Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose
© Sloothaak et al.; licensee Springer 2014
Received: 6 June 2014
Accepted: 8 August 2014
Published: 23 August 2014
Pectin is a structural heteropolysaccharide of the primary cell walls of plants and as such is a significant fraction of agricultural waste residues that is currently insufficiently used. Its main component, D-galacturonic acid, is an attractive substrate for bioconversion. The complete metabolic pathway is present in the genome of Aspergillus niger, that is used in this study. The objective was to identify the D-galacturonic acid transporter in A. niger and to use this transporter to study D-galacturonic acid metabolism.
We have functionally characterized the gene An14g04280 that encodes the D-galacturonic acid transporter in A. niger. In a mixed sugar fermentation it was found that the An14g04280 overexpression strain, in contrast to the parent control strain, has a preference for D-galacturonic acid over D-xylose as substrate. Overexpression of this transporter in A. niger resulted in a strong increase of D-galacturonic acid uptake and induction of the D-galacturonic acid reductase activity, suggesting a metabolite controlled regulation of the endogenous D-galacturonic acid catabolic pathway.
KeywordsD-galacturonic acid Pectin Sustainable resources Aspergillus niger Transmembrane transport
Global limits in food and energy availability are becoming a major concern. Arable land is needed for production of food and large waste streams come from processing of our largest food resources, like grain, maize, potato and rice. These waste streams are currently insufficiently exploited and mainly used for feed and energy production (Howard et al. ). Alternatively, agricultural waste streams can be used as substrate for fermentative production of chemicals by microorganisms.
Historically, Aspergillus species are used for the production of food additives and platform chemicals such as citric acid (A. niger) and itaconic acid (A. terreus) (Willke and Vorlop ). The filamentous fungus Aspergillus niger is additionally exploited for production of enzymes for food and feed applications, many of which have been rewarded the GRAS (Generally Recognized As Safe) status (Howard et al. ; van Dijck et al. ).
Grain, maize and rice waste stream material contains around 40% cellulose, 35% hemicellulose, 20% lignin and 5% pectin, while waste streams from other plants, such as sugar beet and potato, contain around 20% cellulose and hemicellulose, less than 1% lignin and 30% to 40% pectin (Ángel Siles López et al. ; Howard et al. ; Micard et al. ). A. niger has a high capacity for degrading the hemicellulose, pectin and, to a lesser extend, cellulose fractions as the genome of A. niger encodes multiple gene variants of the enzymes required for the efficient degradation of these polysaccharides. (van den Brink and de Vries ).
D-glucose and D-xylose, released from plant wall material, are carbon sources that will yield high energy upon being metabolized. The genome of A. niger is wired to specifically produce and secrete the enzymes involved in degradation of the cellulose and hemicellulose fractions to release D-glucose and D-xylose. These sugars are then taken up and metabolized, before energy is invested in the release of other carbon sources from polysaccharides. This preferential uptake is regulated by the interplay of activating and repressing transcription factors that respond to extracellular concentrations of inducers and sugars.
Expression of genes that code for enzymes involved in cellulose and hemicellulose degradation in A. niger is regulated by the transcription factor XlnR (Gielkens et al. ). XlnR is activated by inducers derived from xylan, like D-xylose, though at a higher concentration this activation is attenuated by CreA (de Vries et al. ; Ruijter et al. ; van Peij et al. ). Tight regulation of the specific genes encoding proteins involved in the release, uptake and metabolism of sugars gives the fungus the ability to utilize the available sugars in a physiologically most efficient way. However, circumventing this regulatory mechanism would potentially lead to simultaneous uptake of all sugar substrates and improved fermentation yields.
Data used for selection of putative D-galacturonic acid transporters (Martens-Uzunova and Schaap)
Relative expression t = 4 h after induction on
Major facilitator superfamily strong similarity to monocarboxylate transporter
Major facilitator superfamily strong similarity to hexose transporter
Major facilitator superfamily strong similarity to hexose transporter
In this study we have functionally identified the D-galacturonic mono-acid sugar transporter by overexpression in A. niger. The effect of the increased uptake of D-galacturonic acid on the preferential uptake and metabolism of substrates has been assessed by mixed sugar fermentations and enzyme activity measurements.
