1
|
Makabe K, Ishida N, Kanezaki N, Shiono Y, Koseki T. Aspergillus oryzae α-l-rhamnosidase: Crystal structure and insight into the substrate specificity. Proteins 2024; 92:236-245. [PMID: 37818702 DOI: 10.1002/prot.26608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/16/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
The subsequent biochemical and structural investigations of the purified recombinant α-l-rhamnosidase from Aspergillus oryzae expressed in Pichia pastoris, designated as rAoRhaA, were performed. The specific activity of the rAoRhaA wild-type was higher toward hesperidin and narirutin, where the l-rhamnose residue was α-1,6-linked to β-d-glucoside, than toward neohesperidin and naringin with an α-1,2-linkage to β-d-glucoside. However, no activity was detected toward quercitrin, myricitrin, and epimedin C. rAoRhaA kinetic analysis indicated that Km values for neohesperidin, naringin, and rutin were lower compared to those for hesperidin and narirutin. kcat values for hesperidin and narirutin were higher than those for neohesperidin, naringin, and rutin. High catalytic efficiency (kcat /Km ) toward hesperidin and narirutin was a result of a considerably high kcat value, while Km values for hesperidin and narirutin were higher than those for naringin, neohesperidin, and rutin. The crystal structure of rAoRhaA revealed that the catalytic domain was represented by an (α/α)6 -barrel with the active site located in a deep cleft and two β-sheet domains were also present in the N- and C-terminal sites of the catalytic domain. Additionally, five asparagine-attached N-acetylglucosamine molecules were observed. The catalytic residues of AoRhaA were suggested to be Asp254 and Glu524, and their catalytic roles were confirmed by mutational studies of D254N and E524Q variants, which lost their activity completely. Notably, three aspartic acids (Asp117, Asp249, and Asp261) located at the catalytic pocket were replaced with asparagine. D117N variant showed reduced activity. D249N and D261N variants activities drastically decreased.
Collapse
Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Japan
| | - Naoki Ishida
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Nanako Kanezaki
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Yoshihito Shiono
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Takuya Koseki
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| |
Collapse
|
2
|
MacCabe A, Sanmartín G, Orejas M. Identification of the genes encoding the catalytic steps corresponding to LRA4 (l-2-keto-3-deoxyrhamnonate aldolase) and l-lactaldehyde dehydrogenase in Aspergillus nidulans: evidence for involvement of the loci AN9425/lraD and AN0544/aldA in the l-rhamnose catabolic pathway. Environ Microbiol 2021; 23:2420-2432. [PMID: 33615657 DOI: 10.1111/1462-2920.15439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/29/2022]
Abstract
l-rhamnose is found in nature mainly as a component of structural plant polysaccharides and can be used as a carbon source by certain microorganisms. Catabolism of this sugar in bacteria, archaea and fungi occurs by two routes involving either phosphorylated or non-phosphorylated intermediates. Unlike the corresponding pathway in yeasts, the metabolic details of the non-phosphorylated pathway in filamentous fungi are not fully defined. The first three genes (lraA, lraB and lraC) of the non-phosphorylated pathway in Aspergillus nidulans have recently been studied revealing dependence on lraA function for growth on l-rhamnose and α-l-rhamnosidase production. In the present work, two genes encoding the subsequent steps catalysed by l-2-keto-3-deoxyrhamnonate (l-KDR) aldolase (AN9425) and l-lactaldehyde dehydrogenase (AN0554) are identified. Loss-of-function mutations cause adverse growth effects on l-rhamnose. Akin to genes lraA-C and those encoding rhamnosidases (rhaA, rhaE), their expression is induced on l-rhamnose via the transcriptional activator RhaR. Interestingly, the aldolase belongs to the ftablamily of bacterial l-KDR aldolases (PF03328/COG3836) and not that of yeasts (PF00701/COG0329). In addition, AN0554 corresponds to the previously characterized aldA gene (encodes aldehyde dehydrogenase involved in ethanol utilization) thus revealing a previously unknown role for this gene in the catabolism of l-rhamnose.
