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Abstract
Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. From 54 SP families described in MEROPS Peptidase Database, 21 are present in fungi. Interestingly, 14 of them are also present in Metazoa and Viridiplantae - this suggests that, except one (S64), all fungal SP families evolved before plants and fungi diverged. Most representatives of sequenced eukaryotic lineages encode a set of 13-16 SP families. The number of SPs from each family varies among the analysed taxa. The most abundant are S8 proteases. In order to verify hypotheses linking lifestyle and expansions of particular SP, we performed statistical analyses and revealed previously undescribed associations. Here, we present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.
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102
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Niu X, Zhou JS, Wang YX, Liu CC, Liu ZH, Yuan S. Heterologous Expression and Characterization of a Novel Chitinase (ChiEn1) from Coprinopsis cinerea and its Synergism in the Degradation of Chitin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6943-6956. [PMID: 28721730 DOI: 10.1021/acs.jafc.7b02278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chitinase ChiEn1 did not hydrolyze insoluble chitin but showed hydrolysis and transglycosylation activities toward chitin-oligosaccharides. Interestingly, the addition of ChiEn1 increased the amount of reducing sugars released from chitin powder by endochitinase ChiIII by 105.0%, and among the released reducing sugars the amount of (GlcNAc)2 was increased by 149.5%, whereas the amount of GlcNAc was decreased by 10.3%. The percentage of GlcNAc in the products of chitin powder with the combined ChiIII and ChiEn1 was close to that in the products of chitin-oligosaccharides with ChiEn1, rather than that with ChiIII. These results indicate that chitin polymers are first degraded into chitin oligosaccharides by ChiIII and the latter are further degraded to monomers and dimers by ChiEn1, and the synergistic action of ChiEn1 and ChiIII is involved in the efficient degradation of chitin in cell walls during pileus autolysis. The structure modeling explores the molecular base of ChiEn1 action.
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Affiliation(s)
- Xin Niu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
| | - Jiang-Sheng Zhou
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
| | - Yan-Xin Wang
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
| | - Cui-Cui Liu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
| | - Zhong-Hua Liu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
| | - Sheng Yuan
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University , Nanjing, PR China 210023
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103
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Cheng XX, Zhao LH, Klosterman SJ, Feng HJ, Feng ZL, Wei F, Shi YQ, Li ZF, Zhu HQ. The endochitinase VDECH from Verticillium dahliae inhibits spore germination and activates plant defense responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:12-23. [PMID: 28483050 DOI: 10.1016/j.plantsci.2017.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/01/2017] [Accepted: 03/06/2017] [Indexed: 05/06/2023]
Abstract
Chitinases function in the digestion of chitin molecules, which are present principally in insects and fungi. In plants, chitinase genes play important roles in defense, and their expression can be triggered in response to both biotic and abiotic stresses. In this study, we cloned and characterized an endochitinase (VDECH) from Verticillium dahliae, strain Vd080. The VDECH coding region consists of 1845bp with two exons and one 54bp intron, encoding a 615 amino acid protein with the predicted molecular weight (MW) of 63.9kDa. The VDECH cDNA without signal peptide-encoding region was introduced into pCold-TF vector and the recombinant protein HIS-VDECH with a predicted MW of ∼114kDa was expressed. HIS-VDECH showed high tolerance to extreme temperature, exhibiting efficient chitinolytic activity at 50°C. In addition, VDECH triggered typical plant defense responses, including a hypersensitive response, oxidative burst, and elicited increased expression of defense-related genes in both Arabidopsis and cotton. VDECH-treatment of the conidial spores of V. dahliae and Fusarium oxysporum resulted in marked reductions in the germination of these spores in both fungi. After 36h of incubation with VDECH, the inhibition rate of germination was recorded at 99.57% for V. dahliae, and 96.89% for F. oxysporum. These results provide evidence that VDECH is recognized by the plant to elicit defense responses, and also that VDECH is an effective inhibitor of conidia germination, both of which may be exploited for disease control.
