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Quan ND, Nguyen NL, Giang TTH, Ngan NTT, Hien NT, Tung NV, Trang NHT, Lien NTK, Nguyen HH. Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don. J Fungi (Basel) 2024; 10:352. [PMID: 38786707 PMCID: PMC11122143 DOI: 10.3390/jof10050352] [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: 03/07/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls.
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Affiliation(s)
- Nguyen Duc Quan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
| | - Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Tran Thi Huong Giang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
| | - Nguyen Thi Thanh Ngan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Thanh Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Hoang Thanh Trang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
| | - Nguyen Thi Kim Lien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Huy Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam; (N.D.Q.); (N.-L.N.); (T.T.H.G.); (N.T.T.N.); (N.T.H.); (N.V.T.); (N.H.T.T.); (N.T.K.L.)
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
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Hassan S, Syun-Ichi U, Shabeer S, Kiran TA, Wu CF, Moriyama H, Coutts RHA, Kotta Loizou I, Jamal A. Molecular and biological characterization of a novel partitivirus from Talaromyces pinophilus. Virus Res 2024; 343:199351. [PMID: 38453057 PMCID: PMC10982079 DOI: 10.1016/j.virusres.2024.199351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/13/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Talaromyces spp. have a worldwide distribution, are ecologically diverse and have been isolated from numerous different substrates. Talaromyces spp. are considered biotechnologically important due to their ability to produce a range of enzymes and pigments. Talaromyces pinophilus, belonging to genus Talaromyces and family Trichocomaceae, is known for producing several important bioactive metabolites. Here we report the isolation and characterisation of a partitivirus from T. pinophilus which we have nominated Talaromyces pinophilus partitivirus-1 (TpPV-1). TpPV-1 possesses a genome consisting of three double stranded (ds) RNA segments i.e., dsRNAs1-3, 1824 bp, 1638 bp and 1451 bp respectively, which are encapsidated in icosahedral particles 35 nm in diameter. Both dsRNA1 and dsRNA2 contain a single open reading frame (ORF) encoding respectively a 572 amino acid (aa) protein of 65 kDa and a 504 aa protein of 50 kDa. The third segment (dsRNA3) is potentially a satellite RNA. Phylogenetic analysis revealed that the TpPV-1 belongs to the family Partitiviridae in the proposed genus Zetapartitivirus. TpPV-1 infection decreases the mycelial growth rate of the host fungus and alters pigmentation as indicated by time course experiments performed on a range of different solid media comparing virus-infected and virus-free isogenic lines. This is the first report of mycovirus infection in T. pinophilus and may provide insights into understanding the effect of the mycovirus on the production of enzymes and pigments by the host fungus.
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Affiliation(s)
- Sidra Hassan
- Department of Plant and Environmental Protection, PARC Institute of Advanced Studies in Agriculture (Affiliated with Quaid-i-Azam University), National Agricultural Research Centre, Islamabad 45500, Pakistan
| | - Urayama Syun-Ichi
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Saba Shabeer
- Department of Bioscience, COMSATS University, Islamabad 44000, Pakistan; Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Tahseen Ali Kiran
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Chien-Fu Wu
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture & Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture & Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical & Biological Science, School of Life and Medical Sciences, University of Hertfordshire, AL10 9AB, Hatfield, United Kingdom
| | - Ioly Kotta Loizou
- Department of Clinical, Pharmaceutical & Biological Science, School of Life and Medical Sciences, University of Hertfordshire, AL10 9AB, Hatfield, United Kingdom; Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, SW7 2AZ, London, United Kingdom.
| | - Atif Jamal
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan.
