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Flipphi M, Márton A, Bíró V, Ág N, Sándor E, Fekete E, Karaffa L. Generation, Transfer, and Loss of Alternative Oxidase Paralogues in the Aspergillaceae Family. J Fungi (Basel) 2023; 9:1195. [PMID: 38132795 PMCID: PMC10744626 DOI: 10.3390/jof9121195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative oxidase (Aox) is a terminal oxidase operating in branched electron transport. The activity correlates positively with overflow metabolisms in certain Aspergilli, converting intracellular glucose by the shortest possible path into organic acids, like citrate or itaconate. Aox is nearly ubiquitous in fungi, but aox gene multiplicity is rare. Nevertheless, within the family of the Aspergillaceae and among its various species of industrial relevance-Aspergillus niger, A. oryzae, A. terreus, Penicillium rubens-paralogous aox genes coexist. Paralogous genes generally arise from duplication and are inherited vertically. Here, we provide evidence of four independent duplication events along the lineage that resulted in aox paralogues (aoxB) in contemporary Aspergillus and Penicillium taxa. In some species, three aox genes are co-expressed. The origin of the A. niger paralogue is different than that of the A. terreus paralogue, but all paralogous clades ultimately arise from ubiquitous aoxA parent genes. We found different patterns of uncorrelated gene losses reflected in the Aspergillus pedigree, albeit the original aoxA orthologues persist everywhere and are never replaced. The loss of acquired paralogues co-determines the contemporary aox gene content of individual species. In Aspergillus calidoustus, the two more ancient paralogues have, in effect, been replaced by two aoxB genes of distinct origins.
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Affiliation(s)
- Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Alexandra Márton
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Vivien Bíró
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
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Flipphi M, Márton A, Bíró V, Ág N, Sándor E, Fekete E, Karaffa L. Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains. J Fungi (Basel) 2023; 9:jof9050570. [PMID: 37233281 DOI: 10.3390/jof9050570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes-A. calidoustus and A. implicatus-as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species.
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Affiliation(s)
- Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Alexandra Márton
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Vivien Bíró
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
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Yoshioka I, Kirimura K. Rapid and marker-free gene replacement in citric acid-producing Aspergillus tubingensis (A. niger) WU-2223L by the CRISPR/Cas9 system-based genome editing technique using DNA fragments encoding sgRNAs. J Biosci Bioeng 2021; 131:579-588. [PMID: 33612423 DOI: 10.1016/j.jbiosc.2021.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/11/2021] [Accepted: 01/30/2021] [Indexed: 01/19/2023]
Abstract
Strains belonging to Aspergillus section Nigri, including Aspergillus niger, are used for industrial production of citric acid from carbohydrates such as molasses and starch. The objective of this study was to construct the genome editing system that could enable rapid and efficient gene replacement in citric acid-producing fungi for genetic breeding. Using the citric acid-hyperproducer A. tubingensis (formerly A. niger) WU-2223L as a model strain, we developed a CRISPR/Cas9 system-based genome editing technique involving co-transformation of Cas9 and the DNA fragment encoding single guide RNA (sgRNA). Using this system, ATP-sulfurylase gene (sC) knock-out strain derived from WU-2223L was generated; the knock-out efficiency was 29 transformants when 5 μg Cas9 was added to 5 × 105 protoplasts. In the gene replacement method based on this system, a DNA fragment encoding sgRNAs that target both the gene of interest and marker gene was used, and replacement of nitrate reductase gene (niaD) using sC gene as a marker gene was attempted. More than 90% of the sC-knock-out transformants exhibited replaced niaD, indicating efficient gene replacement. Moreover, one-step marker rescue of the sC marker gene was accomplished by excising the knock-in donor via intramolecular homologous recombination, enabling marker-free genome editing and drastically shortening the gene replacement period by circumventing the transformation procedure to recover the sC gene. Thus, we succeeded in constructing a CRISPR/Cas9 system-based rapid and marker-free gene replacement system for the citric acid-hyperproducer strain WU-2223L.
