Enhanced production of L-sorbose from D-sorbitol by improving the mRNA abundance of sorbitol dehydrogenase in Gluconobacter oxydansWSH-003
© Xu et al.; licensee BioMed Central Ltd. 2014
Received: 19 July 2014
Accepted: 8 October 2014
Published: 18 October 2014
Production of L-sorbose from D-sorbitol by Gluconobacter oxydans is the first step to produce L-ascorbic acid on industrial scale. The sldhAB gene, which encodes the sorbitol dehydrogenase (SLDH), was overexpressed in an industrial strain G. oxydans WSH-003 with a strong promoter, P tufB . To enhance the mRNA abundance, a series of artificial poly(A/T) tails were added to the 3′-terminal of sldhAB gene. Besides, their role in sldhAB overexpression and their subsequent effects on L-sorbose production were investigated.
The mRNA abundance of the sldhAB gene could be enhanced in G. oxydans by suitable poly(A/T) tails. By self-overexpressing the sldhAB gene in G. oxydans WSH-003 with an optimal poly(A/T) tail under the constitutive promoter P tufB , the titer and the productivity of L-sorbose were enhanced by 36.3% and 25.0%, respectively, in a 1-L fermenter. Immobilization of G. oxydans-sldhAB6 cells further improved the L-sorbose titer by 33.7% after 20 days of semi-continuous fed-batch fermentation.
The artificial poly(A/T) tails could significantly enhance the mRNA abundance of the sldhAB. Immobilized G. oxydans-sldhAB6 cells could further enlarge the positive effect caused by enhanced mRNA abundance of the sldhAB.
L-sorbose is an important carbohydrate that is predominantly used as a starting material in the biosynthesis of L-ascorbic acid ,. The most prominent industrial method of producing L-sorbose is the biotransformation of D-sorbitol to L-sorbose in Gluconobacter species or Acetobacter species ,. During the process, two hydrogen atoms were removed from one molecular of D-sorbitol to form one molecular of L-sorbose. Gluconobacter oxydans is widely used in biotransformation due to its ability to incompletely oxidize D-sorbitol, glycerol, and glucose to L-sorbose , dihydroxypropanone , and gluconic acid , respectively. These oxidation reactions are performed by membrane-bound dehydrogenases located on the outer surface of the cytoplasmic membrane, whereas the oxidation products accumulate in the culture medium.
G. oxydans WSH-003 and its relative derivative strains are commonly used for the industrial production of L-sorbose, which is the first step in the production of L-ascorbic acid via the two-step fermentation process . The most significant feature of G. oxydans WSH-003 is its ability to produce a high titer of L-sorbose. D-sorbitol is oxidized in the periplasm in a chemo-, regio-, and stereoselective manner to L-sorbose by membrane-bound dehydrogenases . The gene clusters encoding D-sorbitol dehydrogenase (sldhAB, 2,670 bp) have been identified from the draft genome sequence of G. oxydans WSH-003 . For industrial production, it is preferable to engineer G. oxydans cells to further enhance their catalytic properties during the biotransformation processes of D-sorbitol ,,. For example, by overexpressing a membrane-bound glycerol dehydrogenase gene in G. oxydans DSM 2343, the titer of dihydroxyacetone from glycerol was enhanced by 75% . This indicated that an engineered G. oxydans strain that overexpresses the sldhAB gene could enhance the L-sorbose production.
To overexpress an enzyme, the stability of the corresponding mRNA of the enzyme plays an important role in the process. Polyadenylation is the process to add a poly(A) tail on the 3′-terminal of a RNA . The poly(A) tail consists of multiple adenosine monophosphates and is a stretch of RNA that has only adenine bases. In eukaryotes, the poly(A) tail could be shortened over time. Once the poly(A) tail is short enough, the mRNA could be enzymatically degraded . In some of eukaryotes, the mRNA with short poly(A) tails could be reactivated by re-polyadenylation in the cytosol . In E. coli mRNA with poly(A) tail could be formed by the activity of poly(A) polymerase . Different from the eukaryotes, some of the previous researches showed that the existence of poly(A) tails may decrease the stability of mRNA ,. However, the current view of mechanism related to the formation and the regulation of poly(A) tails on the mRNA stability or abundance remains to be smatter -.