Materials and methods
All Aspergillus strains used are descendants of A. niger N400 (CBS 120.49). A niger strain NW185 cspA1, fwnA1, goxC17, prtF28) was derived from NW131 and has been described by Ruijter et al. . The recipient strain in all transformation experiments NW186 (ΔargB; pyrA6; prtF28; goxC17; cspA1) is an argB and pyrA derivative of NW185.
Primers used in vector construction
Transformation of Aspergillus niger
For the transformation of A. niger NW186, protoplasts were generated using Novozyme-234 lysing enzyme cocktail. The An14g04280, An03g01620 and An07g00780 constructs were introduced in A. niger by transformation (Kusters-van Someren et al. ) using the pyrA gene as a primary selection marker, relieving uridine auxotrophy. To generate the parent control reference strain, NW186 was transformed using pGW635, the resulting NW185 PYR A+ strain was used as a control strain in our studies. Colonies were randomly picked from the primary transformation plates and re-plated on selective medium to purify the single colonies.
Analysis of A. niger transformants
Screening of randomly picked transformants was done by PCR on genomic DNA isolates. For that, fresh mycelium was disrupted using MP lysing matrix C tubes and 400 μl DNA extraction buffer (0.1 M Tris HCl pH 8.0, 1.2 M NaCl, 5 mM EDTA). DNA was extracted using phenol-chloroform extraction. The pellet was washed with 70% cold ethanol, air-dried and re-suspended in 50 μl MQ water. The presence of An14g04280, An03g01620 and An07g00780 expression constructs was confirmed by PCR using the JS_XlnDp_FW primer, binding to the promoter region of the construct, and JS_gatA_RV, JS_gatB_RV or JS_gatC_RV specifically binding to the complementary strand in the corresponding coding region. Transformants with confirmed gene constructs were re-plated on complete medium. Spores are harvested after 4 days of growth at 30°C.
Growth in shake flasks
Composition of synthetic cell wall hydrolysate (SCH)
D-galacturonic acid; 10%
Growth in fermentors
Strains were grown in duplicate in 500 mL PM medium (Ruijter et al. ) with 100 mM sorbitol as a carbon source in 1 L flasks. For inoculation, a final concentration of 1•106 spores per mL was used. Cultures were incubated for 18 hours at 30°C with 250 rpm orbital shaking. Mycelium was aseptically harvested by filtering over a sterile nylon cloth, washed with PM without carbon source and transferred to 1 L fermentors. Fermentors contained 750 ml PM with 50 mM D-xylose and 50 mM D-galacturonic acid, adjusted to pH6. Air was flushed at a stirrer speed of 600 rpm. Medium and biomass samples were taken as previously described, with an additional sampling of mycelium from 10 ml broth volume for enzymatic assays. Carbon dioxide and oxygen concentrations in off-gas were measured as well as pH.
High-pressure liquid chromatography (HPLC) was used to determine the extracellular concentrations of D-glucose, L-sorbitol, D-xylose, citric acid and D-galacturonic acid in the culture broth samples. A Shodex KC-811 column was used at 30°C that was eluted with 0.01 N H2SO4 at a flow rate of 0.8 mL min−1. A refractive index detector (Spectrasystem RI-150, sample frequency 5.00032 Hz) and a UV–VIS detector (Spectrasystem UV1000, λ = 210 nm) were used for detection of the eluting compounds. Crotonate at a concentration of 6 mM was used as an internal standard.
To determine the activity of the D-galacturonic acid metabolism, the first step in the enzymatic conversion, D-galacturonic acid to L-galactonic acid, was measured. D-galacturonic acid reductase assay based on conversion of NADPH to NADP+, previously described by Kuorelahti et al., was applied (Kuorelahti et al. ). 20 mg of frozen mycelium was added to 400 μl of extraction buffer (100 mM phosphate buffer pH 7.0, 0.1 mM EDTA, 1 mM DTT and fungal protease inhibitor cocktail) in lysing matrix C tubes (MP biomedicals) and disrupted at level 6 for 30 seconds in a bead beater (MP fastprep-24). Cell debris was removed by centrifugation and supernatant was used as cell extract. 25 μl of cell extract was added to 200 μl of assay buffer (100 mM sodium phosphate buffer pH 7.0, 0.25 mM NADPH) and reaction was started by the addition of 25 μl of substrate (1 M D-galacturonic acid pH 6). Decrease of absorbance at 340 nm was measured on a platereader (Biotek Synergy) in parallel with sample controls, for which 25 μl of buffer was added. Background activity of sample control without D-galacturonic acid was substracted from sample measurements with D-galacturonic acid. Protein content was determined by photometric assay (Peterson ).