Collapse
Affiliation(s)
- Andrew MacCabe
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), c/ Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| | - Gemma Sanmartín
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), c/ Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), c/ Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| |
Collapse
|
3
|
Catabolism of L-rhamnose in A. nidulans proceeds via the non-phosphorylated pathway and is glucose repressed by a CreA-independent mechanism. Microb Cell Fact 2020; 19:188. [PMID: 33008411 PMCID: PMC7532622 DOI: 10.1186/s12934-020-01443-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/25/2020] [Indexed: 12/02/2022] Open
Abstract
l-rhamnose (6-deoxy-mannose) occurs in nature mainly as a component of certain plant structural polysaccharides and bioactive metabolites but has also been found in some microorganisms and animals. The release of l-rhamnose from these substrates is catalysed by extracellular enzymes including α-l-rhamnosidases, the production of which is induced in its presence. The free sugar enters cells via specific uptake systems where it can be metabolized. Of two l-rhamnose catabolic pathways currently known in microorganisms a non-phosphorylated pathway has been identified in fungi and some bacteria but little is known of the regulatory mechanisms governing it in fungi. In this study two genes (lraA and lraB) are predicted to be involved in the catabolism of l-rhamnose, along with lraC, in the filamentous fungus Aspergillus nidulans. Transcription of all three is co-regulated with that of the genes encoding α-l-rhamnosidases, i.e. induction mediated by the l-rhamnose-responsive transcription factor RhaR and repression of induction in the presence of glucose via a CreA-independent mechanism. The participation of lraA/AN4186 (encoding l-rhamnose dehydrogenase) in l-rhamnose catabolism was revealed by the phenotypes of knock-out mutants and their complemented strains. lraA deletion negatively affects both growth on l-rhamnose and the synthesis of α-l-rhamnosidases, indicating not only the indispensability of this pathway for l-rhamnose utilization but also that a metabolite derived from this sugar is the true physiological inducer.
Collapse
|
4
|
Tautau FAP, Izumi M, Matsunaga E, Higuchi Y, Takegawa K. Microbial α-L-Rhamnosidases of Glycosyl Hydrolase Families GH78 and GH106 Have Broad Substrate Specificities toward α-L-Rhamnosyl- and α-L-Mannosyl-Linkages. J Appl Glycosci (1999) 2020; 67:87-93. [PMID: 34354534 PMCID: PMC8132073 DOI: 10.5458/jag.jag.jag-2020_0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/10/2020] [Indexed: 11/21/2022] Open
Abstract
α-L-Rhamnosidases (α-L-Rha-ases, EC 3.2.1.40) are glycosyl hydrolases (GHs) that hydrolyze a terminal α-linked L-rhamnose residue from a wide spectrum of substrates such as heteropolysaccharides, glycosylated proteins, and natural flavonoids. As a result, they are considered catalysts of interest for various biotechnological applications. α-L-rhamnose (6-deoxy-L-mannose) is structurally similar to the rare sugar α-L-mannose. Here we have examined whether microbial α-L-Rha-ases possess α-L-mannosidase activity by synthesizing the substrate 4-nitrophenyl α-L-mannopyranoside. Four α-L-Rha-ases from GH78 and GH106 families were expressed and purified from Escherichia coli cells. All four enzymes exhibited both α-L-rhamnosyl-hydrolyzing activity and weak α-L-mannosyl-hydrolyzing activity. SpRhaM, a GH106 family α-L-Rha-ase from Sphingomonas paucimobilis FP2001, was found to have relatively higher α-L-mannosidase activity as compared with three GH78 α-L-Rha-ases. The α-L-mannosidase activity of SpRhaM showed pH dependence, with highest activity observed at pH 7.0. In summary, we have shown that α-L-Rha-ases also have α-L-mannosidase activity. Our findings will be useful in the identification and structural determination of α-L-mannose-containing polysaccharides from natural sources for use in the pharmaceutical and food industries.
Collapse
Affiliation(s)
| | - Minoru Izumi
- 2 Graduate School of Environmental and Life Science, Okayama University
| | - Emiko Matsunaga
- 1 Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University
| | - Yujiro Higuchi
- 1 Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University
| | - Kaoru Takegawa
- 1 Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University
| |
Collapse
|
5
|
Gu X, Ding J, Liu W, Yang X, Yao L, Gao X, Zhang M, Yang S, Wen J. Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean. BMC Genomics 2020; 21:172. [PMID: 32075575 PMCID: PMC7032006 DOI: 10.1186/s12864-020-6581-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/13/2020] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
Collapse
Affiliation(s)
- Xin Gu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingzhi Wen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China.
| |
Collapse
|
6
|
Lyu Y, Zeng W, Du G, Chen J, Zhou J. Efficient bioconversion of epimedin C to icariin by a glycosidase from Aspergillus nidulans. BIORESOURCE TECHNOLOGY 2019; 289:121612. [PMID: 31203178 DOI: 10.1016/j.biortech.2019.121612] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/25/2023]
Abstract
Herba Epimedii is a traditional Chinese herbal medicine that contains a mixture of bioactive flavonoid glycosides. Among them, icariin has the most outstanding bioactive functions, while epimedin C exhibits substantial toxicity. A recombinant α-L-rhamnosidase (synAnRhaE) from Aspergillus nidulans was expressed in Escherichia coli to promote the efficient bioconversion of epimedin C to icariin. A hydrolase activity of 574.5 U L-1 was acquired via optimized fed-batch fermentation in a 5-L bioreactor. The enzyme proved to be stable in an acidulous pH range below 55 °C with an optimal pH of 4.5 and optimal temperature of 55 °C. Epimedin C (1 g L-1) was 100% converted to icariin within 90 min using recombinant cells. The resting cells proved to be selective for epimedin C and 2″-O-rhamnosylicariside II in crude extracts of the epimedium plant. This work provides an original and efficient biocatalyst system that can be applied in industrialized production of icariin.