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Affiliation(s)
- Isato Yoshioka
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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Yoshioka I, Kobayashi K, Kirimura K. Overexpression of the gene encoding alternative oxidase for enhanced glucose consumption in oxalic acid producing Aspergillus niger expressing oxaloacetate hydrolase gene. J Biosci Bioeng 2020; 129:172-176. [DOI: 10.1016/j.jbiosc.2019.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/13/2019] [Accepted: 08/28/2019] [Indexed: 10/25/2022]
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Kirimura K, Kobayashi K, Yoshioka I. Decrease of citric acid produced by Aspergillus niger through disruption of the gene encoding a putative mitochondrial citrate-oxoglutarate shuttle protein. Biosci Biotechnol Biochem 2019; 83:1538-1546. [DOI: 10.1080/09168451.2019.1574205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ABSTRACT
The transporter that exports citric acid (CA) generated in mitochondria to the cytosol is an important component of the CA production machinery of Aspergillus niger. In this report, we cloned and identified the gene cocA, encoding a 33.7-kDa putative mitochondrial citrate-oxoglutarate shuttle protein of the CA hyper-producer A. niger WU-2223L. The amount of CA produced by a representative cocA disruptant (35 g/L) was significantly lower than that produced by strain WU-2223L (63 g/L) after culture for 12 days under CA production conditions, and the phenotype of the cocA disruptant differed in part from that of strain WU-2223L. A cocA disruptant complemented with cocA exhibited the same phenotypes as those of strain WU-2223L. This report is the first to show that cocA and its protein product clearly contribute to substantial CA production by A. niger, and provides a significant insight into microbial organic acid production by fermentation.
Abbreviations: CA: citric acid; CD medium: Czapek-Dox medium; CS: citrate synthase; CTP: citrate transport protein; HR: homologous recombination; MCF: mitochondrial carrier family; RT-PCR: reverse-transcription PCR; TCA: tricarboxylic acid
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Affiliation(s)
- Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Keiichi Kobayashi
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Isato Yoshioka
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
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Hartmann SK, Stockdreher Y, Wandrey G, Hosseinpour Tehrani H, Zambanini T, Meyer AJ, Büchs J, Blank LM, Schwarzländer M, Wierckx N. Online in vivo monitoring of cytosolic NAD redox dynamics in Ustilago maydis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1015-1024. [DOI: 10.1016/j.bbabio.2018.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/06/2018] [Accepted: 05/20/2018] [Indexed: 12/20/2022]
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Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production. Sci Rep 2017; 7:41040. [PMID: 28106122 PMCID: PMC5247736 DOI: 10.1038/srep41040] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
Despite a long and successful history of citrate production in Aspergillus niger, the molecular mechanism of citrate accumulation is only partially understood. In this study, we used comparative genomics and transcriptome analysis of citrate-producing strains—namely, A. niger H915-1 (citrate titer: 157 g L−1), A1 (117 g L−1), and L2 (76 g L−1)—to gain a genome-wide view of the mechanism of citrate accumulation. Compared with A. niger A1 and L2, A. niger H915-1 contained 92 mutated genes, including a succinate-semialdehyde dehydrogenase in the γ-aminobutyric acid shunt pathway and an aconitase family protein involved in citrate synthesis. Furthermore, transcriptome analysis of A. niger H915-1 revealed that the transcription levels of 479 genes changed between the cell growth stage (6 h) and the citrate synthesis stage (12 h, 24 h, 36 h, and 48 h). In the glycolysis pathway, triosephosphate isomerase was up-regulated, whereas pyruvate kinase was down-regulated. Two cytosol ATP-citrate lyases, which take part in the cycle of citrate synthesis, were up-regulated, and may coordinate with the alternative oxidases in the alternative respiratory pathway for energy balance. Finally, deletion of the oxaloacetate acetylhydrolase gene in H915-1 eliminated oxalate formation but neither influence on pH decrease nor difference in citrate production were observed.