Strains that overexpress GatA have increased D-galacturonic acid uptake in shakeflask cultures
To study the effect of the expression of the putative D-galacturonic acid transporter encoding gene, the D-galacturonic acid concentration in the medium was measured during growth. A faster uptake of D-galacturonic acid from the medium was observed for the cultures with the An14g04280 overexpression strains (transformant) in comparison to the NW185 PYR A+ control strain. At 6 hours after induction, the strains that overexpress An14g04280 had taken up over 50% of D-galacturonic acid present at the start of the cultivation, while no D-galacturonic acid had been taken up by the control strain. The strains containing the other constructs did not show any difference in D-galacturonic acid uptake in comparison to the NW185 PYR A+ control strain. The effect of the An14g04280 overexpression strain is most pronounced between time points 6 and 30 h.
Growth of transporter overexpression strains in fermentors
Phylogenetic analysis of GatA
Three genes that potentially encode the D-galacturonic acid transporter in A. niger are investigated. A. niger transformants that overexpress the An14g04280 gene under control of the D-xylose induced xlnD promoter show a significant increase in D-galacturonic acid uptake. From this we conclude that this gene, gatA, encodes for the D-galacturonic acid transporter, GatA.
By analysis of the amino acid sequence using the α-helical transmembrane protein topology prediction software (PRODIV-TNHMM) (Viklund and Elofsson ) GatA is predicted to be part of the Major Facilitator Superfamily (MFS). MFS transporter proteins consist of 12 transmembrane helices and have both C- and N-termini located in the cytoplasm.
This study shows that the overexpression of gatA, using a D-xylose inducible promoter, leads to differences in the uptake of sugars when the strains are grown on various mixed sugar substrates. GatA overproducing strains preferentially use D-galacturonic acid over D-xylose, while the wild type strains prefer D-xylose. D-xylose is used for overexpression of the GatA transporter in all growth experiments and it is also used as a substrate. However, the main carbon source present in the medium is sorbitol, a non-inducing, non-repressing carbon source. Our extensive previous studies have shown that in this condition induction of expression occurs at concentrations of 0.1 to 50 mM D-xylose (van der Veen et al. ; Mach-Aigner et al. ).
The increased D-galacturonic acid uptake of the transformant was not reflected in the basal GaaA enzyme activity during the first hours of growth on D-xylose and D-galacturonic acid. It is, however, reflected in an increased GaaA enzyme activity after 8 hours. This time delay suggests that GaaA enzyme activity is not limiting D-galacturonic acid uptake and metabolism during the first few hours of growth on these substrates and that regulation of expression of GaaA is taking place “at the gate”, via import of D-galacturonic acid. The repression of induction of GaaA in the presence of D-xylose in the parent strain, is bypassed by an increased influx of substrate in the GatA overexpressing strain, suggesting that the endogenous D-galacturonic acid catabolic pathway is controlled by a pathway intermediate such as L-galactonate or keto-deoxy-L-galactonate as has been suggested for T. reesei (Kuivanen et al. ).
Several repressing and inducing regulatory systems are known to be functioning in Aspergillus niger. The glucose carbon catabolite repressor creA is the most studied and is known to be dominant in most cases (de Vries et al. ). The promoter region of the gatA gene shows two consensus sequences for binding of this protein, which suggests that D-glucose is repressing the expression of the endogenous gene. The xlnR xylanolytic induction system is also well studied and an inducer consensus binding sequence is known (van Peij et al. ). This consensus sequence can not be found in the upstream region of the endogenous gatA gene and it is therefore not induced by the presence of D-xylose. Additionally, GatA expression has been found to be stricktly coregulated with D-galacturonic acid catabolic enzymes and a number of extracellular galacturonases (Martens-Uzunova and Schaap ). The regulator of the D-galacturonic acid metabolism, however, remains unknown for now.