Collapse
Affiliation(s)
- Yunbin Lyu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
7
|
Li LJ, Liu XQ, Du XP, Wu L, Jiang ZD, Ni H, Li QB, Chen F. Preparation of isoquercitrin by biotransformation of rutin using α-L-rhamnosidase from Aspergillus niger JMU-TS528 and HSCCC purification. Prep Biochem Biotechnol 2019; 50:1-9. [PMID: 31441715 DOI: 10.1080/10826068.2019.1655763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isoquercitrin is a flavonoid with important applications in the pharmaceutical and nutraceutical industries. However, a low yield and high production cost hinders the industrial preparation of isoquercitrin. In the present study, isoquercitrin was prepared by biotransformation of rutin using α-L-rhamnosidase from Aspergillus niger JMU-TS528 combined with high-speed countercurrent chromatography (HSCCC) purification. As a result, the optimum transformation pH, temperature, and time were pH 4.0, 60 °C, and 60 min, respectively. The Km and Vmax were 0.36 mM and 0.460 mmol/min, respectively. For isoquercitrin production, the optimal rutin concentration and transformation time were approximately 1000 mg/L and 60 min. The rutin transformation rate reached 96.44%. The isoquercitrin was purified to a purity of 97.83% using one-step purification with HSCCC. The isoquercitrin was identified using UPLC-Q-TOF-MS. The comprehensive results indicated that the biotransformation procedure using the α-L-rhamnosidase from A. niger JMU-TS528 combined with HSCCC was a simple and effective process to prepare isoquercitrin, which might facilitate the production of isoquercitrin for industrial use.
Collapse
Affiliation(s)
- Li Jun Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xiao Qing Liu
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Xi Ping Du
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Ling Wu
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Ze Dong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Qing Biao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Feng Chen
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Department of Food, Nutrition and Packaging Sciences, Clemson University, Clemson, SC, USA
| |
Collapse
|
8
|
CreA-independent carbon catabolite repression of cellulase genes by trimeric G-protein and protein kinase A in Aspergillus nidulans. Curr Genet 2019; 65:941-952. [PMID: 30796472 DOI: 10.1007/s00294-019-00944-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Cellulase production in filamentous fungi is repressed by various carbon sources. In our preliminary survey in Aspergillus nidulans, degree of de-repression differed depending on carbon sources in a mutant of creA, encoding the transcriptional repressor for carbon catabolite repression (CCR). To further understand mechanisms of CCR of cellulase production, we compared the effects of creA deletion with deletion of protein kinase A (pkaA) and G (ganB) genes, which constitute a nutrient sensing and signaling pathway. In plate culture with carboxymethyl cellulose and D-glucose, deletion of pkaA and ganB, but not creA, led to significant de-repression of cellulase production. In submerged culture with cellobiose and D-glucose or 2-deoxyglucose, both creA or pkaA single deletion led to partial de-repression of cellulase genes with the highest level by their double deletion, while ganB deletion caused de-repression comparable to that of the creA/pkaA double deletion. With ball-milled cellulose and D-glucose, partial de-repression was detected by deletion of creA but not of pkaA or ganB. The creA/pkaA or creA/ganB double deletion led to earlier expression than the creA deletion. Furthermore, the effect of each deletion with D-xylose or L-arabinose as the repressing carbon source was significantly different from that with D-glucose, D-fructose, and D-mannose. Consequently, this study revealed that PkaA and GanB participate in CreA-independent CCR and that contribution of CreA, PkaA, and GanB in CCR differs depending on the inducers, repressing carbon sources, and culture conditions (plate or submerged). Further study of CreA-independent mechanisms is needed to fully understand CCR in filamentous fungi.
Collapse
|
9
|
Guillotin L, Kim H, Traore Y, Moreau P, Lafite P, Coquoin V, Nuccio S, de Vaumas R, Daniellou R. Biochemical Characterization of the α-l-Rhamnosidase DtRha from Dictyoglomus thermophilum: Application to the Selective Derhamnosylation of Natural Flavonoids. ACS OMEGA 2019; 4:1916-1922. [PMID: 31459445 PMCID: PMC6649072 DOI: 10.1021/acsomega.8b03186] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/10/2019] [Indexed: 05/25/2023]
Abstract
α-l-Rhamnosidases are catalysts of industrial tremendous interest, but their uses are still somewhat limited by their poor thermal stabilities and selectivities. The thermophilic DtRha from Dictyoglomus thermophilum was cloned, and the recombinant protein was easily purified to homogeneity to afford 4.5 mg/L culture of biocatalyst. Michaelis-Menten parameters demonstrated it to be fully specific for α-l-rhamnose. Most significantly, DtRha demonstrated to have a stronger preference for α(1 → 2) linkage rather than α(1 → 6) linkage when removing rhamnosyl moiety from natural flavonoids. This selectivity was fully explained by the difference of binding of the corresponding substrates in the active site of the protein.