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Affiliation(s)
- Xiao-Xiao Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Li-Hong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | | | - Hong-Jie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Zi-Li Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yong-Qiang Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Zhi-Fang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - He-Qin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
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104
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Applying Unconventional Secretion in Ustilago maydis for the Export of Functional Nanobodies. Int J Mol Sci 2017; 18:ijms18050937. [PMID: 28468279 PMCID: PMC5454850 DOI: 10.3390/ijms18050937] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022] Open
Abstract
Exploiting secretory pathways for production of heterologous proteins is highly advantageous with respect to efficient downstream processing. In eukaryotic systems the vast majority of heterologous proteins for biotechnological application is exported via the canonical endoplasmic reticulum–Golgi pathway. In the endomembrane system target proteins are often glycosylated and may thus be modified with foreign glycan patterns. This can be destructive for their activity or cause immune reactions against therapeutic proteins. Hence, using unconventional secretion for protein expression is an attractive alternative. In the fungal model Ustilago maydis, chitinase Cts1 is secreted via an unconventional pathway connected to cell separation which can be used to co-export heterologous proteins. Here, we apply this mechanism for the production of nanobodies. First, we achieved expression and unconventional secretion of a functional nanobody directed against green fluorescent protein (Gfp). Second, we found that Cts1 binds to chitin and that this feature can be applied to generate a Gfp-trap. Thus, we demonstrated the dual use of Cts1 serving both as export vehicle and as purification tag. Finally, we established and optimized the production of a nanobody against botulinum toxin A and hence describe the first pharmaceutically relevant target exported by Cts1-mediated unconventional secretion.
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105
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Kelliher CM, Haase SB. Connecting virulence pathways to cell-cycle progression in the fungal pathogen Cryptococcus neoformans. Curr Genet 2017; 63:803-811. [PMID: 28265742 PMCID: PMC5605583 DOI: 10.1007/s00294-017-0688-5] [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: 02/16/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 11/01/2022]
Abstract
Proliferation and host evasion are critical processes to understand at a basic biological level for improving infectious disease treatment options. The human fungal pathogen Cryptococcus neoformans causes fungal meningitis in immunocompromised individuals by proliferating in cerebrospinal fluid. Current antifungal drugs target "virulence factors" for disease, such as components of the cell wall and polysaccharide capsule in C. neoformans. However, mechanistic links between virulence pathways and the cell cycle are not as well studied. Recently, cell-cycle synchronized C. neoformans cells were profiled over time to identify gene expression dynamics (Kelliher et al., PLoS Genet 12(12):e1006453, 2016). Almost 20% of all genes in the C. neoformans genome were periodically activated during the cell cycle in rich media, including 40 genes that have previously been implicated in virulence pathways. Here, we review important findings about cell-cycle-regulated genes in C. neoformans and provide two examples of virulence pathways-chitin synthesis and G-protein coupled receptor signaling-with their putative connections to cell division. We propose that a "comparative functional genomics" approach, leveraging gene expression timing during the cell cycle, orthology to genes in other fungal species, and previous experimental findings, can lead to mechanistic hypotheses connecting the cell cycle to fungal virulence.
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Affiliation(s)
- Christina M Kelliher
- Department of Biology, Duke University, Box 90338, 130 Science Drive, Durham, NC, 27708-0338, USA
| | - Steven B Haase
- Department of Biology, Duke University, Box 90338, 130 Science Drive, Durham, NC, 27708-0338, USA.
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106
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Cheba BA, Zaghloul TI, EL-Massry MH, EL-Mahdy AR. Kinetics Properties of Marine Chitinase from Novel Red Sea Strain of Bacillus. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.proeng.2017.02.383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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107
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Thatcher LF, Williams AH, Garg G, Buck SAG, Singh KB. Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors. BMC Genomics 2016; 17:860. [PMID: 27809762 PMCID: PMC5094085 DOI: 10.1186/s12864-016-3192-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume Medicago truncatula and a pathogenic F. oxysporum forma specialis (f. sp.) medicaginis (Fom). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession. RESULTS High coverage RNA-Seq of Fom infected root samples harvested from susceptible (DZA315) or resistant (A17) M. truncatula seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of in planta differentially expressed genes. This included enrichment, particularly in DZA315 in planta up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high in-planta induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other F. oxysporum ff. spp. as well as other Fusaria (F. solani, F. fujikori, F. verticilloides, F. graminearum and F. pseudograminearum), and from another wilt pathogen of the same class, a Verticillium species. Overall, this suggests these novel effector candidates may play important roles in Fusaria and wilt pathogen virulence. CONCLUSION Combining high coverage in planta RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible M. truncatula host. The knowledge from this first in depth in planta transcriptome sequencing of any F. oxysporum ff. spp. pathogenic on legumes will facilitate the dissection of Fusarium wilt pathogenicity mechanisms on many important legume crops.