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Kirimura K, Kobayashi K, Ueda Y, Hattori T. Phenotypes of gene disruptants in relation to a putative mitochondrial malate–citrate shuttle protein in citric acid-producing Aspergillus niger. Biosci Biotechnol Biochem 2016; 80:1737-46. [DOI: 10.1080/09168451.2016.1164583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
The mitochondrial citrate transport protein (CTP) functions as a malate–citrate shuttle catalyzing the exchange of citrate plus a proton for malate between mitochondria and cytosol across the inner mitochondrial membrane in higher eukaryotic organisms. In this study, for functional analysis, we cloned the gene encoding putative CTP (ctpA) of citric acid-producing Aspergillus niger WU-2223L. The gene ctpA encodes a polypeptide consisting 296 amino acids conserved active residues required for citrate transport function. Only in early-log phase, the ctpA disruptant DCTPA-1 showed growth delay, and the amount of citric acid produced by strain DCTPA-1 was smaller than that by parental strain WU-2223L. These results indicate that the CTPA affects growth and thereby citric acid metabolism of A. niger changes, especially in early-log phase, but not citric acid-producing period. This is the first report showing that disruption of ctpA causes changes of phenotypes in relation to citric acid production in A. niger.
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Affiliation(s)
- Kohtaro Kirimura
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Tokyo, Japan
| | - Keiichi Kobayashi
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Tokyo, Japan
| | - Yuka Ueda
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Tokyo, Japan
| | - Takasumi Hattori
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Tokyo, Japan
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Characterizing MttA as a mitochondrial cis-aconitic acid transporter by metabolic engineering. Metab Eng 2016; 35:95-104. [DOI: 10.1016/j.ymben.2016.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/25/2016] [Accepted: 02/03/2016] [Indexed: 01/05/2023]
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Kobayashi K, Hattori T, Hayashi R, Kirimura K. Overexpression of the NADP+-specific isocitrate dehydrogenase gene (icdA) in citric acid-producing Aspergillus niger WU-2223L. Biosci Biotechnol Biochem 2014; 78:1246-53. [DOI: 10.1080/09168451.2014.918483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
In the tricarboxylic acid (TCA) cycle, NADP+-specific isocitrate dehydrogenase (NADP+-ICDH) catalyzes oxidative decarboxylation of isocitric acid to form α-ketoglutaric acid with NADP+ as a cofactor. We constructed an NADP+-ICDH gene (icdA)-overexpressing strain (OPI-1) using Aspergillus niger WU-2223L as a host and examined the effects of increase in NADP+-ICDH activity on citric acid production. Under citric acid-producing conditions with glucose as the carbon source, the amounts of citric acid produced and glucose consumed by OPI-1 for the 12-d cultivation period decreased by 18.7 and 10.5%, respectively, compared with those by WU-2223L. These results indicate that the amount of citric acid produced by A. niger can be altered with the NADP+-ICDH activity. Therefore, NADP+-ICDH is an important regulator of citric acid production in the TCA cycle of A. niger. Thus, we propose that the icdA gene is a potentially valuable tool for modulating citric acid production by metabolic engineering.