Collapse
Affiliation(s)
- Laure Guillotin
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Hyuna Kim
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Yasmina Traore
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Philippe Moreau
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Pierre Lafite
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Véronique Coquoin
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - Sylvie Nuccio
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - René de Vaumas
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - Richard Daniellou
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| |
Collapse
|
10
|
Schmitz K, Protzko R, Zhang L, Benz JP. Spotlight on fungal pectin utilization-from phytopathogenicity to molecular recognition and industrial applications. Appl Microbiol Biotechnol 2019; 103:2507-2524. [PMID: 30694345 DOI: 10.1007/s00253-019-09622-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 11/29/2022]
Abstract
Pectin is a complex polysaccharide with D-galacturonic acid as its main component that predominantly accumulates in the middle lamella of the plant cell wall. Integrity and depolymerization of pectic structures have long been identified as relevant factors in fungal phytosymbiosis and phytopathogenicity in the context of tissue penetration and carbon source supply. While the pectic content of a plant cell wall can vary significantly, pectin was reported to account for up to 20-25% of the total dry weight in soft and non-woody tissues with non- or mildly lignified secondary cell walls, such as found in citrus peel, sugar beet pulp, and apple pomace. Due to their potential applications in various industrial sectors, pectic sugars from these and similar agricultural waste streams have been recognized as valuable targets for a diverse set of biotechnological fermentations.Recent advances in uncovering the molecular regulation mechanisms for pectinase expression in saprophytic fungi have led to a better understanding of fungal pectin sensing and utilization that could help to improve industrial, pectin-based fermentations. Related research in phytopathogenic fungi has furthermore added to our knowledge regarding the relevance of pectinases in plant cell wall penetration during onset of disease and is therefore highly relevant for agricultural sciences and the agricultural industry. This review therefore aims at summarizing (i) the role of pectinases in phytopathogenicity, (ii) the global regulation patterns for pectinase expression in saprophytic filamentous fungi as a highly specialized class of pectin degraders, and (iii) the current industrial applications in pectic sugar fermentations and transformations.
Collapse
Affiliation(s)
- Kevin Schmitz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Ryan Protzko
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - J Philipp Benz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany.
| |
Collapse
|
11
|
l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans. Fungal Genet Biol 2018; 123:53-59. [PMID: 30496805 DOI: 10.1016/j.fgb.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/03/2018] [Accepted: 11/25/2018] [Indexed: 11/22/2022]
Abstract
l-Arabinose and d-galactose are the principal constituents of l-arabinogalactan, and also co-occur in other hemicelluloses and pectins. In this work we hypothesized that similar to the induction of relevant glycoside hydrolases by monomers liberated from these plant heteropolymers, their respective catabolisms in saprophytic and phytopathogenic fungi may respond to the presence of the other sugar to promote synergistic use of the complex growth substrate. We showed that these two sugars are indeed consumed simultaneously by Aspergillus nidulans, while l-arabinose is utilised faster in the presence than in the absence of d-galactose. Furthermore, the first two genes of the Leloir pathway for d-galactose catabolism - encoding d-galactose 1-epimerase and galactokinase - are induced more rapidly by l-arabinose than by d-galactose eventhough deletion mutants thereof grow as well as a wild type strain on the pentose. d-Galactose 1-epimerase is hyperinduced by l-arabinose, d-xylose and l-arabitol but not by xylitol. The results suggest that in A. nidulans, l-arabinose and d-xylose - both requiring NADPH for their catabolisation - actively promote the enzyme infrastructure necessary to convert β-d-galactopyranose via the Leloir pathway with its α-anomer specific enzymes, into β-d-glucose-6-phosphate (the starting substrate of the oxidative part of the pentose phosphate pathway) even in the absence of d-galactose.
Collapse
|
12
|
Pachl P, Škerlová J, Šimčíková D, Kotik M, Křenková A, Mader P, Brynda J, Kapešová J, Křen V, Otwinowski Z, Řezáčová P. Crystal structure of native α-L-rhamnosidase from Aspergillus terreus. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1078-1084. [DOI: 10.1107/s2059798318013049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022]
Abstract
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.