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Zhao S, Zhang T, Hasunuma T, Kondo A, Zhao XQ, Feng JX. Every road leads to Rome: diverse biosynthetic regulation of plant cell wall-degrading enzymes in filamentous fungi Penicillium oxalicum and Trichoderma reesei. Crit Rev Biotechnol 2023:1-21. [PMID: 38035670 DOI: 10.1080/07388551.2023.2280810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Cellulases and xylanases are plant cell wall-degrading enzymes (CWDEs) that are critical to sustainable bioproduction based on renewable lignocellulosic biomass to reduce carbon dioxide emission. Currently, these enzymes are mainly produced from filamentous fungi, especially Trichoderma reesei and Penicillium oxalicum. However, an in-depth comparison of these two producers has not been performed. Although both P. oxalicum and T. reesei harbor CWDE systems, they exhibit distinct features regulating the production of these enzymes, mainly through different transcriptional regulatory networks. This review presents the strikingly different modes of genome-wide regulation of cellulase and xylanase biosynthesis in P. oxalicum and T. reesei, including sugar transporters, signal transduction cascades, transcription factors, chromatin remodeling, and three-dimensional organization of chromosomes. In addition, different molecular breeding approaches employed, based on the understanding of the regulatory networks, are summarized. This review highlights the existence of very different regulatory modes leading to the efficient regulation of CWDE production in filamentous fungi, akin to the adage that "every road leads to Rome." An understanding of this divergence may help further improvements in fungal enzyme production through the metabolic engineering and synthetic biology of certain fungal species.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
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Hu X, Qian Y, Gao Z, Li G, Fu F, Guo J, Shan Y. Safety evaluation and whole genome sequencing for revealing the ability of Penicillium oxalicum WX-209 to safely and effectively degrade citrus segments. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Nguyen TTT, Lee HB. A New Species and Five New Records of Talaromyces ( Eurotiales, Aspergillaceae) Belonging to Section Talaromyces in Korea. MYCOBIOLOGY 2023; 51:320-332. [PMID: 37929009 PMCID: PMC10621255 DOI: 10.1080/12298093.2023.2265645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Talaromyces is a genus within the phylum Ascomycota (class Eurotiomycetes, order Eurotiales, family Trichocomaceae). Many species in this genus are known to produce diverse secondary metabolites with great potential for agricultural, medical, and pharmaceutical applications. During a survey on fungal diversity in the genus Talaromyces in Korea, six strains were isolated from soil, indoor air, and freshwater environments. Based on morphological, physiological, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses, we identified five previously unrecorded species in Korea (T. brevis, T. fusiformis, T. muroii, T. ruber, and T. soli) and a new species (T. echinulatus sp. nov.) belonging to section Talaromyces. Herein, detailed descriptions, illustrations, and phylogenetic tree are provided.
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Affiliation(s)
- Thuong T. T. Nguyen
- Environmental Microbiology Lab, Department of Agricultural Biological Chemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hyang Burm Lee
- Environmental Microbiology Lab, Department of Agricultural Biological Chemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
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Pasari N, Gupta M, Sinha T, Ogunmolu FE, Yazdani SS. Systematic identification of CAZymes and transcription factors in the hypercellulolytic fungus Penicillium funiculosum NCIM1228 involved in lignocellulosic biomass degradation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:150. [PMID: 37794424 PMCID: PMC10552389 DOI: 10.1186/s13068-023-02399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Penicillium funiculosum NCIM1228 is a filamentous fungus that was identified in our laboratory to have high cellulolytic activity. Analysis of its secretome suggested that it responds to different carbon substrates by secreting specific enzymes capable of digesting those substrates. This phenomenon indicated the presence of a regulatory system guiding the expression of these hydrolyzing enzymes. Since transcription factors (TFs) are the key players in regulating the expression of enzymes, this study aimed first to identify the complete repertoire of Carbohydrate Active Enzymes (CAZymes) and TFs coded in its genome. The regulation of CAZymes was then analysed by studying the expression pattern of these CAZymes and TFs in different carbon substrates-Avicel (cellulosic substrate), wheat bran (WB; hemicellulosic substrate), Avicel + wheat bran, pre-treated wheat straw (a potential substrate for lignocellulosic ethanol), and glucose (control). RESULTS The P. funiculosum NCIM1228 genome was sequenced, and 10,739 genes were identified in its genome. These genes included a total of 298 CAZymes and 451 TF coding genes. A distinct expression pattern of the CAZymes was observed in different carbon substrates tested. Core cellulose hydrolyzing enzymes were highly expressed in the presence of Avicel, while pre-treated wheat straw and Avicel + wheat bran induced a mixture of CAZymes because of their heterogeneous nature. Wheat bran mainly induced hemicellulases, and the least number of CAZymes were expressed in glucose. TFs also exhibited distinct expression patterns in each of the carbon substrates. Though most of these TFs have not been functionally characterized before, homologs of NosA, Fcr1, and ATF21, which have been known to be involved in fruiting body development, protein secretion and stress response, were identified. CONCLUSIONS Overall, the P. funiculosum NCIM1228 genome was sequenced, and the CAZymes and TFs present in its genome were annotated. The expression of the CAZymes and TFs in response to various polymeric sugars present in the lignocellulosic biomass was identified. This work thus provides a comprehensive mapping of transcription factors (TFs) involved in regulating the production of biomass hydrolyzing enzymes.
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Affiliation(s)
- Nandita Pasari
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mayank Gupta
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Tulika Sinha
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Funso Emmanuel Ogunmolu
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
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Cheng CY, Zhang MY, Niu YC, Zhang M, Geng YH, Deng H. Comparison of Fungal Genera Isolated from Cucumber Plants and Rhizosphere Soil by Using Various Cultural Media. J Fungi (Basel) 2023; 9:934. [PMID: 37755042 PMCID: PMC10532442 DOI: 10.3390/jof9090934] [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: 06/09/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All fungal strains were identified through sequence similarity of the ITS1-5.8s-ITS2 rDNA region. The potato dextrose agar (PDA) media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the four media for the isolation of all cucumber endophytic fungi. However, in the roots, the number of endophytic fungi isolated by MRBA was significantly higher than that isolated on malt extract agar (MEA), while in the stems, the number of fungi isolated with PDA was significantly higher than that isolated with Martin's rose bengal agar medium (MRBA). PDA had significantly higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were significantly more isolated by MEA than those of MRBA. It is suggested that PDA can be used as a basic medium, and different cultural media can be considered for specific fungal genera.