We have investigated the application of our findings by growing our strains on a synthetic medium mimicking a plant cell wall hydrolysate. Under these conditions the gatA overexpressing strains preferentially use D-galacturonic acid over D-xylose. In these experiments it was found that GatA overexpression strains had a higher citric acid yield. While the effect seems pronounced on a simulated hydrolysate substrate, further experiments are needed to study the benefit on second generation feedstocks with high D-galacturonic acid content like sugar beet pulp to investigate the potential of GatA in biotechnological applications.
This work has been carried out on the basis of a grant in the framework of the BE- BASIC program F01.011 Transport processes in the production of organic acids by Aspergillus niger. We would like to thank Tom Schonewille for his assistance with the analysis equipment.
- Ángel Siles López J, Li Q, Thompson IP: Biorefinery of waste orange peel. CRC Cr Rev Biotechn 2010, 30: 63–69. doi:10.3109/07388550903425201 10.3109/07388550903425201View ArticleGoogle Scholar
- Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR: The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res 2012, 40: D653-D659. 10.1093/nar/gkr875PubMed CentralView ArticlePubMedGoogle Scholar
- Benz J, Protzko RJ, Andrich JM, Bauer S, Dueber JE, Somerville CR: Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes. Biotechnol Biofuels 2014, 7: 20–14. doi:10.1111/j.1567–1364.2009.00523.x 10.1186/1754-6834-7-20PubMed CentralView ArticlePubMedGoogle Scholar
- Carlsen M, Nielsen J: Influence of carbon source on alpha-amylase production by Aspergillus oryzae . Appl Microbiol Biotechnol 2001, 57: 346–349. 10.1007/s002530100772View ArticlePubMedGoogle Scholar
- Carpita NC, Gibeaut DM: Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Plant J 1993, 3: 1–30. 10.1111/j.1365-313X.1993.tb00007.xView ArticlePubMedGoogle Scholar
- de Vries RP, Visser J, de Graaff LH: CreA modulates the XlnR-induced expression on xylose of Aspergillus niger genes involved in xylan degradation. Res Microbiol 1999, 150(4):281–285. 10.1016/S0923-2508(99)80053-9View ArticlePubMedGoogle Scholar
- Gielkens MMC, Dekkers E, Visser J, de Graaff LH: Two cellobiohydrolase-encoding genes from Aspergillus niger require D-xylose and the xylanolytic transcriptional activator XlnR for their expression. Appl Environ Microbiol 1999, 65: 4340–4345.PubMed CentralPubMedGoogle Scholar
- Howard RL, Abotsi E, van Rensburg EJ, Howard S: Lignocellulose biotechnology: issues of bioconversion and enzyme production. Afr J Biotechnol 2003, 2: 602–619. doi:10.4314/ajb.v2i12.14892View ArticleGoogle Scholar
- Kuivanen J, Mojzita D, Wang Y, Hilditch S, Penttila M, Richard P, Wiebe MG: Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid. Appl Environ Microbiol 2012, 78: 8676–8683. doi:10.1128/AEM.02171–12 10.1128/AEM.02171-12PubMed CentralView ArticlePubMedGoogle Scholar
- Kuorelahti S, Kalkkinen N, Penttil M, Londesborough J, Richard P: Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase. Biochemistry 2005, 44: 11234–11240. doi:10.1021/bi050792f 10.1021/bi050792fView ArticlePubMedGoogle Scholar
- Kusters-van Someren MA, Harmsen JA, Kester HC, Visser J: Structure of the Aspergillus niger pelA gene and its expression in Aspergillus niger and Aspergillus nidulans . Curr Genet 1991, 20: 293–299. 10.1007/BF00318518View ArticlePubMedGoogle Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23: 2947–2948. doi:10.1093/bioinformatics/btm404 10.1093/bioinformatics/btm404View ArticlePubMedGoogle Scholar
- Mach-Aigner AR, Omony J, Jovanovic B, van Boxtel AJB, de Graaff LH: D-Xylose concentration-dependent hydrolase expression profiles and the function of CreA and XlnR in Aspergillus niger . Appl Environ Microbiol 2012, 78(9):3145–3155. doi:10.1128/AEM.07772–11 10.1128/AEM.07772-11PubMed CentralView ArticlePubMedGoogle Scholar