Collapse
|
13
|
Ahn HJ, You HJ, Park MS, Johnston TV, Ku S, Ji GE. Biocatalysis of Platycoside E and Platycodin D3 Using Fungal Extracellular β-Glucosidase Responsible for Rapid Platycodin D Production. Int J Mol Sci 2018; 19:ijms19092671. [PMID: 30205574 PMCID: PMC6163259 DOI: 10.3390/ijms19092671] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/21/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Platycodi radix (i.e., Platycodon grandiflorum root) products (e.g., tea, cosmetics, and herbal supplements) are popular in East Asian nutraceutical markets due to their reported health benefits and positive consumer perceptions. Platycosides are the key drivers of Platycodi radixes' biofunctional effects; their nutraceutical and pharmaceutical activities are primarily related to the number and varieties of sugar side-chains. Among the various platycosides, platycodin D is a major saponin that demonstrates various nutraceutical activities. Therefore, the development of a novel technology to increase the total platycodin D content in Platycodi radix extract is important, not only for consumers' health benefits but also producers' commercial applications and manufacturing cost reduction. It has been reported that hydrolysis of platycoside sugar moieties significantly modifies the compound's biofunctionality. Platycodi radix extract naturally contains two major platycodin D precursors (platycoside E and platycodin D3) which can be enzymatically converted to platycodin D via β-d-glucosidase hydrolysis. Despite evidence that platycodin D precursors can be changed to platycodin D in the Platycodi radix plant, there is little research on increasing platycodin D concentrations during processing. In this work, platycodin D levels in Platycodi radix extracts were significantly increased via extracellular Aspergillus usamii β-d-glucosidase (n = 3, p < 0.001). To increase the extracellular β-d-glucosidase activity, A. usamii was cultivated in a culture media containing cellobiose as its major carbon source. The optimal pH and temperature of the fungal β-d-glucosidase were 6.0 and 40.0 °C, respectively. Extracellular A. usamii β-d-glucosidase successfully converted more than 99.9% (w/v, n = 3, p < 0.001) of platycoside E and platycodin D3 into platycodin D within 2 h under optimal conditions. The maximum level of platycodin D was 0.4 mM. Following the biotransformation process, the platycodin D was recovered using preparatory High Performance Liquid Chromatography (HPLC) and applied to in vitro assays to evaluate its quality. Platycodin D separated from the Platycodi radix immediately following the bioconversion process showed significant anti-inflammatory effects from the Lipopolysaccharide (LPS)-induced macrophage inflammatory responses with decreased nitrite and IL-6 production (n = 3, p < 0.001). Taken together, these results provide evidence that biocatalysis of Platycodi radix extracts with A. usamii may be used as an efficient method of platycodin D-enriched extract production and novel Platycodi radix products may thereby be created.
Collapse
Affiliation(s)
- Hyung Jin Ahn
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 08826, Korea.
| | - Hyun Ju You
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Korea.
| | - Myung Su Park
- Department of Hotel Culinary Arts, Yeonsung University, Anyang 14001, Korea.
| | - Tony V Johnston
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 08826, Korea.
- Research Center, BIFIDO Co., Ltd., Hongcheon 25117, Korea.
| |
Collapse
|
14
|
Mäkelä MR, Aguilar-Pontes MV, van Rossen-Uffink D, Peng M, de Vries RP. The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA. Sci Rep 2018; 8:6655. [PMID: 29703914 PMCID: PMC5923239 DOI: 10.1038/s41598-018-25152-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/17/2018] [Indexed: 11/09/2022] Open
Abstract
In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.
Collapse
Affiliation(s)
- Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - María Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands. .,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
15
|
Lameiras F, Ras C, Ten Pierick A, Heijnen JJ, van Gulik WM. Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger. Bioprocess Biosyst Eng 2017; 41:157-170. [PMID: 29052015 PMCID: PMC5773628 DOI: 10.1007/s00449-017-1854-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 10/11/2017] [Indexed: 01/28/2023]
Abstract
In its natural environment, the filamentous fungus Aspergillus niger grows on decaying fruits and plant material, thereby enzymatically degrading the lignocellulosic constituents (lignin, cellulose, hemicellulose, and pectin) into a mixture of mono- and oligosaccharides. To investigate the kinetics and stoichiometry of growth of this fungus on lignocellulosic sugars, we carried out batch cultivations on six representative monosaccharides (glucose, xylose, mannose, rhamnose, arabinose, and galacturonic acid) and a mixture of these. Growth on these substrates was characterized in terms of biomass yields, oxygen/biomass ratios, and specific conversion rates. Interestingly, in combination, some of the carbon sources were consumed simultaneously and some sequentially. With a previously developed protocol, a sequential chemostat cultivation experiment was performed on a feed mixture of the six substrates. We found that the uptake of glucose, xylose, and mannose could be described with a Michaelis–Menten-type kinetics; however, these carbon sources seem to be competing for the same transport systems, while the uptake of arabinose, galacturonic acid, and rhamnose appeared to be repressed by the presence of other substrates.
Collapse
Affiliation(s)
- Francisca Lameiras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Cor Ras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Angela Ten Pierick
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Joseph J Heijnen
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Walter M van Gulik
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands.
| |
Collapse
|
16
|
Ishikawa M, Shiono Y, Koseki T. Biochemical characterization of Aspergillus oryzae recombinant α-l-rhamnosidase expressed in Pichia pastoris. J Biosci Bioeng 2017; 124:630-634. [PMID: 28800907 DOI: 10.1016/j.jbiosc.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 11/30/2022]
Abstract
An α-l-rhamnosidase-encoding gene from Aspergillus oryzae, which belongs to the glycoside hydrolase family 78, was cloned and expressed in Pichia pastoris. SDS-PAGE of the purified recombinant α-l-rhamnosidase protein revealed smeared bands with apparent molecular mass of 90-130 kDa. After N-deglycosylation, the recombinant enzyme showed a molecular mass of 70 kDa. The enzyme exhibited optimal activity at a pH of 5.0 and a temperature of 70 °C. Specific activity of the enzyme was higher toward hesperidin than toward naringin, which consist of α-1,6 and α-1,2 linkages, respectively. The activity was also higher toward hesperidin than toward rutin, which consist of 7-O- and 3-O-glycosyl linkages of flavonoids, respectively. Kinetic analysis of the enzyme showed that the Michaelis constant (Km) was lowest toward rutin, moderate toward naringin, and higher toward p-nitrophenyl-α-l-rhamnopyranoside and hesperidin. Its high catalytic efficiency (kcat/Km) toward rutin was results of its low Km value while its high catalytic efficiency toward hesperidin was results of a considerably high kcat value.