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Affiliation(s)
- Chong-Yang Cheng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Ming-Yuan Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Yong-Chun Niu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Meng Zhang
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Yue-Hua Geng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Hui Deng
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
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Leschonski KP, Kaasgaard SG, Spodsberg N, Krogh KBRM, Kabel MA. Two Subgroups within the GH43_36 α-l-Arabinofuranosidase Subfamily Hydrolyze Arabinosyl from Either Mono-or Disubstituted Xylosyl Units in Wheat Arabinoxylan. Int J Mol Sci 2022; 23:ijms232213790. [PMID: 36430284 PMCID: PMC9693073 DOI: 10.3390/ijms232213790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Fungal arabinofuranosidases (ABFs) catalyze the hydrolysis of arabinosyl substituents (Ara) and are key in the interplay with other glycosyl hydrolases to saccharify arabinoxylans (AXs). Most characterized ABFs belong to GH51 and GH62 and are known to hydrolyze the linkage of α-(1→2)-Ara and α-(1→3)-Ara in monosubstituted xylosyl residues (Xyl) (ABF-m2,3). Nevertheless, in AX a substantial number of Xyls have two Aras (i.e., disubstituted), which are unaffected by ABFs from GH51 and GH62. To date, only two fungal enzymes have been identified (in GH43_36) that specifically release the α-(1→3)-Ara from disubstituted Xyls (ABF-d3). In our research, phylogenetic analysis of available GH43_36 sequences revealed two major clades (GH43_36a and GH43_36b) with an expected substrate specificity difference. The characterized fungal ABF-d3 enzymes aligned with GH43_36a, including the GH43_36 from Humicola insolens (HiABF43_36a). Hereto, the first fungal GH43_36b (from Talaromyces pinophilus) was cloned, purified, and characterized (TpABF43_36b). Surprisingly, TpABF43_36b was found to be active as ABF-m2,3, albeit with a relatively low rate compared to other ABFs tested, and showed minor xylanase activity. Novel specificities were also discovered for the HiABF43_36a, as it also released α-(1→2)-Ara from a disubstitution on the non-reducing end of an arabinoxylooligosaccharide (AXOS), and it was active to a lesser extent as an ABF-m2,3 towards AXOS when the Ara was on the second xylosyl from the non-reducing end. In essence, this work adds new insights into the biorefinery of agricultural residues.
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Affiliation(s)
| | | | | | | | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Li CX, Liu L, Zhang T, Luo XM, Feng JX, Zhao S. Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum. Microbiol Spectr 2022; 10:e0212121. [PMID: 35499317 PMCID: PMC9241887 DOI: 10.1128/spectrum.02121-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
Higher-order spatial organization of the chromatin in the nucleus plays crucial roles in the maintenance of cell functions and the regulation of gene expression. Three-dimensional (3D) genome sequencing has been used to great effect in mammal and plants, but the availability of 3D genomes of filamentous fungi is severely limited. Here, we performed a chromosome-level genome assembly of Penicillium oxalicum through single-molecule real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C), with a scaffold N50 of 4.07 Mb and a contig N50 of 3.81 Mb, and further elucidated the 3D genome architecture of P. oxalicum. High-frequency interchromosomal contacts occurred within the centromeres and telomeres, as well as within individual chromosomes. There were 12,203 cis-interactions and 7,884 trans-interactions detected at a resolution of 1 kb. Moreover, a total of 1,099 topologically associated domains (or globules) were found, ranging in size from 2.0 to 76.0 kb. Interestingly, transcription factor-bound motifs were enriched in the globule boundaries. All the cellulase and xylanase genes were discretely distributed in the 3D model of the P. oxalicum genome as a result of few cis- and trans-interactions. Our results from this study provide a global view of chromatin interactions in the P. oxalicum genome and will act as a resource for studying spatial regulation of gene expression in filamentous fungi. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and the regulation of gene expression. The three-dimensional (3D) architectures of the genomes of many mammals and plants have been elucidated, but corresponding studies on filamentous fungi, which play vital roles as decomposers of organic matter in the soil, are very limited. Penicillium oxalicum is one of the predominant cellulolytic aerobic fungi in subtropical and tropical forest soils and can secrete integrative cellulase and xylanase under integrated regulatory control, degrading plant biomass highly efficiently. In the present study, we employed Hi-C technology to construct the 3D genome model of P. oxalicum strain HP7-1 and to further investigate cellulase and xylanase as well as transcription factor genes in 3D genome. These results provide a resource to achieve a deeper understanding of cell function and the regulation of gene expression in filamentous fungi.