In this work, the sldhAB gene, which encodes the sorbitol dehydrogenase in G. oxydans, was overexpressed with a strong promoter, P tufB . Inspired by the mechanims from most of the eukaryotes, it is proposed that the mRNA stability could be enhanced by the introduction of extra poly(A) or other similar tails at the 3′-end, such as AAATTT, AAATTTAAA, AAATTTAAATTT, AAATTTAAAAAAA and AAAAAAAAATTT. The mRNA abundance of the sldhAB gene with suitable poly(A/T) tails in G. oxydans could be significantly enhanced. As a result, both the L-sorbose titer and the stability of the immobilized cells were improved. These results showed that adding some suitable short poly(A/T) tails could significantly improve the mRNA abundance of a specific enzyme, thus facilitate the bioprocesses associated with the enzyme.
Results and discussion
qRT-PCR analysis of the sldhAB gene
The mRNA level in G. oxydans is a dynamic process, which was dominated by both the transcription and mRNA degradation processes. The poly(A) and poly(A/T) tails was located in the downstream of the 3′-UTR and should have minor impact on the expression of mRNA. Therefore, the final mRNA level in vivo is actually dominated by the mRNA degradation process. From this point, the improved mRNA level of sldhAB should be caused by the decreased RNA degradation process. Thus, this process could be directly reflected from the mRNA level (Figure 1). Compared to eukaryotes, prokaryotes have mRNA of lower stability. Degradation of mRNA in prokaryotes is generally attributed to the combined action of endonucleases and 3′-exonucleases ,. Posttranscriptional mRNA processing includes 5′-capping, splicing, and poly-adenylation at the 3′ end, which contribute to mRNA stability and establish the translational efficiency of mRNA in eukaryotes -. However, posttranscriptional mRNA processing is not completed independently in prokaryotes. Therefore, an artificial poly(A/T) tail was proposed to slow down the mRNA degradation process in bacteria. As expected, the high sldhAB expression levels were achieved when the poly(A/T) tails were linked.
Effects of poly(A/T) tails on enzyme activity
As expected, the high SLDH activity levels were achieved when the poly(A/T) tails were linked to the sldhAB gene. The enzyme is highly abundant in G. oxydan-sldhAB6, so that the proper poly(A/T) tail of the encoding gene led to an increase of the sldhAB transcription level when the sldhAB gene was overexpressesed. The result indicates that the transcription and expression of the sldhAB gene in G. oxydans were markedly enhanced by poly(A/T) tails. The results showed that existence of short poly(A/T) tails on mRNA could significantly enhanced the following translational process by enhancing the mRNA stability.
Effects of poly(A/T) tails on L-sorbose production in shake flasks
Effects of poly(A/T) tails on L-sorbose production in a 1-L fermenter
Biotransformation of D-sorbitol to L-sorbose by immobilized G. oxydans-sldhAB6
Furthermore, to avoid potential delays or inhibition caused by the increased concentration of L-sorbose, an intermittent feeding approach was applied in fed-batch culture. An initial D-sorbitol concentration of 150 g/L was applied. According to the results of Figure 5A, 50 g (G. oxydans WSH-003) or 70 g (G. oxydans-sldhAB6) of D-sorbitol in a total volume of 0.25 L were fed into the 1-L bioreactor every 24 h. Equal volume of the culture broth was removed before the feeding (Figure 5B,C). The long-term performance of immobilized cells in a 1-L fermenter over a period of 20 days was highly stable. Consequently, the maximal L-sorbose titers were verified for G. oxydans-sldhAB6 and G. oxydans WSH-003 at 21 days (Figure 5B,C). Both the D-sorbitol consumption and L-sorbose titer decreased sharply after the 20th day. Compared to G. oxydans WSH-003, the L-sorbose accumulation for G. oxydans-sldhAB6 was improved by 33.7%. The result further demonstrated that the positive effect of the overexpression could be enlarged by immobilization process.