Collapse
Affiliation(s)
- Mai Ishikawa
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan
| | - Yoshihito Shiono
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan
| | - Takuya Koseki
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan.
| |
Collapse
|
17
|
Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger. PLoS Genet 2016; 12:e1006468. [PMID: 27984587 PMCID: PMC5161314 DOI: 10.1371/journal.pgen.1006468] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/07/2016] [Indexed: 11/19/2022] Open
Abstract
The study of plant biomass utilization by fungi is a research field of great interest due to its many implications in ecology, agriculture and biotechnology. Most of the efforts done to increase the understanding of the use of plant cell walls by fungi have been focused on the degradation of cellulose and hemicellulose, and transport and metabolism of their constituent monosaccharides. Pectin is another important constituent of plant cell walls, but has received less attention. In relation to the uptake of pectic building blocks, fungal transporters for the uptake of galacturonic acid recently have been reported in Aspergillus niger and Neurospora crassa. However, not a single L-rhamnose (6-deoxy-L-mannose) transporter has been identified yet in fungi or in other eukaryotic organisms. L-rhamnose is a deoxy-sugar present in plant cell wall pectic polysaccharides (mainly rhamnogalacturonan I and rhamnogalacturonan II), but is also found in diverse plant secondary metabolites (e.g. anthocyanins, flavonoids and triterpenoids), in the green seaweed sulfated polysaccharide ulvan, and in glycan structures from viruses and bacteria. Here, a comparative plasmalemma proteomic analysis was used to identify candidate L-rhamnose transporters in A. niger. Further analysis was focused on protein ID 1119135 (RhtA) (JGI A. niger ATCC 1015 genome database). RhtA was classified as a Family 7 Fucose: H+ Symporter (FHS) within the Major Facilitator Superfamily. Family 7 currently includes exclusively bacterial transporters able to use different sugars. Strong indications for its role in L-rhamnose transport were obtained by functional complementation of the Saccharomyces cerevisiae EBY.VW.4000 strain in growth studies with a range of potential substrates. Biochemical analysis using L-[3H(G)]-rhamnose confirmed that RhtA is a L-rhamnose transporter. The RhtA gene is located in tandem with a hypothetical alpha-L-rhamnosidase gene (rhaB). Transcriptional analysis of rhtA and rhaB confirmed that both genes have a coordinated expression, being strongly and specifically induced by L-rhamnose, and controlled by RhaR, a transcriptional regulator involved in the release and catabolism of the methyl-pentose. RhtA is the first eukaryotic L-rhamnose transporter identified and functionally validated to date. The growth of filamentous fungi on plant biomass, which occurs through the utilization of its components (e.g. D-glucose, D-xylose, L-arabinose, L-rhamnose) as carbon sources, is a highly regulated event. L-rhamnose (6-deoxy-L-mannose) is a deoxy-sugar present in plant cell wall pectic polysaccharides (mainly rhamnogalacturonan I and rhamnogalacturonan II), but also in diverse plant secondary metabolites, ulvan from green seaweeds and glycan structures from virus and bacteria. The utilization, transformation or detoxification of this monosaccharide by fungi involves a first step of chemical hydrolysis, performed by alpha-L-rhamnosidases, and a second step of transport into the cell, prior to its metabolization. While many rhamnosidases have been identified, not a single eukaryotic plasma membrane L-rhamnose transporter is known to date. In this study we identified and characterized, for the first time, a fungal L-rhamnose transporter (RhtA), from the industrial workhorse Aspergillus niger. We also found that RhtA putative orthologs are conserved throughout different fungal orders, opening the possibility of identifying new transporters of its kind.