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Affiliation(s)
- Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
- Anhui Key Laboratory of Infection and Immunity, Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Troiano D, Orsat V, Dumont MJ. Solid-state co-culture fermentation of simulated food waste with filamentous fungi for production of bio-pigments. Appl Microbiol Biotechnol 2022; 106:4029-4039. [PMID: 35608668 DOI: 10.1007/s00253-022-11984-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
The use of waste stream residues as feedstock for material production simultaneously helps reduce dependence on fossil-based resources and to shift toward a circular economy. This study explores the conversion of food waste into valuable chemicals, namely, bio-pigments. Here, a simulated food waste feedstock was converted into pigments via solid-state fermentation with the filamentous fungus Talaromyces albobiverticillius (NRRL 2120). Pigments including monascorubrin, rubropunctatin, and 7-(2-hydroxyethyl)-monascorubramine were identified as products of the fermentation via ultra-performance liquid chromatography coupled with quadrupole-time-of-flight electrospray ionization mass spectrometry. Pigments were obtained at concentrations of 32.5, 20.9, and 22.4 AU/gram dry substrate for pigments absorbing at 400, 475, and 500 nm, respectively. Pigment production was further enhanced by co-culturing T. albobiverticillius with Trichoderma reesei (NRRL 3652), and ultimately yielded 63.8, 35.6, and 43.6 AU/gds at the same respective wavelengths. This represents the highest reported production of pigments via solid-state fermentation of a non-supplemented waste stream feedstock. KEY POINTS: • Simulated food waste underwent solid-state fermentation via filamentous fungi. • Bio-pigments were obtained from fermentation of the simulated food waste. • Co-culturing multiple fungal species substantially improved pigment production.
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Affiliation(s)
- Derek Troiano
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| | - Valérie Orsat
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Marie-Josée Dumont
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.,Deptartment of Chemical Engineering, Université Laval, Québec, QC, G1V 0A6, Canada
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11
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Platinum Nanoparticles as Potent Anticancer and Antimicrobial Agent: Green Synthesis, Physical Characterization, and In-Vitro Biological Activity. J CLUST SCI 2022. [DOI: 10.1007/s10876-022-02225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Zhang T, Sun Y, Ma Z, Zhang J, Lv B, Li C. Developing iterative and quantified transgenic manipulations of non-conventional filamentous fungus Talaromyces pinophilus Li-93. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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13
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Fiorito F, Cerracchio C, Salvatore MM, Serra F, Pucciarelli A, Amoroso MG, Nicoletti R, Andolfi A. Antiviral Property of the Fungal Metabolite 3-O-Methylfunicone in Bovine Herpesvirus 1 Infection. Microorganisms 2022; 10:microorganisms10010188. [PMID: 35056637 PMCID: PMC8781729 DOI: 10.3390/microorganisms10010188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 02/05/2023] Open
Abstract
Bovine herpesvirus type-1 (BoHV-1) is a widespread pathogen that provokes infectious rhinotracheitis and polymicrobial infections in cattle, resulting in serious economic losses to the farm animal industry and trade restrictions. To date, non-toxic active drugs against BoHV-1 are not available. The exploitation of bioactive properties of microbial products is of great pharmaceutical interest. In fact, fungi are a promising source of novel drugs with a broad spectrum of activities and functions, including antiviral properties. Hence, the potential antiviral properties of 3-O-methylfunicone (OMF), a secondary metabolite produced by Talaromyces pinophilus, were evaluated on BoHV-1. In this study, during BoHV-1 infection in bovine cells (MDBK), the non-toxic concentration of 5 µM OMF considerably reduced signs of cell death and increased cell proliferation. Furthermore, OMF significantly decreased the virus titer as well as the cytopathic effect and strongly inhibited the expression of bICP0, the major regulatory protein in the BoHV-1 lytic cycle. These findings were accompanied by a considerable up-regulation in the expression of the aryl hydrocarbon receptor (AhR), a multifunctional transcription factor also linked to the host’s response to a herpesvirus infection. Overall, our results suggest that by involving AhR, OMF shows potential against a BoHV-1 infection.
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Affiliation(s)
- Filomena Fiorito
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Naples, Italy; (C.C.); (A.P.)
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Portici, Naples, Italy
- Correspondence: (F.F.); (M.G.A.); (A.A.); Tel.: +39-081-2539179 (A.A.)
| | - Claudia Cerracchio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Naples, Italy; (C.C.); (A.P.)
| | - Maria Michela Salvatore
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Naples, Italy;
- Institute for Sustainable Plant Protection, National Research Council, 80055 Portici, Naples, Italy
| | - Francesco Serra
- Istituto Zooprofilattico del Mezzogiorno, 80055 Portici, Naples, Italy;
| | - Alessia Pucciarelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Naples, Italy; (C.C.); (A.P.)