In order to decrease the cost and enhance the production efficiency, oxygen-carriers have been successfully used to enhance the productivity of L-sorbose in batch and fed-batch fermentation . Besides, previous research indicated it was possible to decrease the cost of L-sorbose production by using immobilized G. oxydans cells ,,. However, oxygen-carriers may make downstream processing difficult and the immobilized fermentation requires a longer fermentation period. In this work, enhanced expression of the sldhAB gene in G. oxydans due to the introduction of poly(A/T) tails improved the production of L-sorbose from D-sorbitol. Besides, the leakage of cells from the beads during repeated usage of immobilized beads should also be monitored to facilitate the downstream process. Compared with the previous strategies, G. oxydans-sldhAB6 resulted in a higher productivity without the need for oxygen-carriers. Besides, our method requires a shorter fermentation time than previous research ,.
In summary, poly(A/T) tails were linked to the gene sldhAB to enhance mRNA stability and translational efficiency. The results suggested that the mRNA stability and transcription of the sldhAB gene in G. oxydans were markedly enhanced by poly(A/T) tails. The L-sorbose titer was 33.7% higher in the immobilized G. oxydans-sldhAB6 cells. In addition, fed-batch fermentation with immobilized G. oxydans-sldhAB6 cells was examined. The long-term performance of immobilized cells in a 1-L fermenter over a period of 20 days showed that the long-term culture process could further amplify the advantage gained by the presence of the poly(A/T) tails. The L-sorbose titer was improved by 33.7% by the immobilization of G. oxydans-sldhAB6 cells. The cost of L-sorbose production by G. oxydans can be decreased by using this biotransformation process. Therefore, the high activity and stability of immobilized cells make them ideal for large-scale industrial applications.
Strains, plasmids, and growth conditions
G. oxydans WSH-003 (CICIM-CU B7004) was obtained from Jiangsu Jiangshan Pharmaceutical Co., Ltd (Jiangsu, China) and stored at −80°C . G. oxydans strains were cultivated in D-sorbitol medium (D-sorbitol 150 g/L, yeast extract 6 g/L, CaCO3 2 g/L), at 30°C, 200 rpm . Escherichia coli JM109 and E. coli pRK2013 were cultivated at 37°C, 200 rpm on Luria-Bertani medium (yeast extract 5 g/L, tryptone 10 g/L, NaCl 10 g/L) with appropriate antibiotics (50 mg/L of kanamycin and/or 100 mg/L ampicillin). All culture media were sterilized at 121°C for 15 min.
Overexpression of genes in G. oxydans WSH-003
Primers used in this study
Quantitative real-time PCR (qRT-PCR)
Cells at the beginning of the stationary phase (at 24 h) were harvested at room temperature and immediately frozen in liquid nitrogen. Cells were then stored at -80°C until RNA extraction. Total RNA was extracted with RNAiso™Plus from Takara (Dalian, China). The quantity of total RNA was verified using an Eppendorf Biophotometer (Eppendorf, Hamburg, Germany). The cDNA was synthesized from the total RNA using a PrimeScript RT Reagent Kit (Perfect Real Time) (Takara) according to the manufacturer’s protocol.
Oligonucleotides sequence used in qRT-PCR in this study
Products length (bp)
Measurement of enzyme activity
Cells were harvested at the late-log phase by centrifugation at 9,000gg for 10 min. The cells (0.5 g wet weight) were suspended in 1 mL of 50 mm phosphate buffer (pH 7.0) and passed through a French pressure cell press at 20,000psi. After centrifugation to remove intact cells, the supernatant (cell-free extract) was centrifuged at 80,000gg for 1 h. The membrane fraction was resuspended into the above buffer (1 mL) .
The basal reaction mixture for assaying SLDH activity consisted of 50 mm potassium phosphate buffer (pH 6.0), 0.25 mm DCIP, and 0.325 mm phenazine methosulfate (PMS), which was prepared just before the assay. The cuvette had a 1-cm light path and contained 0.8 mL of the basal reaction mixture, 0.2 mL of 0.4 M D-sorbitol, and the enzyme solution plus water, with a total volume of 1.01 mL. The reference cuvette contained all components except the substrate. The reaction was started at 25°C with D-sorbitol, and the enzyme activity was measured as the initial reduction rate of DCIP at 600 nm. One unit of enzyme activity is defined as the amount of enzyme that catalyzes the reduction of 1 mmol of DCIP per minute .