- Martens-Uzunova ES, Schaap PJ: An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet Biol 2008, 45: 1449–1457. doi:10.1016/j.fgb.2008.08.002 10.1016/j.fgb.2008.08.002View ArticlePubMedGoogle Scholar
- Micard V, Renard CMGC, Thibault JF: Enzymatic saccharification of sugar-beet pulp. Enzyme Microb Technol 1996, 19: 162–170. doi:10.1016/0141–0229(95)00224–3 10.1016/0141-0229(95)00224-3View ArticleGoogle Scholar
- Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 1999, 96: 2896–2901. 10.1073/pnas.96.6.2896PubMed CentralView ArticlePubMedGoogle Scholar
- Peterson GL: A simplification of the protein assay method of Lowry et al. which is more generally applicable. Anal Biochem 1977, 83: 346–356. doi:10.1016/0003–2697(77)90043–4 10.1016/0003-2697(77)90043-4View ArticlePubMedGoogle Scholar
- Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29: 45e-45. doi:10.1093/nar/29.9.e45 10.1093/nar/29.9.e45View ArticleGoogle Scholar
- Ruijter GJG, van de Vondervoort PJI, Visser J: Oxalic acid production by Aspergillus niger : an oxalate-non-producing mutant produces citric acid at pH 5 and in the presence of manganese. Microbiology 1999, 145(Pt 9):2569–2576.View ArticlePubMedGoogle Scholar
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S: MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013, 30: 2725–2729. doi:10.1093/molbev/mst197 10.1093/molbev/mst197PubMed CentralView ArticlePubMedGoogle Scholar
- van den Brink J, de Vries RP: Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 2011, 91: 1477–1492. doi:10.1007/s00253–011–3473–2 10.1007/s00253-011-3473-2PubMed CentralView ArticlePubMedGoogle Scholar
- van der Veen D, Oliveira JM, van den Berg WAM, de Graaff LH: Analysis of variance components reveals the contribution of sample processing to transcript variation. Appl Environ Microbiol 2009, 75: 2414–2422. 10.1128/AEM.02270-08PubMed CentralView ArticlePubMedGoogle Scholar
- van Dijck PWM, Selten GCM, Hempenius RA: On the safety of a new generation of DSM Aspergillus niger enzyme production strains. Regul Toxicol Pharmacol 2003, 38: 27–35. doi:10.1016/S0273–2300(03)00049–7 10.1016/S0273-2300(03)00049-7View ArticlePubMedGoogle Scholar
- van Peij NNME, Visser J, de Graaff LH: Isolation and analysis of xlnR , encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger . Mol Microbiol 1998, 27: 131–142. doi:10.1046/j.1365–2958.1998.00666.x 10.1046/j.1365-2958.1998.00666.xView ArticlePubMedGoogle Scholar
- vanKuyk PA, Diderich JA, MacCabe AP, Hererro O, Ruijter G, Visser J: Aspergillus niger mstA encodes a high-affinity sugar/H + symporter which is regulated in response to extracellular pH. Biochemical J 2004, 379: 375–383. 10.1042/BJ20030624View ArticleGoogle Scholar
- Viklund H, Elofsson A: Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 2004, 13: 1908–1917. doi:10.1110/ps.04625404 10.1110/ps.04625404PubMed CentralView ArticlePubMedGoogle Scholar
- Willke T, Vorlop KD: Biotechnological production of itaconic acid. Appl Microbiol Biotechnol 2001, 56: 289–295. 10.1007/s002530100685View ArticlePubMedGoogle Scholar
- Yan N: Structural advances for the major facilitator superfamily (MFS) transporters. Trends Biochem Sci 2013, 38: 151–159. doi:10.1016/j.tibs.2013.01.003 10.1016/j.tibs.2013.01.003View ArticlePubMedGoogle Scholar
- Zhang L, Hua C, Stassen JHM, Chatterjee S, Cornelissen M, van Kan JAL (2013) Genome-wide analysis of pectate-induced gene expression in Botrytis cinerea: Identification and functional analysis of putative D-galacturonate transporters. Fungal Genet Biol, doi:10.1016/j.fgb.2013.10.002
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.