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Sgro M, Chow N, Olyaei F, Arentshorst M, Geoffrion N, Ram AFJ, Powlowski J, Tsang A. Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger. J Biol Chem 2023; 299:105003. [PMID: 37399977 PMCID: PMC10406623 DOI: 10.1016/j.jbc.2023.105003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl-CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate.
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Affiliation(s)
- Michael Sgro
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Nicholas Chow
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Farnaz Olyaei
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
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van Leeuwe TM, Arentshorst M, Forn-Cuní G, Geoffrion N, Tsang A, Delvigne F, Meijer AH, Ram AFJ, Punt PJ. Deletion of the Aspergillus niger Pro-Protein Processing Protease Gene kexB Results in a pH-Dependent Morphological Transition during Submerged Cultivations and Increases Cell Wall Chitin Content. Microorganisms 2020; 8:E1918. [PMID: 33276589 PMCID: PMC7761569 DOI: 10.3390/microorganisms8121918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
There is a growing interest in the use of post-fermentation mycelial waste to obtain cell wall chitin as an added-value product. In the pursuit to identify suitable production strains that can be used for post-fermentation cell wall harvesting, we turned to an Aspergillus niger strain in which the kexB gene was deleted. Previous work has shown that the deletion of kexB causes hyper-branching and thicker cell walls, traits that may be beneficial for the reduction in fermentation viscosity and lysis. Hyper-branching of ∆kexB was previously found to be pH-dependent on solid medium at pH 6.0, but was absent at pH 5.0. This phenotype was reported to be less pronounced during submerged growth. Here, we show a series of controlled batch cultivations at a pH range of 5, 5.5, and 6 to examine the pellet phenotype of ΔkexB in liquid medium. Morphological analysis showed that ΔkexB formed wild type-like pellets at pH 5.0, whereas the hyper-branching ΔkexB phenotype was found at pH 6.0. The transition of phenotypic plasticity was found in cultivations at pH 5.5, seen as an intermediate phenotype. Analyzing the cell walls of ΔkexB from these controlled pH-conditions showed an increase in chitin content compared to the wild type across all three pH values. Surprisingly, the increase in chitin content was found to be irrespective of the hyper-branching morphology. Evidence for alterations in cell wall make-up are corroborated by transcriptional analysis that showed a significant cell wall stress response in addition to the upregulation of genes encoding other unrelated cell wall biosynthetic genes.
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Affiliation(s)
- Tim M. van Leeuwe
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Gabriel Forn-Cuní
- Institute of Biology Leiden, Animal Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (G.F.-C.); (A.H.M.)
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B1R6, Canada; (N.G.); (A.T.)
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B1R6, Canada; (N.G.); (A.T.)
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, 2B, 5030 Gembloux, Belgium;
| | - Annemarie H. Meijer
- Institute of Biology Leiden, Animal Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (G.F.-C.); (A.H.M.)
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Peter J. Punt
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, The Netherlands
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van Leeuwe TM, Wattjes J, Niehues A, Forn-Cuní G, Geoffrion N, Mélida H, Arentshorst M, Molina A, Tsang A, Meijer AH, Moerschbacher BM, Punt PJ, Ram AF. A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan. Cell Surf 2020; 6:100039. [PMID: 32743151 PMCID: PMC7389268 DOI: 10.1016/j.tcsw.2020.100039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/12/2020] [Accepted: 03/17/2020] [Indexed: 11/05/2022] Open
Abstract
Chitin is an important fungal cell wall component that is cross-linked to β-glucan for structural integrity. Acquisition of chitin to glucan cross-links has previously been shown to be performed by transglycosylation enzymes in Saccharomyces cerevisiae, called Congo Red hypersensitive (Crh) enzymes. Here, we characterized the impact of deleting all seven members of the crh gene family (crhA-G) in Aspergillus niger on cell wall integrity, cell wall composition and genome-wide gene expression. In this study, we show that the seven-fold crh knockout strain shows slightly compact growth on plates, but no increased sensitivity to cell wall perturbing compounds. Additionally, we found that the cell wall composition of this knockout strain was virtually identical to that of the wild type. In congruence with these data, genome-wide expression analysis revealed very limited changes in gene expression and no signs of activation of the cell wall integrity response pathway. However, deleting the entire crh gene family in cell wall mutants that are deficient in either galactofuranose or α-glucan, mainly α-1,3-glucan, resulted in a synthetic growth defect and an increased sensitivity towards Congo Red compared to the parental strains, respectively. Altogether, these results indicate that loss of the crh gene family in A. niger does not trigger the cell wall integrity response, but does play an important role in ensuring cell wall integrity in mutant strains with reduced galactofuranose or α-glucan.
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Affiliation(s)
- Tim M. van Leeuwe
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jasper Wattjes
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Anna Niehues
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Gabriel Forn-Cuní
- Leiden University, Institute of Biology Leiden, Animal Science and Health, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Quebec H4B1R6, Canada
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Mark Arentshorst
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Quebec H4B1R6, Canada
| | - Annemarie H. Meijer
- Leiden University, Institute of Biology Leiden, Animal Science and Health, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Bruno M. Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Peter J. Punt
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arthur F.J. Ram
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
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