Measurement of L-sorbose and D-sorbitol
Production of D-sorbitol and L-sorbose was evaluated by HPLC (Agilent 1100 series, Santa Clara, CA), with an Aminex HPX-87H column (300 mm × 7.8 mm; Bio-Rad, Hercules, CA) at 35°C with a flow rate of 0.6 mL/min and 5 mm H2SO4 as the eluent .
Immobilization of G. oxydans
An 18-h culture was harvested during the exponential growth phase and mixed with sodium alginate solution. To prepare the calcium alginate beads, 35 mL of G. oxydans sldhAB6 seed culture were added to sodium alginate solution prepared by dissolving 2.5 g of sodium alginate powder to make a 2.5% (w/v) solution in 100 mL of deionized water. The mixture of sodium alginate and seed culture was passed through a peristaltic pump into a 0.15 M CaCl2 solution. The beads were uniformly packed and stored in CaCl2 solution at 4°C for 3 h and then washed with deionized water to remove residual CaCl2 before fermentation .
Student’s t-test was employed to investigate statistical differences, and samples with P <0.05 were considered significant.
SX and XW performed the experiments and drafted the manuscript. GD, JW and JC participated in the design of the study and supervised the study. All authors revised and approved the final manuscript.
This work was supported by the National High Technology Research and Development Program of China (863 Program, 2012AA022103) the National Natural Science Foundation of China (21406087), the Program for New Century Excellent Talents in University (NCET-12-0876), the Foundation for the Author of National Excellent Doctoral Dissertation of PR China (FANEDD, 201256), the Priority Academic Program Development of Jiangsu Higher Education Institutions, the Fundamental Research Funds for the Central Universities (JUSRP211A25), and the 111 Project (111-2-06).
- Gao LL, Du GC, Zhou JW, Chen J, Liu J: Characterization of a group of pyrroloquinoline quinone-dependent dehydrogenases that are involved in the conversion of L-sorbose to 2-keto-L-gulonic acid in Ketogulonicigenium vulgare WSH-001. Biotechnol Progr. 2013, 29: 1398-1404. 10.1002/btpr.1803.View ArticleGoogle Scholar
- Gao LL, Hu YD, Liu J, Du GC, Zhou JW, Chen J: Stepwise metabolic engineering of Gluconobacter oxydans WSH-003 for the direct production of 2-keto-l-gulonic acid from d-sorbitol. Metab Eng. 2014, 24: 30-37. 10.1016/j.ymben.2014.04.003.View ArticleGoogle Scholar
- Zebiri I, Balieu S, Guilleret A, Reynaud R, Haudrechy A: The chemistry of L-Sorbose. Eur J Org Chem. 2011, 2011: 2905-2910. 10.1002/ejoc.201001578.View ArticleGoogle Scholar
- Macauley-Patrick S, McNeil B, Harvey LM: By-product formation in the d-sorbitol to l-sorbose biotransformation by Gluconobacter suboxydans ATCC 621 in batch and continuous cultures. Process Biochem. 2005, 40: 2113-2122. 10.1016/j.procbio.2004.07.014.View ArticleGoogle Scholar
- Gupta A, Singh VK, Qazi G, Kumar A: Gluconobacter oxydans: its biotechnological applications. J Mol Microbiol Biotechnol. 2001, 3: 445-456.Google Scholar
- Lu LF, Wei LJ, Zhu K, Wei DZ, Hua Q: Combining metabolic engineering and adaptive evolution to enhance the production of dihydroxyacetone from glycerol by Gluconobacter oxydans in a low-cost way. Bioresour Technol. 2012, 117: 317-324. 10.1016/j.biortech.2012.03.013.View ArticleGoogle Scholar