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Affiliation(s)
- Keiichi Kobayashi
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Shinjuku-ku, Japan
| | - Takasumi Hattori
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Shinjuku-ku, Japan
| | - Rie Hayashi
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Shinjuku-ku, Japan
| | - Kohtaro Kirimura
- Faculty of Science and Engineering, Department of Applied Chemistry, Waseda University, Shinjuku-ku, Japan
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Increases in Gene-Targeting Frequencies Due to Disruption ofkueAas aku80Homolog in Citric Acid-ProducingAspergillus niger. Biosci Biotechnol Biochem 2014; 75:1594-6. [DOI: 10.1271/bbb.110015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gene Identification and Functional Analysis of Methylcitrate Synthase in Citric Acid-ProducingAspergillus nigerWU-2223L. Biosci Biotechnol Biochem 2014; 77:1492-8. [DOI: 10.1271/bbb.130139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kobayashi K, Hattori T, Honda Y, Kirimura K. Oxalic acid production by citric acid-producing Aspergillus niger overexpressing the oxaloacetate hydrolase gene oahA. J Ind Microbiol Biotechnol 2014; 41:749-56. [PMID: 24615146 DOI: 10.1007/s10295-014-1419-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/11/2014] [Indexed: 12/01/2022]
Abstract
The filamentous fungus Aspergillus niger is used worldwide in the industrial production of citric acid. However, under specific cultivation conditions, citric acid-producing strains of A. niger accumulate oxalic acid as a by-product. Oxalic acid is used as a chelator, detergent, or tanning agent. Here, we sought to develop oxalic acid hyperproducers using A. niger as a host. To generate oxalic acid hyperproducers by metabolic engineering, transformants overexpressing the oahA gene, encoding oxaloacetate hydrolase (OAH; EC 3.7.1.1), were constructed in citric acid-producing A. niger WU-2223L as a host. The oxalic acid production capacity of this strain was examined by cultivation of EOAH-1 under conditions appropriate for oxalic acid production with 30 g/l glucose as a carbon source. Under all the cultivation conditions tested, the amount of oxalic acid produced by EOAH-1, a representative oahA-overexpressing transformant, exceeded that produced by A. niger WU-2223L. A. niger WU-2223L and EOAH-1 produced 15.6 and 28.9 g/l oxalic acid, respectively, during the 12-day cultivation period. The yield of oxalic acid for EOAH-1 was 64.2 % of the maximum theoretical yield. Our method for oxalic acid production gave the highest yield of any study reported to date. Therefore, we succeeded in generating oxalic acid hyperproducers by overexpressing a single gene, i.e., oahA, in citric acid-producing A. niger as a host.
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Affiliation(s)
- Keiichi Kobayashi
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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Mallo N, Lamas J, Leiro JM. Evidence of an alternative oxidase pathway for mitochondrial respiration in the scuticociliate Philasterides dicentrarchi. Protist 2013; 164:824-36. [PMID: 24211656 DOI: 10.1016/j.protis.2013.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 11/17/2022]
Abstract
The presence of an alternative oxidase (AOX) in the mitochondria of the scuticociliate P. dicentrarchi was investigated. The mitochondrial oxygen consumption was measured in the presence of KCN, an inhibitor of cytochrome pathway (CP) respiration and salicylhydroxamic acid (SHAM), a specific inhibitor of alternative pathway (AP) respiration. AOX expression was monitored by western blotting with an AOX polyclonal antibody. The results showed that P. dicentrarchi possesses a branched mitochondrial electron transport chain with both cyanide-sensitive and -insensitive oxygen consumption. Mitochondrial respiration was partially inhibited by cyanide and completely inhibited by the combination of cyanide and SHAM, which is direct evidence for the existence of an AP in this ciliate. SHAM significantly inhibited in vitro growth of trophozoites both under normoxic and hypoxic conditions. AOX is a 42kD monomeric protein inducible by hypoxic conditions in experimental infections and by CP inhibitors such as cyanide and antimycin A, or by AP inhibitors such as SHAM. CP respiration was greatly stimulated during the exponential growth phase, while AP respiration increased during the stationary phase, in which AOX expression is induced. As the host does not possess AOX, and because during infection P. dicentrarchi respires via AP, it may be possible to develop inhibitors targeting the AP as a novel anti-scuticociliate therapy.
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Affiliation(s)
- Natalia Mallo
- Laboratorio de Parasitología, Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentarios, c/ Constantino Candeira s/n, 15782, Universidad de Santiago de Compostela; Santiago de Compostela (La Coruña, Spain)
| | - Jesús Lamas
- Departamento de Biología Celular y Ecología; Universidad de Santiago de Compostela; Santiago de Compostela, (La Coruña, Spain)
| | - José Manuel Leiro
- Laboratorio de Parasitología, Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentarios, c/ Constantino Candeira s/n, 15782, Universidad de Santiago de Compostela; Santiago de Compostela (La Coruña, Spain).