- Istituto Zooprofilattico del Mezzogiorno, 80055 Portici, Naples, Italy;
| | - Maria Grazia Amoroso
- Istituto Zooprofilattico del Mezzogiorno, 80055 Portici, Naples, Italy;
- Correspondence: (F.F.); (M.G.A.); (A.A.); Tel.: +39-081-2539179 (A.A.)
| | - Rosario Nicoletti
- Council for Agricultural Research and Economics, Research Centre for Olive, Fruit and Citrus Crops, 81100 Caserta, Caserta, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
| | - Anna Andolfi
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Portici, Naples, Italy
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Naples, Italy;
- Correspondence: (F.F.); (M.G.A.); (A.A.); Tel.: +39-081-2539179 (A.A.)
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14
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Ptitsyn LR, Yampolskaya TA, Kutukova EA, Altman IB. Identification of Core Cellulolytic Enzymes from the Talaromyces cellulolyticus Strains Y-94 and S6-25. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Diversity of Endophytic and Pathogenic Fungi of Saffron (Crocus sativus) Plants from Cultivation Sites in Italy. DIVERSITY 2021. [DOI: 10.3390/d13110535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Crocus sativus is an important crop for the production of saffron and bioactive compounds. Plant endophytic fungi are a source of secondary metabolites additional to those produced by the plant itself. We analysed the biodiversity of endophytic fungi present in corms, stems, leaves, tepals, and stigmas of C. sativus from ten Italian sites; furthermore, we isolated putative pathogenic fungi from rotten plants. We used an in vitro isolation approach followed by molecular analysis of the internal transcribed spacer (ITS rDNA) region. We obtained 165 strains belonging to 39 OTUs, spreading over 26 genera and 29 species. Dark septate endophytes of the genus Cadophora and the species Talaromyces pinophilus dominated in corms, while Alternaria alternata, Epicoccum spp., T. pinophilus, Mucor fragilis, and Stemphylium vesicarium dominated in other tissues. The most frequently isolated pathogens were Fusarium oxysporum and Rhizopus oryzae. Endophytic communities significantly differed among tissues and life stages, whereas differences among cultivation sites were not statistically supported. Several endophytes were hypothesized to have changing trophic modes and/or to be latent pathogens in C. sativus. All strains were conserved ex-situ for future bioactivity tests and production of metabolites.
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Prieto A, de Eugenio L, Méndez-Líter JA, Nieto-Domínguez M, Murgiondo C, Barriuso J, Bejarano-Muñoz L, Martínez MJ. Fungal glycosyl hydrolases for sustainable plant biomass valorization: Talaromyces amestolkiae as a model fungus. Int Microbiol 2021; 24:545-558. [PMID: 34417929 DOI: 10.1007/s10123-021-00202-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/26/2022]
Abstract
As the main decomposers and recyclers in nature, fungi secrete complex mixtures of extracellular enzymes for degradation of plant biomass, which is essential for mobilization of the organic carbon fixed by the photosynthesis in vegetal cells. Biotechnology can emulate the closed natural biological cycles, using lignocellulosic biomass as a renewable resource and lignocellulolytic fungal enzymes as catalysts to sustainably produce consumer goods. Cellulose and hemicellulose are the major polysaccharides on Earth, and the main enzymes involved in their hydrolytic depolymerization are cellulases (endoglucanases, cellobiohydrolases, and β-glucosidases) and hemicellulases (mainly endoxylanases and β-xylosidases). This work will focus on the enzymes secreted by the filamentous ascomycete Talaromyces amestolkiae and on some of their biotechnological applications. Their excellent hydrolytic activity was demonstrated by the partial degradation of xylans to prebiotic oligosaccharides by the endoxylanase XynN, or by the saccharification of lignocellulosic wastes to monosaccharides (fermentable to ethanol) either by the whole secretomes or by isolated enzymes used as supplements of commercial cocktails. However, apart from their expected hydrolytic activity, some of the β-glycosidases produced by this strain catalyze the transfer of a sugar molecule to specific aglycons by transglycosylation. As the synthesis of customized glycoconjugates is a major goal for biocatalysis, mutant variants of the β-xyloxidase BxTW1 and the ß-glucosidases BGL-1 and BGL-2 were obtained by directed mutagenesis, substantially improving the regioselective production yields of bioactive glycosides since they showed reduced or null hydrolytic activity.
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Affiliation(s)
- Alicia Prieto
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain.
| | - Laura de Eugenio
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - Juan A Méndez-Líter
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - Manuel Nieto-Domínguez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - Carlos Murgiondo
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - Lara Bejarano-Muñoz
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28022, Madrid, Spain.
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Wang B, Guo L, Ye K, Wang L. Chromosome-Scale Genome Assembly of Talaromyces rugulosus W13939, a Mycoparasitic Fungus and Promising Biocontrol Agent. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1446-1450. [PMID: 33048598 DOI: 10.1094/mpmi-06-20-0163-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, we report a chromosome-level genome assembly of Talaromyces rugulosus (syn. Penicillium rugulosum) W13939 (six chromosomes; contig N50: 5.90 Mb), generated using a combination of PacBio long-read and Illumina paired-end data. T. rugulosus is not only a potent enzyme producer, but also a mycoparasite of Aspergillus flavus, which is a notorious plant pathogen and mycotoxin producer, making it a promising biocontrol agent. The T. rugulosus genome is rich in genes encoding proteases, carbohydrate-active enzymes, fungal cell wall-degrading enzymes, lectin, and secondary metabolite biosynthetic enzymes, reflecting its mycoparasitic life style and mycotoxigenic capability. This high-quality assembly of the T. rugulosus genome will be a valuable resource to assist us in the understanding of the molecular basis of mycoparasitism and facilitate the agricultural and biotechnological applications of Talaromyces spp.