Collapse
|
18
|
Kelly CL, Liu Z, Yoshihara A, Jenkinson SF, Wormald MR, Otero J, Estévez A, Kato A, Marqvorsen MHS, Fleet GWJ, Estévez RJ, Izumori K, Heap JT. Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter. ACS Synth Biol 2016; 5:1136-1145. [PMID: 27247275 DOI: 10.1021/acssynbio.6b00030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
External control of gene expression is crucial in synthetic biology and biotechnology research and applications, and is commonly achieved using inducible promoter systems. The E. coli rhamnose-inducible rhaBAD promoter has properties superior to more commonly used inducible expression systems, but is marred by transient expression caused by degradation of the native inducer, l-rhamnose. To address this problem, 35 analogues of l-rhamnose were screened for induction of the rhaBAD promoter, but no strong inducers were identified. In the native configuration, an inducer must bind and activate two transcriptional activators, RhaR and RhaS. Therefore, the expression system was reconfigured to decouple the rhaBAD promoter from the native rhaSR regulatory cascade so that candidate inducers need only activate the terminal transcription factor RhaS. Rescreening the 35 compounds using the modified rhaBAD expression system revealed several promising inducers. These were characterized further to determine the strength, kinetics, and concentration-dependence of induction; whether the inducer was used as a carbon source by E. coli; and the modality (distribution) of induction among populations of cells. l-Mannose was found to be the most useful orthogonal inducer, providing an even greater range of induction than the native inducer l-rhamnose, and crucially, allowing sustained induction instead of transient induction. These findings address the key limitation of the rhaBAD expression system and suggest it may now be the most suitable system for many applications.
Collapse
Affiliation(s)
- Ciarán L. Kelly
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Zilei Liu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Akihide Yoshihara
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Sarah F. Jenkinson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Mark R. Wormald
- Glycobiology
Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Jose Otero
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Amalia Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Atsushi Kato
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - Mikkel H. S. Marqvorsen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - George W. J. Fleet
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Ramón J. Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Ken Izumori
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - John T. Heap
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| |
Collapse
|
19
|
Wu Z, Mao Y, Zhang X, Weng P. Symbolic Metabolite Analysis of Pickled Wax Gourd in Eastern China by 1H-NMR Spectroscopy and Multivariate Data. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2016. [DOI: 10.1080/10942912.2015.1099044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Zufang Wu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yijun Mao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Peifang Weng
- School of Marine Sciences, Ningbo University, Ningbo, China
| |
Collapse
|
20
|
Kiesenhofer D, Mach-Aigner AR, Mach RL. Understanding the Mechanism of Carbon Catabolite Repression to Increase Protein Production in Filamentous Fungi. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
21
|
Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR. RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica. PLoS One 2015; 10:e0136899. [PMID: 26332397 PMCID: PMC4558045 DOI: 10.1371/journal.pone.0136899] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.
Collapse
Affiliation(s)
- Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- * E-mail:
| | - Darren P. Cullerne
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Pernelyn Torreña
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
| | - Jen Taylor
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
| |
Collapse
|
22
|
Niño-Sánchez J, Tello V, Casado-Del Castillo V, Thon MR, Benito EP, Díaz-Mínguez JM. Gene expression patterns and dynamics of the colonization of common bean (Phaseolus vulgaris L.) by highly virulent and weakly virulent strains of Fusarium oxysporum. Front Microbiol 2015; 6:234. [PMID: 25883592 PMCID: PMC4383042 DOI: 10.3389/fmicb.2015.00234] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The dynamics of root and hypocotyl colonization, and the gene expression patterns of several fungal virulence factors and plant defense factors have been analyzed and compared in the interaction of two Fusarium oxysporum f. sp. phaseoli strains displaying clear differences in virulence, with a susceptible common bean cultivar. The growth of the two strains on the root surface and the colonization of the root was quantitatively similar although the highly virulent (HV) strain was more efficient reaching the central root cylinder. The main differences between both strains were found in the temporal and spatial dynamics of crown root and hypocotyl colonization. The increase of fungal biomass in the crown root was considerably larger for the HV strain, which, after an initial stage of global colonization of both the vascular cylinder and the parenchymal cells, restricted its growth to the newly differentiated xylem vessels. The weakly virulent (WV) strain was a much slower and less efficient colonizer of the xylem vessels, showing also growth in the intercellular spaces of the parenchyma. Most of the virulence genes analyzed showed similar expression patterns in both strains, except SIX1, SIX6 and the gene encoding the transcription factor FTF1, which were highly upregulated in root crown and hypocotyl. The response induced in the infected plant showed interesting differences for both strains. The WV strain induced an early and strong transcription of the PR1 gene, involved in SAR response, while the HV strain preferentially induced the early expression of the ethylene responsive factor ERF2.
