACCTCG
The flux redirections and mutations for GDP-fucose and fucosyllated oligosaccharide biosynthesis in a split metabolism are shown in
When the genes pgi, pfkA, and pfkB are knocked out, carbon, taken up as glucose can only be metabolised via the pentose phosphate pathway. Due to the biochemical properties of this pathway, fructose-6-phosphate is formed (
The mutant strain in which the genes lacZ, glgC, agp, pfkA, pfkB, pgi, arcA, ic/R, wcaJ are knocked out and lacY was expressed via constitutive expression to ensure expression under all culturing conditions, was transformed further with a fucosyltransferase originating from Helicobacter pylori and a sucrose phosphorylase originating from Bifidobacterium adolescentis, which were also constitutively expressed. The constitutive promoters originate from the promoter library described by De Mey et al. 2007. This strain was cultured in a medium as described in the materials and methods, however with 30 g/l of sucrose and 50 g/l of lactose. This resulted in the formation of 2-fucosyllactose as shown in
The mutant strain in which the genes lacZ, glgC, agp, pfkA, pfkB, pgi, arcA, ic/R, wcaJ are knocked out and lacY was expressed via constitutive expression to ensure expression under all culturing conditions, was transformed further with a fucosyltransferase originating from Dictyostellium discoideum and a sucrose phosphorylase originating from Bifidobacterium adolescentis, which were also expressed constitutively. The constitutive promoters originate from the promoter library described by De Mey et al. 2007. This strain was cultured in a medium as described in the materials and methods, however with 30 g/l of sucrose and 50 g/l of lactose. This resulted in the formation of 2-fucosyllactose as shown in
To accumulate the GDP-mannose precursors fructose and fructose-6-phosphate, a sucrose phosphorylase or invertase is introduced. Because fructose-6-phosphate is easily degraded in the glycolysis, the glycolysis is interrupted in order to steer all fructose-6-phosphate in the direction of GDP-fucose. The genes pgi, pfkA and pfkB are thus knocked out, coding for glucose-6-phosphate isomerase and phosphofructokinase A and B. Finally a mannosyltransferase is introduced to link mannose to an acceptor molecule. To avoid GDP-mannose degradation the genes gmm and gmd have to be knocked out in the colanic acid operon. In addition, the genes that do not code for GDP-mannose biosynthesis reactions are knocked out, such as wcaA, wcaB, wcaC, wcaD, wcaE, wcaF, wcaI, wcaJ, wcaK, wcaL and/or, wcaM.
Similar to the colanic acid operon upregulation, acid resistance related genes are also upregulated in a ΔarcAΔiclR double mutant strain in comparison to the wild type strain and the single mutant strains. These genes make a strain more resistant to low pH, which is beneficial for the production of acids (4) or the production of glucosamine (12) which is not stable at neutral and high pH.
A mutant strain was constructed via the genetic engineering methodologies described above with the following genotype:
ΔlacZYA::P22-lacYΔglgCΔagpΔpgiΔpfkA-P22-baSPΔpfkBΔarcAΔiclR::slΔwcaJΔIonΔadhE-P14-frk+pCXP14-FT—H. pylori (a vector with sequence SEQ ID No 1). The promoter P22 and P14 originate from the promoter library constructed by De Mey et al (11) and was cloned similar to the methodology described by Aerts et al (2). “::sl” marks a scarless gene deletion, thus without a FRT site that remains in the chromosome.
This strain was cultured in a bioreactor as described above in materials and methods, in the mineral medium with 30 g/l of sucrose and 50 g/l of lactose. After the batch phase the bioreactor was fed with 500 g/l of sucrose, 50 g/l lactose and 1 g/l of magnesium sulphate heptahydrate. This led to the accumulation of 27.5 g/l of fucosyllactose in the supernatant.