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Barbu EM, Shirazi F, McGrath DM, Albert N, Sidman RL, Pasqualini R, Arap W, Kontoyiannis DP. An antimicrobial peptidomimetic induces Mucorales cell death through mitochondria-mediated apoptosis. PLoS One 2013; 8:e76981. [PMID: 24098573 PMCID: PMC3789667 DOI: 10.1371/journal.pone.0076981] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
The incidence of mucormycosis has dramatically increased in immunocompromised patients. Moreover, the array of cellular targets whose inhibition results in fungal cell death is rather limited. Mitochondria have been mechanistically identified as central regulators of detoxification and virulence in fungi. Our group has previously designed and developed a proteolytically-resistant peptidomimetic motif D(KLAKLAK)2 with pleiotropic action ranging from targeted (i.e., ligand-directed) activity against cancer and obesity to non-targeted activity against antibiotic resistant gram-negative rods. Here we evaluated whether this non-targeted peptidomimetic motif is active against Mucorales. We show that D(KLAKLAK)2 has marked fungicidal action, inhibits germination, and reduces hyphal viability. We have also observed cellular changes characteristic of apoptosis in D(KLAKLAK)2-treated Mucorales cells. Moreover, the fungicidal activity was directly correlated with vacuolar injury, mitochondrial swelling and mitochondrial membrane depolarization, intracellular reactive oxygen species accumulation (ROS), and increased caspase-like enzymatic activity. Finally, these apoptotic features were prevented by the addition of the ROS scavenger N-acetyl-cysteine indicating mechanistic pathway specificity. Together, these findings indicate that D(KLAKLAK)2 makes Mucorales exquisitely susceptible via mitochondrial injury-induced apoptosis. This prototype may serve as a candidate drug for the development of translational applications against mucormycosis and perhaps other fungal infections.
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Affiliation(s)
- E. Magda Barbu
- David H. Koch Center, Department of Genitourinary Medical Oncology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Department of Infectious Diseases, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Fazal Shirazi
- Department of Infectious Diseases, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Danielle M. McGrath
- David H. Koch Center, Department of Genitourinary Medical Oncology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Nathaniel Albert
- Department of Infectious Diseases, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Richard L. Sidman
- Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Renata Pasqualini
- David H. Koch Center, Department of Genitourinary Medical Oncology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (DPK); (WA); (RP)
| | - Wadih Arap
- David H. Koch Center, Department of Genitourinary Medical Oncology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (DPK); (WA); (RP)
| | - Dimitrios P. Kontoyiannis
- Department of Infectious Diseases, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (DPK); (WA); (RP)
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Blumhoff ML, Steiger MG, Mattanovich D, Sauer M. Targeting enzymes to the right compartment: Metabolic engineering for itaconic acid production by Aspergillus niger. Metab Eng 2013; 19:26-32. [DOI: 10.1016/j.ymben.2013.05.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/10/2013] [Accepted: 05/22/2013] [Indexed: 11/27/2022]
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Honda Y, Kirimura K. Generation of circularly permuted fluorescent-protein-based indicators for in vitro and in vivo detection of citrate. PLoS One 2013; 8:e64597. [PMID: 23717638 PMCID: PMC3661591 DOI: 10.1371/journal.pone.0064597] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/15/2013] [Indexed: 11/30/2022] Open
Abstract
Indicators for citrate, particularly those applicable to its in vivo detection and quantitation, have attracted much interest in both biochemical studies and industrial applications since citrate is a key metabolic intermediate playing important roles in living cells. We generated novel fluorescence indicators for citrate by fusing the circularly permuted fluorescent protein (cpFP) and the periplasmic domain of the bacterial histidine kinase CitA, which can bind to citrate with high specificity. The ratiometric fluorescent signal change was observed with one of these cpFP-based indicators, named CF98: upon addition of citrate, the excitation peak at 504 nm increased proportionally to the decrease in the peak at 413 nm, suitable for build-in quantitative estimation of the binding compound. We confirmed that CF98 can be used for detecting citrate in vitro at millimolar levels in the range of 0.1 to 50 mM with high selectivity; even in the presence of other organic acids such as isocitrate and malate, the fluorescence intensity of CF98 remains unaffected. We finally demonstrated the in vivo applicability of CF98 to estimation of the intracellular citrate concentration in Escherichia coli co-expressing the genes encoding CF98 and the citrate carrier CitT. The novel indicator CF98 can be a specific and simple detection tool for citrate in vitro and a non-invasive tool for real-time estimation of intracellular concentrations of the compound in vivo.