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Affiliation(s)
- Louise F. Thatcher
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Angela H. Williams
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Sally-Anne G. Buck
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
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108
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Bösch K, Frantzeskakis L, Vraneš M, Kämper J, Schipper K, Göhre V. Genetic Manipulation of the Plant Pathogen Ustilago maydis to Study Fungal Biology and Plant Microbe Interactions. J Vis Exp 2016. [PMID: 27768088 DOI: 10.3791/54522] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene deletion plays an important role in the analysis of gene function. One of the most efficient methods to disrupt genes in a targeted manner is the replacement of the entire gene with a selectable marker via homologous recombination. During homologous recombination, exchange of DNA takes place between sequences with high similarity. Therefore, linear genomic sequences flanking a target gene can be used to specifically direct a selectable marker to the desired integration site. Blunt ends of the deletion construct activate the cell's DNA repair systems and thereby promote integration of the construct either via homologous recombination or by non-homologous-end-joining. In organisms with efficient homologous recombination, the rate of successful gene deletion can reach more than 50% making this strategy a valuable gene disruption system. The smut fungus Ustilago maydis is a eukaryotic model microorganism showing such efficient homologous recombination. Out of its about 6,900 genes, many have been functionally characterized with the help of deletion mutants, and repeated failure of gene replacement attempts points at essential function of the gene. Subsequent characterization of the gene function by tagging with fluorescent markers or mutations of predicted domains also relies on DNA exchange via homologous recombination. Here, we present the U. maydis strain generation strategy in detail using the simplest example, the gene deletion.
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Affiliation(s)
- Kristin Bösch
- Institute for Microbiology, Heinrich-Heine University Düsseldorf; Bioeconomy Science Center (BioSC)
| | | | - Miroslav Vraneš
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich-Heine University Düsseldorf; Bioeconomy Science Center (BioSC)
| | - Vera Göhre
- Institute for Microbiology, Heinrich-Heine University Düsseldorf; Bioeconomy Science Center (BioSC); Cluster of Excellence in Plant Sciences (CEPLAS), Heinrich-Heine University Düsseldorf;
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109
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McCotter SW, Horianopoulos LC, Kronstad JW. Regulation of the fungal secretome. Curr Genet 2016; 62:533-45. [DOI: 10.1007/s00294-016-0578-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 02/07/2023]
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110
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Stock J, Terfrüchte M, Schipper K. A Reporter System to Study Unconventional Secretion of Proteins Avoiding N-Glycosylation in Ustilago maydis. Methods Mol Biol 2016; 1459:149-60. [PMID: 27665557 DOI: 10.1007/978-1-4939-3804-9_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Unconventional secretion of proteins in eukaryotes is characterized by the circumvention of the Endoplasmic Reticulum (ER). As a consequence proteins exported by unconventional pathways lack N-glycosylation, a post-transcriptional modification that is initiated in the ER during classical secretion. We are exploiting the well-established enzyme β-glucuronidase (GUS) to assay unconventional protein secretion (UPS). This bacterial protein is perfectly suited for this purpose because it carries a eukaryotic N-glycosylation motif. Modification of this residue by attachment of sugar moieties during the passage of the ER apparently causes a very strong reduction in GUS activity. Hence, this enzyme can only be secreted in an active state, if the export mechanism does not involve ER passage. Here, we describe a reporter system applied in the corn smut fungus Ustilago maydis that is based on this observation and can be used to test if candidate proteins are secreted to the culture supernatant via alternative pathways avoiding N-glycosylation. Importantly, this system is the basis for the establishment of genetic screens providing mechanistic insights into unknown UPS pathways in the future.
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Affiliation(s)
- Janpeter Stock
- Heinrich Heine University Düsseldorf, Institute for Microbiology, Bldg. 26.12.01, 40204, Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Marius Terfrüchte
- Heinrich Heine University Düsseldorf, Institute for Microbiology, Bldg. 26.12.01, 40204, Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Kerstin Schipper
- Heinrich Heine University Düsseldorf, Institute for Microbiology, Bldg. 26.12.01, 40204, Düsseldorf, Germany.
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425, Jülich, Germany.
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