CGCGTTGGATGCAGGCATGCAAGCTTGGCTGTTTTGGCGGATGAGAGA
AGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGA
TAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACC
CCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGG
GGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGA
AAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCG
GTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC
GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAA
ACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTT
TTTGCGTTTCTACAAACTCTTTTTGTTTATTTTTCTAAATACATTCAA
ATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAAT
ATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTA
TTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAA
CGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGG
GTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTC
GCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTAT
GTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTC
GCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCA
CAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTG
CTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAA
CGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGG
ATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCA
TACCAAACGACGAGCGTGACACCACGATGCCTACAGCAATGGCAACAA
CGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGC
AACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTC
TGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAG
CCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATG
GTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAA
CTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGA
TTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGA
TTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCC
TTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCC
ACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATC
CTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGC
TACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTC
CGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTC
TAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGC
CTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTG
GCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGG
ATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCA
GCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGC
TATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATC
CGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAG
GGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCT
GACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTAT
GGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCT
GGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGG
ATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCC
GAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCC
TGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCA
TATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCC
AGTATACACTCCGCTATCGCTACGTGACTGGGTCATGGCTGCGCCCCG
ACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCC
GGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGAGCTCGATA
TCCCGGGCGGCCGCCTTCATTCTATAAGTTTCTTGACATCTTGGCCGG
CATATGGTATAATAGGGAAATTTCCATGGCGGCCGCTCTAGAAGAAGC
TTGGGATCCGTCGACCTCGAATTCGGAGGAAACAAAGATGGCCTTTAA
AGTTGTTCAGATTTGTGGTGGTCTGGGCAATCAGATGTTTCAGTATGC
ATTTGCAAAAAGCCTGCAGAAACATAGCAATACACCGGTTCTGCTGGA
TATTACCAGCTTTGATTGGAGCAATCGTAAAATGCAGCTGGAACTGTT
TCCGATTGATCTGCCGTATGCAAGCGAAAAAGAAATTGCAATTGCCAA
AATGCAGCATCTGCCGAAACTGGTTCGTAATGTTCTGAAATGCATGGG
TTTTGATCGTGTGAGCCAAGAAATCGTGTTTGAATATGAACCGAAACT
GCTGAAAACCAGCCGTCTGACCTATTTTTATGGCTATTTTCAGGATCC
GCGTTATTTTGATGCAATTAGTCCGCTGATCAAACAGACCTTTACCCT
GCCTCCGCCTCCGGAAAATGGTAATAACAAAAAAAAAGAAGAAGAGTA
TCATCGTAAACTGGCACTGATTCTGGCAGCAAAAAATAGCGTGTTTGT
GCATATTCGTCGCGGTGATTATGTTGGTATTGGTTGTCAGCTGGGCAT
CGATTATCAGAAAAAAGCACTGGAATACATGGCAAAACGTGTTCCGAA
TATGGAACTGTTTGTGTTTTGCGAGGACCTGGAATTTACCCAGAATCT
GGATCTGGGCTATCCGTTTATGGATATGACCACCCGTGATAAAGAGGA
AGAGGCATATTGGGATATGCTGCTGATGCAGAGCTGTAAACATGGTAT
TATTGCCAACAGCACCTATAGTTGGTGGGCAGCATATCTGATTAATAA
CCCGGAAAAAATCATTATTGGTCCGAAACATTGGCTGTTTGGCCATGA
AAACATCCTGTGTAAAGAATGGGTGAAAATCGAAAGCCACTTTGAAGT
GAAAAGCCAGAAATATAATGCCTAATAAGAGCTCCCAA
A hybrid colanic acid promoter was constructed based on the genome information and the sequences from the promoter library described by De Mey et al (11).
ΔlacZYA::P22-lacYΔglgCΔagpΔpgiΔpfkA::P22-BaSPΔpfkB ΔarcAΔiclR:sl ΔwcaJ ΔIon ΔadhE-P14-frk ΔldhA::P14-FT—H. pylori ΔpromCA:P14
This strain was cultured in a bioreactor as described above in materials and methods, in the mineral medium with 30 g/l of sucrose and 20 g/l of lactose. After the batch phase the bioreactor was fed with 500 g/l of sucrose, 20 g/l lactose and 1 g/l of magnesium sulphate heptahydrate. This led to the accumulation of 26 g/l of fucosyllactose in the supernatant with nearly stoichiometric conversion of lactose. Increasing the lactose feed concentrations leads further to increased final fucosyllactose titers and stoichiometric lactose conversion.
| Number | Date | Country | Kind |
|---|---|---|---|
| 11194103.5 | Dec 2011 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP12/75639 | 12/14/2012 | WO | 00 | 6/12/2014 |