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Affiliation(s)
- Yuki Honda
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- * E-mail:
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18
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Honda Y, Hattori T, Kirimura K. Visual expression analysis of the responses of the alternative oxidase gene (aox1) to heat shock, oxidative, and osmotic stresses in conidia of citric acid-producing Aspergillus niger. J Biosci Bioeng 2012; 113:338-42. [DOI: 10.1016/j.jbiosc.2011.10.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/28/2011] [Accepted: 10/31/2011] [Indexed: 11/16/2022]
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McDonald AE. Alternative oxidase: what information can protein sequence comparisons give us? PHYSIOLOGIA PLANTARUM 2009; 137:328-341. [PMID: 19493309 DOI: 10.1111/j.1399-3054.2009.01242.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The finding that alternative oxidase (AOX) is present in most kingdoms of life has resulted in a large number of AOX sequences that are available for analyses. Multiple sequence alignments of AOX proteins from evolutionarily divergent organisms represent a valuable tool and can be used to identify amino acids and domains that may play a role in catalysis, membrane association and post-translational regulation, especially when these data are coupled with the structural model for the enzyme. I validate the use of this approach by demonstrating that it detects the conserved glutamate and histidine residues in AOX that initially led to its identification as a di-iron carboxylate protein and the generation of a structural model for the protein. A comparative analysis using a larger dataset identified 35 additional amino acids that are conserved in all AOXs examined, 30 of which have not been investigated to date. I hypothesize that these residues will be involved in the quinol terminal oxidase activity or membrane association of AOX. Major differences in AOX protein sequences between kingdoms are revealed, and it is hypothesized that two angiosperm-specific domains may be responsible for the non-covalent dimerization of AOX, whereas two indels in the aplastidic AOXs may play a role in their post-translational regulation. A scheme for predicting whether a particular AOX protein will be recognized by the alternative oxidase monoclonal antibody generated against the AOX of Sauromatum guttatum (Voodoo lily) is presented. The number of functional sites in AOX is greater than expected, and determining the structure of AOX will prove extremely valuable to future research.
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Affiliation(s)
- Allison E McDonald
- Department of Biology, The University of Western Ontario, 1151 Richmond St. N., London, Ontario N6A5B7, Canada.
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20
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Vrabl P, Mutschlechner W, Burgstaller W. Dynamics of energy charge and adenine nucleotides during uncoupling of catabolism and anabolism in Penicillium ochrochloron. ACTA ACUST UNITED AC 2009; 113:1422-32. [PMID: 19818403 DOI: 10.1016/j.mycres.2009.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Filamentous fungi are able to spill energy when exposed to energy excess by uncoupling catabolism from anabolism, e.g. via overflow metabolism. In current study we tested the hypothesis that overflow metabolism is regulated via the energetic status of the hyphae (i.e. energy charge, ATP concentration). This hypothesis was studied in Penicillium ochrochloron during the steady state of glucose- or ammonium-limited chemostat cultures as well as during three transient states ((i) glucose pulse to a glucose-limited chemostat, (ii) shift from glucose-limited to ammonium-limited conditions in a chemostat, and (iii) ammonium exhaustion in batch culture). Organic acids were excreted under all conditions, even during exponential growth in batch culture as well as under glucose-limited conditions in a chemostat. Partial uncoupling of catabolism and anabolism via overflow metabolism was thus constitutively present. Under all tested conditions, overflow metabolism was independent of the energy charge or the ATP concentration of the hyphae. There was a reciprocal correlation between glucose uptake rate and intracellular adenine nucleotide content. During all transients states a rapid decrease in energy charge and the concentrations of nucleotides was observed shortly after a change in glycolytic flux ("ATP paradoxon"). A possible connection between the change in adenine nucleotide concentrations and the purine salvage pathway is discussed.