Collapse
Affiliation(s)
- Jonathan Niño-Sánchez
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Vega Tello
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Virginia Casado-Del Castillo
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Michael R Thon
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - José María Díaz-Mínguez
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| |
Collapse
|
23
|
Pardo E, Orejas M. The Aspergillus nidulans Zn(II)2Cys6 transcription factor AN5673/RhaR mediates L-rhamnose utilization and the production of α-L-rhamnosidases. Microb Cell Fact 2014; 13:161. [PMID: 25416526 PMCID: PMC4245848 DOI: 10.1186/s12934-014-0161-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/01/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Various plant-derived substrates contain L-rhamnose that can be assimilated by many fungi and its liberation is catalyzed by α-L-rhamnosidases. Initial data obtained in our laboratory focussing on two Aspergillus nidulans α-L-rhamnosidase genes (rhaA and rhaE) showed α-L-rhamnosidase production to be tightly controlled at the level of transcription by the carbon source available. Whilst induction is effected by L-rhamnose, unlike many other glycosyl hydrolase genes repression by glucose and other carbon sources occurs in a manner independent of CreA. To date regulatory genes affecting L-rhamnose utilization and the production of enzymes that yield L-rhamnose as a product have not been identified in A. nidulans. The purpose of the present study is to characterize the corresponding α-L-rhamnosidase transactivator. RESULTS In this study we have identified the rhaR gene in A. nidulans and Neurospora crassa (AN5673, NCU9033) encoding a putative Zn(II)2Cys6 DNA-binding protein. Genetic evidence indicates that its product acts in a positive manner to induce transcription of the A. nidulans L-rhamnose regulon. rhaR-deleted mutants showed reduced ability to induce expression of the α-L-rhamnosidase genes rhaA and rhaE and concomitant reduction in α-L-rhamnosidase production. The rhaR deletion phenotype also results in a significant reduction in growth on L-rhamnose that correlates with reduced expression of the L-rhamnonate dehydratase catabolic gene lraC (AN5672). Gel mobility shift assays revealed RhaR to be a DNA binding protein recognizing a partially symmetrical CGG-X11-CCG sequence within the rhaA promoter. Expression of rhaR alone is insufficient for induction since its mRNA accumulates even in the absence of L-rhamnose, therefore the presence of both functional RhaR and L-rhamnose are absolutely required. In N. crassa, deletion of rhaR also impairs growth on L-rhamnose. CONCLUSIONS To define key elements of the L-rhamnose regulatory circuit, we characterized a DNA-binding Zn(II)2Cys6 transcription factor (RhaR) that regulates L-rhamnose induction of α-L-rhamnosidases and the pathway for its catabolism in A. nidulans, thus extending the list of fungal regulators of genes encoding plant cell wall polysaccharide degrading enzymes. These findings can be expected to provide valuable information for modulating α-L-rhamnosidase production and L-rhamnose utilization in fungi and could eventually have implications in fungal pathogenesis and pectin biotechnology.
Collapse
Affiliation(s)
- Ester Pardo
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Agustín Escardino 7, 46980 Paterna, Valencia Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Agustín Escardino 7, 46980 Paterna, Valencia Spain
| |
Collapse
|
24
|
Kowalczyk JE, Benoit I, de Vries RP. Regulation of plant biomass utilization in Aspergillus. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:31-56. [PMID: 24767425 DOI: 10.1016/b978-0-12-800260-5.00002-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability of fungi to survive in every known biotope, both natural and man-made, relies in part on their ability to use a wide range of carbon sources. Fungi degrade polymeric carbon sources present in the environment (polysaccharides, proteins, and lignins) to use the monomeric components as nutrients. However, the available carbon sources vary strongly in nature, both between biotopes and in time. The degradation of polymeric carbon sources is mediated through the production of a broad range of enzymes, the production of which is tightly controlled by a network of regulators and linked to the activation of catabolic pathways to convert the released monomers. This review summarizes the knowledge of Aspergillus regulators involved in plant biomass utilization.
Collapse
Affiliation(s)
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | | |
Collapse
|
25
|
Wang J, Sun GX, Yu L, Wu FA, Guo XJ. Enhancement of the selective enzymatic biotransformation of rutin to isoquercitrin using an ionic liquid as a co-solvent. BIORESOURCE TECHNOLOGY 2013; 128:156-163. [PMID: 23201508 DOI: 10.1016/j.biortech.2012.10.098] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 05/25/2023]
Abstract
An ionic liquid (IL)-containing buffer system was first applied in the conversion of rutin to isoquercitrin. High substrate solubility was achieved to enhance the selectivity and efficiency of hesperidinase-catalyzed reaction. Ten ILs were selected as co-solvents to assist catalytic reactions in this biotransformation process. The transformed products of rutin were identified by LC-MS. The [Bmim][BF(4)]-glycine-sodium hydroxide buffer (pH 9) (10:90, v/v) was found to be the best medium for the biotransformation of isoquercitrin from rutin with higher selectivity and efficiency. The reaction time was reduced by 0.33-fold while the conversion of rutin and the yield of isoquercitrin were increased by 1.67-fold and 2.33-fold. The results suggest that IL co-solvents have great potential to enhance the selectively enzymatic hydrolysis of rutin for isoquercitrin production.
Collapse
Affiliation(s)
- Jun Wang
- School of Biology and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | | | | | | | | |
Collapse
|
26
|
Yadav S, Yadav RSS, Yadav KDS. An α-l-rhamnosidase fromAspergillus awamoriMTCC-2879 and its role in debittering of orange juice. Int J Food Sci Technol 2012. [DOI: 10.1111/ijfs.12043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarita Yadav
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur; 273009; India
| | - Rama S. S. Yadav
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur; 273009; India
| | - Kapil D. S. Yadav
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur; 273009; India
| |
Collapse
|