- Kazemi MA, Bamdad H, Papari S, Yaghmaei S: Modeling and control of dissolved oxygen concentration in the fermentation of glucose to gluconic acid. Chem Eng. 2013, 57: 63-70.Google Scholar
- Gao LL, Zhou JW, Liu J, Du GC, Chen J: Draft genome sequence of Gluconobacter oxydans WSH-003, a strain that is extremely tolerant of saccharides and alditols. J Bacteriol. 2012, 194: 4455-4456. 10.1128/JB.00837-12.View ArticleGoogle Scholar
- Deppenmeier U, Hoffmeister M, Prust C: Biochemistry and biotechnological applications of Gluconobacter strains. Appl Microbiol Biotechnol. 2002, 60: 233-242. 10.1007/s00253-002-1114-5.View ArticleGoogle Scholar
- Gatgens C, Degner U, Bringer-Meyer S, Herrmann U: Biotransformation of glycerol to dihydroxyacetone by recombinant Gluconobacter oxydans DSM 2343. Appl Microbiol Biotechnol. 2007, 76: 553-559. 10.1007/s00253-007-1003-z.View ArticleGoogle Scholar
- Zhu K, Lu LF, Wei LJ, Wei DZ, Imanaka T, Hua Q: Modification and evolution of Gluconobacter oxydans for enhanced growth and biotransformation capabilities at low glucose concentration. Mol Biotechnol. 2011, 49: 56-64. 10.1007/s12033-011-9378-6.View ArticleGoogle Scholar
- Richter JD: Cytoplasmic polyadenylation in development and beyond. Microbiol Mol Biol Rev. 1999, 63: 446-456.Google Scholar
- Wu XY, Brewer G: The regulation of mRNA stability in mammalian cells: 2.0. Gene. 2012, 500: 10-21. 10.1016/j.gene.2012.03.021.View ArticleGoogle Scholar
- Xu F, Cohen SN: RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature. 1995, 374: 180-183. 10.1038/374180a0.View ArticleGoogle Scholar
- Kushner SR: mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life. 2004, 56: 585-594. 10.1080/15216540400022441.View ArticleGoogle Scholar
- Slomovica S, Portnoya V, Liveanua V, Schustera G: RNA polyadenylation in prokaryotes and organelles: Different tails tell different tales. Crit Rev Plant Sci. 2006, 25: 65-77. 10.1080/07352680500391337.View ArticleGoogle Scholar
- Régnier P, Marujo PE: Polyadenylation and Degradation of RNA in Prokaryotes. Translation Mechanisms. Edited by: Lapointe J, Brakier-Gingras L. 2003, Landes Bioscience, Austin, TX, 185-196.Google Scholar
- Steege DA: Emerging features of mRNA decay in bacteria. RNA. 2000, 6: 1079-1090. 10.1017/S1355838200001023.View ArticleGoogle Scholar
- Lin H-H, Hsu C-C, Yang C-D, Ju Y-W, Chen Y-P, Tseng C-P: Negative effect of glucose on ompA mRNA stability: a potential role of cyclic AMP in the repression of hfq in Escherichia coli. J Bacteriol. 2011, 193: 5833-5840. 10.1128/JB.05359-11.View ArticleGoogle Scholar
- Arnold TE, Yu J, Belasco JG: mRNA stabilization by the ompA 5′untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA. 1998, 4: 319-330.Google Scholar
- Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR: Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic Acids Res. 2013, 41: 509-517. 10.1093/nar/gks1019.View ArticleGoogle Scholar
- Gallie DR: The cap and poly (A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev. 1991, 5: 2108-2116. 10.1101/gad.5.11.2108.View ArticleGoogle Scholar
- Kumar GR, Shum L, Glaunsinger BA: Importin α-mediated nuclear import of cytoplasmic poly (A) binding protein occurs as a direct consequence of cytoplasmic mRNA depletion. Mol Cell Biol. 2011, 31: 3113-3125. 10.1128/MCB.05402-11.View ArticleGoogle Scholar