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Affiliation(s)
- Pamela Vrabl
- University of Innsbruck, Institute of Microbiology, Technikerstrasse 25, 6020 Innsbruck, Austria.
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21
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Hattori T, Kino K, Kirimura K. Regulation of Alternative Oxidase at the Transcription Stage in Aspergillus niger Under the Conditions of Citric Acid Production. Curr Microbiol 2009; 58:321-5. [DOI: 10.1007/s00284-009-9369-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 01/09/2009] [Accepted: 01/09/2009] [Indexed: 10/21/2022]
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22
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McDonald AE. Alternative oxidase: an inter-kingdom perspective on the function and regulation of this broadly distributed 'cyanide-resistant' terminal oxidase. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:535-552. [PMID: 32688810 DOI: 10.1071/fp08025] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Accepted: 07/11/2008] [Indexed: 06/11/2023]
Abstract
Alternative oxidase (AOX) is a terminal quinol oxidase located in the respiratory electron transport chain that catalyses the oxidation of quinol and the reduction of oxygen to water. However, unlike the cytochrome c oxidase respiratory pathway, the AOX pathway moves fewer protons across the inner mitochondrial membrane to generate a proton motive force that can be used to synthesise ATP. The energy passed to AOX is dissipated as heat. This appears to be very wasteful from an energetic perspective and it is likely that AOX fulfils some physiological function(s) that makes up for its apparent energetic shortcomings. An examination of the known taxonomic distribution of AOX and the specific organisms in which AOX has been studied has been used to explore themes pertaining to AOX function and regulation. A comparative approach was used to examine AOX function as it relates to the biochemical function of the enzyme as a quinol oxidase and associated topics, such as enzyme structure, catalysis and transcriptional expression and post-translational regulation. Hypotheses that have been put forward about the physiological function(s) of AOX were explored in light of some recent discoveries made with regard to species that contain AOX. Fruitful areas of research for the AOX community in the future have been highlighted.
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Affiliation(s)
- Allison E McDonald
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building, London, Ontario N6A 5B7, Canada. Email
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Sun J, Lu X, Rinas U, Zeng AP. Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol 2008; 8:R182. [PMID: 17784953 PMCID: PMC2375020 DOI: 10.1186/gb-2007-8-9-r182] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 07/13/2007] [Accepted: 09/04/2007] [Indexed: 11/10/2022] Open
Abstract
A genome-scale metabolic network and an in-depth genomic comparison of Aspergillus niger with seven other fungi is presented, revealing more than 1,100 enzyme-coding genes that are unique to A. niger. Background Aspergillus niger is an important industrial microorganism for the production of both metabolites, such as citric acid, and proteins, such as fungal enzymes or heterologous proteins. Despite its extensive industrial applications, the genetic inventory of this fungus is only partially understood. The recently released genome sequence opens a new horizon for both scientific studies and biotechnological applications. Results Here, we present the first genome-scale metabolic network for A. niger and an in-depth genomic comparison of this species to seven other fungi to disclose its metabolic peculiarities. The raw genomic sequences of A. niger ATCC 9029 were first annotated. The reconstructed metabolic network is based on the annotation of two A. niger genomes, CBS 513.88 and ATCC 9029, including enzymes with 988 unique EC numbers, 2,443 reactions and 2,349 metabolites. More than 1,100 enzyme-coding genes are unique to A. niger in comparison to the other seven fungi. For example, we identified additional copies of genes such as those encoding alternative mitochondrial oxidoreductase and citrate synthase in A. niger, which might contribute to the high citric acid production efficiency of this species. Moreover, nine genes were identified as encoding enzymes with EC numbers exclusively found in A. niger, mostly involved in the biosynthesis of complex secondary metabolites and degradation of aromatic compounds. Conclusion The genome-level reconstruction of the metabolic network and genome-based metabolic comparison disclose peculiarities of A. niger highly relevant to its biotechnological applications and should contribute to future rational metabolic design and systems biology studies of this black mold and related species.