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Affiliation(s)
- Bo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Li Guo
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Kai Ye
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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18
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Liu F, Wang Z, Manglekar RR, Geng A. Enhanced cellulase production through random mutagenesis of Talaromyces pinophilus OPC4-1 and fermentation optimization. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Hadj Taieb K, Gharsallah H, Ksentini I, Leclerque A, Schuster C, Cheffi M, Naayma S, Triki MA, Ksantini M. Screening of biological activities of fungi associated with pistachio bark beetle, Chaetoptelius vestitus (Coleoptera, Curculionidae), infesting pistachio cultivations in Tunisia. J Appl Microbiol 2020; 128:1472-1485. [PMID: 31913566 DOI: 10.1111/jam.14572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/30/2019] [Indexed: 11/26/2022]
Abstract
AIMS In this study, we aimed to explore the enzymatic diversity, the entomopathogenic and the antimicrobial potentialities of fungi associated with the pistachio bark beetle, Chaetoptelius vestitus. METHODS AND RESULTS A total of 40 isolates were screened for enzymatic diversity. Most of them, 92·5%, were able to produce at least two of the screened enzymes. Pathogenic assays performed on C. vestitus showed a high entomopathogenic activity of the isolates Ata_io_1 (A. tamarii), Fve_io_1 (F. verticillioides), Tpi_io_1 (T. pinophilus), Pal_io_1 (P. album), Pbi_io_2 (Penicillium bilaiae) and Pch_io_1 (P. chrysogenum), as based on mean mortality of C. vestitus. A screening of antimicrobial activity using well diffusion method showed that the isolates Tro_io_1 (T. pinophilus), Tat_io_1 (T. atroroseus) and Pch_io_1 (P. chrysogenum) presented the highest antibacterial activity. Furthermore, Mgu_io_1 (M. guilliermondii), Asc_io_1 (A. sclerotiorum), Ata_io_1 (A. tamarii), G. lavendula (Gla_io_1), Pva_io_1 (P. variotii), Pul_io_1 (P. ulaiense), Tat_io_1 (T. atroroseus) and Tro_io_1 (T. roseum) were active against at least two of the three tested fungal phytopathogens. CONCLUSIONS Fungal isolates representing entomopathogenic activity and a broad spectrum of antimicrobial activities can be considered as promising resources for biological pistachio trees protection. SIGNIFICANCE AND IMPACT OF THE STUDY Fungi associated with C. vestitus were investigated for detecting their potential biotechnological applications.
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Affiliation(s)
- K Hadj Taieb
- Institut Supérieur Agronomique de Chott Meriem, Université de Sousse, Sousse, Tunisie.,Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - H Gharsallah
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - I Ksentini
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - A Leclerque
- Institute for Microbiology and Biochemistry, Geisenheim University, Geisenheim, Germany
| | - C Schuster
- Institute for Microbiology and Biochemistry, Geisenheim University, Geisenheim, Germany
| | - M Cheffi
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - S Naayma
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - M A Triki
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
| | - M Ksantini
- Institut de l'Olivier, Université de Sfax, Sfax, Tunisie
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Zhang T, Liao LS, Li CX, Liao GY, Lin X, Luo XM, Zhao S, Feng JX. Identification of a Novel Transcription Factor TP05746 Involved in Regulating the Production of Plant-Biomass-Degrading Enzymes in Talaromyces pinophilus. Front Microbiol 2020; 10:2875. [PMID: 31921053 PMCID: PMC6923684 DOI: 10.3389/fmicb.2019.02875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/28/2019] [Indexed: 12/31/2022] Open
Abstract
Limited information on transcription factor (TF)-mediated regulation exists for most filamentous fungi, specifically for regulation of the production of plant-biomass-degrading enzymes (PBDEs). The filamentous fungus, Talaromyces pinophilus, can secrete integrative cellulolytic and amylolytic enzymes, suggesting a promising application in biotechnology. In the present study, the regulatory roles of a Zn2Cys6 protein, TP05746, were investigated in T. pinophilus through the use of biochemical, microbiological and omics techniques. Deletion of the gene TP05746 in T. pinophilus led to a 149.6% increase in soluble-starch-degrading enzyme (SSDE) production at day one of soluble starch induction but an approximately 30% decrease at days 2 to 4 compared with the parental strain ΔTpKu70. In contrast, the T. pinophilus mutant ΔTP05746 exhibited a 136.8-240.0% increase in raw-starch-degrading enzyme (RSDE) production, as well as a 90.3 to 519.1% increase in cellulase and xylanase production following induction by culturing on wheat bran plus Avicel, relative to that exhibited by ΔTpKu70. Additionally, the mutant ΔTP05746 exhibited accelerated mycelial growth at the early stage of cultivation and decreased conidiation. Transcriptomic profiling and real-time quantitative reverse transcription-PCR (RT-qPCR) analyses revealed that TP05746 dynamically regulated the expression of genes encoding major PBDEs and their regulatory genes, as well as fungal development-regulated genes. Furthermore, in vitro binding experiments confirmed that TP05746 bound to the promoter regions of the genes described above. These results will contribute to our understanding of the regulatory mechanism of PBDE genes and provide a promising target for genetic engineering for improved PBDE production in filamentous fungi.