- Perez C, McKinney C, Chulunbaatar U, Mohr I: Translational control of the abundance of cytoplasmic poly (A) binding protein in human cytomegalovirus-infected cells. J Virol. 2011, 85: 156-164. 10.1128/JVI.01778-10.View ArticleGoogle Scholar
- Shi LL, Li KF, Zhang H, Liu X, Lin JP, Wei DZ: Identification of a novel promoter gHp0169 for gene expression in Gluconobacter oxydans. J Biotechnol. 2014, 175: 69-74. 10.1016/j.jbiotec.2014.01.035.View ArticleGoogle Scholar
- Wang XB, Liu J, Du GC, Zhou JW, Chen J: Efficient production of L-sorbose from D-sorbitol by whole cell immobilization of Gluconobacter oxydans WSH-003. Biochem Eng J. 2013, 77: 171-176. 10.1016/j.bej.2013.06.008.View ArticleGoogle Scholar
- Park YM, Choi ES, Rhee SK: Effect of toluene-permeabilization on oxidation of D-sorbitol to L-sorbose by Gluconobacter suboxydans cells immobilized in calcium alginate. Biotechnol Lett. 1994, 16: 345-348.Google Scholar
- Goldbeck CP, Jensen HM, TerAvest MA, Beedle N, Appling Y, Hepler M, Cambray G, Mutalik V, Angenent LT, Ajo-Franklin CM: Tuning promoter strengths for improved synthesis and function of electron conduits in Escherichia coli. ACS Synth Biol. 2013, 2: 150-159. 10.1021/sb300119v.View ArticleGoogle Scholar
- Giridhar R, Srivastava A: Productivity enhancement in L-sorbose fermentation using oxygen vector. Enzyme Microb Technol. 2000, 27: 537-541. 10.1016/S0141-0229(00)00252-0.View ArticleGoogle Scholar
- Kim HJ, Jong HK, Chul SS: Conversion of D-sorbitol to L-sorbose by Gluconobacter suboxydans cells co-immobilized with oxygen-carriers in alginate beads. Process Biochem. 1999, 35: 243-248. 10.1016/S0032-9592(99)00091-6.View ArticleGoogle Scholar
- Fidaleo M, Charaniya S, Solheid C, Diel U, Laudon M, Ge H, Scriven L, Flickinger M: A model system for increasing the intensity of whole-cell biocatalysis: Investigation of the rate of oxidation of D-sorbitol to L-sorbose by thin bi-layer latex coatings of non-growing Gluconobacter oxydans. Biotechnol Bioeng. 2006, 95: 446-458. 10.1002/bit.21051.View ArticleGoogle Scholar
- Holscher T, Gorisch H: Knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in Gluconobacter oxydans 621H. J Bacteriol. 2006, 188: 7668-7676. 10.1128/JB.01009-06.View ArticleGoogle Scholar
- Yin XX, Madzak C, Du GC, Zhou JW, Chen J: Enhanced α-ketoglutaric acid production in Yarrowia lipolytica WSH-Z06 by regulation of the pyruvate carboxylation pathway. Appl Microbiol Biotechnol. 2012, 96: 1527-1537. 10.1007/s00253-012-4192-z.View ArticleGoogle Scholar
- Sugisawa T, Hoshino T: Purification and properties of membrane-bound D-sorbitol dehydrogenase from Gluconobacter suboxydans IFO 3255. Biosci Biotechnol Biochem. 2002, 66: 57-64. 10.1271/bbb.66.57.View ArticleGoogle Scholar
- Hattori H, Yakushi T, Matsutani M, Moonmangmee D, Toyama H, Adachi O, Matsushita K: High-temperature sorbose fermentation with thermotolerant Gluconobacter frateurii CHM43 and its mutant strain adapted to higher temperature. Appl Microbiol Biotechnol. 2012, 95: 1531-1540. 10.1007/s00253-012-4005-4.View ArticleGoogle Scholar
- Zhu YB, Liu J, Du GC, Zhou JW, Chen J: A high throughput method to screen companion bacterium for 2-keto-L-gulonic acid biosynthesis by co-culturing Ketogulonicigenium vulgare. Process Biochem. 2012, 47: 1428-1432. 10.1016/j.procbio.2012.05.010.View ArticleGoogle Scholar
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