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Affiliation(s)
- Jibin Sun
- Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany
| | - Xin Lu
- Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany
| | - An Ping Zeng
- Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering, Denickestr., 21071 Hamburg, Germany
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Hattori T, Honda Y, Kino K, Kirimura K. Expression of alternative oxidase gene (aox1) at the stage of single-cell conidium in citric acid-producing Aspergillus niger. J Biosci Bioeng 2008; 105:55-7. [PMID: 18295720 DOI: 10.1263/jbb.105.55] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 10/03/2007] [Indexed: 11/17/2022]
Abstract
Mycelia of citric acid-producing Aspergillus niger WU-2223L show cyanide-insensitive respiration catalyzed by alternative oxidase. In this study, the constitutive expression of alternative oxidase gene (aox1) even at the stage of single-cell conidium in A. niger WU-2223L was found using the visual expression analysis system of aox1 with green fluorescent protein under microscopy observation.
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Affiliation(s)
- Takasumi Hattori
- Department of Applied Chemistry, School of Science and Engineering, Waseda University, Tokyo, Japan
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Andersen MR, Nielsen ML, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008; 4:178. [PMID: 18364712 PMCID: PMC2290933 DOI: 10.1038/msb.2008.12] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 01/28/2008] [Indexed: 11/09/2022] Open
Abstract
The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the reportings of 371 articles and comprises 1190 biochemically unique reactions and 871 ORFs. Inclusion of isoenzymes increases the total number of reactions to 2240. A graphical map of the metabolic network is presented. All levels of the reconstruction process were based on manual curation. From the reconstructed metabolic network, a mathematical model was constructed and validated with data on yields, fluxes and transcription. The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform.
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Affiliation(s)
- Mikael Rørdam Andersen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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Production of oxalic acid by overexpression of oxaloacetate hydrolase gene (oahA) in Aspergillus niger WU-2223L. J Biotechnol 2007. [DOI: 10.1016/j.jbiotec.2007.07.910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Zhang Q, Bai G, Cheng J, Yu Y, Tian W, Yang W. Use of an enhanced green fluorescence protein linked to a single chain fragment variable antibody to localize Bursaphelenchus xylophilus cellulase. Biosci Biotechnol Biochem 2007; 71:1514-20. [PMID: 17587683 DOI: 10.1271/bbb.70022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The pine wilt disease caused by Bursaphelenchus xylophilus (BX), also known as pine wood nematode (PWN), is the most devastating disease of pine trees. In this study, we engineered a highly specific antibody (single-chain fragment variable, scFv) against B. xylophilus cellulase antigen (BXCa). The antibody was raised against highly antigenic cellulase purified from PWN that efficiently hydrolyzed carboxymethyl cellulose. Total RNA was extracted from fresh spleens from BALB/c mice immunized with BXCa, and V(H) and V(L) were assembled with a linker following reverse transcriptase-polymerase chain reaction. The final phage display antibody library had a repertoire of about 5 x 10(4). We obtained specific engineered antibodies against BXCa after five rounds of affinity selection. The positive phage clones were used to infect Escherichia coli HB2151, and enzyme-linked immunosorbent assay and dot blotting showed that the soluble scFv specifically binded to BXCa. The scFv was sequenced and expressed in E. coli BL21 fused to enhanced green fluorescence protein, which had both green fluorescence and anti-BXCa functions. Using the fusion protein, we located cellulase in live PWN using an inverted fluorescence microscope and a laser scanning confocal microscope. The results strongly suggested that the cellulase was synthesized in the esophageal gland cells. This novel method of detecting and localizing proteins in live PWN might further our understanding of the underlying pathology of pine wilt disease.
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Affiliation(s)
- Qi Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, China
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