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Affiliation(s)
- Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Gui-Yan Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiong Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
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Transcription Factor NsdD Regulates the Expression of Genes Involved in Plant Biomass-Degrading Enzymes, Conidiation, and Pigment Biosynthesis in Penicillium oxalicum. Appl Environ Microbiol 2018; 84:AEM.01039-18. [PMID: 29980558 DOI: 10.1128/aem.01039-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/29/2018] [Indexed: 11/20/2022] Open
Abstract
Soil fungi produce a wide range of chemical compounds and enzymes with potential for applications in medicine and biotechnology. Cellular processes in soil fungi are highly dependent on the regulation under environmentally induced stress, but most of the underlying mechanisms remain unclear. Previous work identified a key GATA-type transcription factor, Penicillium oxalicum NsdD (PoxNsdD; also called POX08415), that regulates the expression of cellulase and xylanase genes in P. oxalicum PoxNsdD shares 57 to 64% identity with the key activator NsdD, involved in asexual development in Aspergillus In the present study, the regulatory roles of PoxNsdD in P. oxalicum were further explored. Comparative transcriptomic profiling revealed that PoxNsdD regulates major genes involved in starch, cellulose, and hemicellulose degradation, as well as conidiation and pigment biosynthesis. Subsequent experiments confirmed that a ΔPoxNsdD strain lost 43.9 to 78.8% of starch-digesting enzyme activity when grown on soluble corn starch, and it produced 54.9 to 146.0% more conidia than the ΔPoxKu70 parental strain. During cultivation, ΔPoxNsdD cultures changed color, from pale orange to brick red, while the ΔPoxKu70 cultures remained bluish white. Real-time quantitative reverse transcription-PCR showed that PoxNsdD dynamically regulated the expression of a glucoamylase gene (POX01356/Amy15A), an α-amylase gene (POX09352/Amy13A), and a regulatory gene (POX03890/amyR), as well as a polyketide synthase gene (POX01430/alb1/wA) for yellow pigment biosynthesis and a conidiation-regulated gene (POX06534/brlA). Moreover, in vitro binding experiments showed that PoxNsdD bound the promoter regions of the above-described genes. This work provides novel insights into the regulatory mechanisms of fungal cellular processes and may assist in genetic engineering of Poxalicum for potential industrial and medical applications.IMPORTANCE Most filamentous fungi produce a vast number of extracellular enzymes that are used commercially for biorefineries of plant biomass to produce biofuels and value-added chemicals, which might promote the transition to a more environmentally friendly economy. The expression of these extracellular enzyme genes is tightly controlled at the transcriptional level, which limits their yields. Hitherto our understanding of the regulation of expression of plant biomass-degrading enzyme genes in filamentous fungi has been rather limited. In the present study, regulatory roles of a key regulator, PoxNsdD, were further explored in the soil fungus Penicillium oxalicum, contributing to the understanding of gene regulation in filamentous fungi and revealing the biotechnological potential of Poxalicum via genetic engineering.
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Talarodiolide, a New 12-Membered Macrodiolide, and GC/MS Investigation of Culture Filtrate and Mycelial Extracts of Talaromyces pinophilus. Molecules 2018; 23:molecules23040950. [PMID: 29671776 PMCID: PMC6017668 DOI: 10.3390/molecules23040950] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022] Open
Abstract
Talarodiolide, a new 12-membered macrodiolide, was isolated and characterized from the culture filtrate of strain LT6 of Talaromyces pinophilus. The structure of (Z)-4,10-dimethyl-1,7-dioxa-cyclododeca-3,9-diene-2,8-dione was assigned essentially based on NMR and MS data. Furthermore, several known compounds were isolated and identified in the crude extract of the culture filtrate and mycelium of this strain. EI mass spectrum at 70 eV of all isolated metabolites was acquired and compiled in a custom GC/MS library to be employed to detect metabolites in the crude extracts.
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Panek J, Frąc M. Development of a qPCR assay for the detection of heat-resistant Talaromyces flavus. Int J Food Microbiol 2018; 270:44-51. [PMID: 29555595 DOI: 10.1016/j.ijfoodmicro.2018.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 11/18/2022]
Abstract
Heat-resistant fungi of the species Talaromyces flavus, which inhabits soil and can contaminate fruits, constitutes significant impact on spoilage of heat-processed food. T. flavus possess the ability to produce numerous mycotoxins and is able to survive the process of pasteurization what makes it a treat to food industry. Up to date there is no rapid and reliable method to detect and identify T. flavus. Therefore in this study, a sensitive method for detecting T. flavus was developed. The primers (Tf1_F/R) specific to detection of DNA replication licensing factor gene of T. flavus were designed. With this set of primers, a qPCR reaction with SybrGreen detection was developed. The specificity of assay with use of 5 T. flavus strains and 35 other fungal isolates was tested. The detection threshold was 200 fg of T. flavus genomic DNA. The developed method was able to detect 640 ascospores in 1 g of strawberry fruits and soil samples.
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Affiliation(s)
- Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
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Liao GY, Zhao S, Zhang T, Li CX, Liao LS, Zhang FF, Luo XM, Feng JX. The transcription factor TpRfx1 is an essential regulator of amylase and cellulase gene expression in Talaromyces pinophilus. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:276. [PMID: 30337955 PMCID: PMC6174557 DOI: 10.1186/s13068-018-1276-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/26/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Perfect and low cost of fungal amylolytic and cellulolytic enzymes are prerequisite for the industrialization of plant biomass biorefinergy to biofuels. Genetic engineering of fungal strains based on regulatory network of transcriptional factors (TFs) and their targets is an efficient strategy to achieve the above described aim. Talaromyces pinophilus produces integrative amylolytic and cellulolytic enzymes; however, the regulatory mechanism associated with the expression of amylase and cellulase genes in T. pinophilus remains unclear. In this study, we screened for and identified novel TFs regulating amylase and/or cellulase gene expression in T. pinophilus 1-95 through comparative transcriptomic and genetic analyses. RESULTS Comparative analysis of the transcriptomes from T. pinophilus 1-95 grown on media in the presence and absence of glucose or soluble starch as the sole carbon source screened 33 candidate TF-encoding genes that regulate amylase gene expression. Thirty of the 33 genes were successfully knocked out in the parental strain T. pinophilus ∆TpKu70, with seven of the deletion mutants firstly displaying significant changes in amylase production as compared with the parental strain. Among these, ∆TpRfx1 (TpRfx1: Talaromyces pinophilus Rfx1) showed the most significant decrease (81.5%) in amylase production, as well as a 57.7% reduction in filter paper cellulase production. Real-time quantitative reverse transcription PCR showed that TpRfx1 dynamically regulated the expression of major amylase and cellulase genes during cell growth, and in vitro electrophoretic mobility shift assay revealed that TpRfx1 bound the promoter regions of genes encoding α-amylase (TP04014/Amy13A), glucoamylase (TP09267/Amy15A), cellobiohydrolase (TP09412/cbh1), β-glucosidase (TP05820/bgl1), and endo-β-1,4-glucanase (TP08514/eg1). TpRfx1 protein containing a regulatory factor X (RFX) DNA-binding domain belongs to RFX family. CONCLUSION We identified a novel RFX protein TpRFX1 that directly regulates the expression of amylase and cellulase genes in T. pinophilus, which provides new insights into the regulatory mechanism of fungal amylase and cellulase gene expression.
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Affiliation(s)
- Gui-Yan Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Feng-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
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Deletion of TpKu70 facilitates gene targeting in Talaromyces pinophilus and identification of TpAmyR involvement in amylase production. World J Microbiol Biotechnol 2017; 33:171. [PMID: 28849313 DOI: 10.1007/s11274-017-2331-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
Talaromyces pinophilus is a promising filamentous fungus for industrial production of biomass-degrading enzymes used in biorefining, and its genome was recently sequenced and reported. However, functional analysis of genes in T. pinophilus is rather limited owing to lack of genetic tools. In this study, a putative TpKu70 encoding the Ku70 homolog involved in the classic non-homologous end-joining pathway was deleted in T. pinophilus 1-95. ΔTpKu70 displayed no apparent defect in vegetative growth and enzyme production, and presented similar sensitivity to benomyl, bleomycin, and UV, when compared with the wild-type T. pinophilus strain 1-95. Seven genes that encode putative transcription factors, including TpAmyR, were successfully knocked out in ΔTpKu70 at 61.5-100% of homologous recombination frequency, which is significantly higher than that noted in the wild-type. Interestingly, ΔTpAmyR produced approximately 20% of amylase secreted by the parent strain ΔTpKu70 in medium containing soluble starch from corn as the sole carbon source. Real-time quantitative reverse transcription PCR showed that TpAmyR positively regulated the expression of genes encoding α-amylase and glucoamylase. Thus, this study provides a useful tool for genetic analysis of T. pinophilus, and identification of a key role for the transcription factor TpAmyR in amylase production in T. pinophilus.
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