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Li X, Li Z, Li M, Li J, Wang Q, Wang S, Li S, Li H. Transcriptomic and metabolomic analysis reveals the influence of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens. Front Microbiol 2024; 15:1224855. [PMID: 38333584 PMCID: PMC10850570 DOI: 10.3389/fmicb.2024.1224855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction Ligninolytic bacteria can secrete extracellular enzymes to depolymerize lignin into small-molecular aromatics that are subsequently metabolized and funneled into the TCA cycle. Carbohydrates, which are the preferred carbon sources of bacteria, influence the metabolism of lignin-derived aromatics through bacteria. Methods In this study, untargeted metabolomics and transcriptomics analyses were performed to investigate the effect of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens MN-13, a strain with lignin-degrading activity that was isolated in our previous work. Results The results demonstrated that the cell growth of the MN-13 strain and lignin removal were promoted when carbohydrates such as glucose and sodium carboxymethyl cellulose were added to an alkaline lignin-minimal salt medium (AL-MSM) culture. Metabolomics analysis showed that lignin depolymerization took place outside the cells, and the addition of glucose regulated the uptake and metabolism of lignin-derived monomers and activated the downstream metabolism process in cells. In the transcriptomics analysis, 299 DEGs were screened after 24 h of inoculation in AL-MSM with free glucose and 2 g/L glucose, respectively, accounting for 8.3% of the total amount of annotated genes. These DEGs were primarily assigned to 30 subcategories, including flagellar assembly, the PTS system, RNA degradation, glycolysis/gluconeogenesis, the TCA cycle, pyruvate metabolism, and tryptophan metabolism. These subcategories were closely associated with the cell structure, generation of cellular energy, and precursors for biosynthetic pathways, based on a - log 10 (P adjust) value in the KEGG pathway analysis. Conclusion In summary, the addition of glucose increased lignin degradation mediated by the MN-13 strain through regulating glycolysis, TCA cycle, and central carbon metabolism.
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Affiliation(s)
- Xiaodan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhuofan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ming Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jingwen Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Quan Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuxiang Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuna Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Hongya Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
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Ortiz-Álvarez J, Becerra S, Baroncelli R, Hernández-Rodríguez C, Sukno SA, Thon MR. Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions. BMC Genomics 2024; 25:56. [PMID: 38216891 PMCID: PMC10785452 DOI: 10.1186/s12864-023-09858-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/29/2023] [Indexed: 01/14/2024] Open
Abstract
The genomes of species belonging to the genus Colletotrichum harbor a substantial number of cytochrome P450 monooxygenases (CYPs) encoded by a broad diversity of gene families. However, the biological role of their CYP complement (CYPome) has not been elucidated. Here, we investigated the putative evolutionary scenarios that occurred during the evolution of the CYPome belonging to the Colletotrichum Graminicola species complex (s.c.) and their biological implications. The study revealed that most of the CYPome gene families belonging to the Graminicola s.c. experienced gene contractions. The reductive evolution resulted in species restricted CYPs are predominant in each CYPome of members from the Graminicola s.c., whereas only 18 families are absolutely conserved among these species. However, members of CYP families displayed a notably different phylogenetic relationship at the tertiary structure level, suggesting a putative convergent evolution scenario. Most of the CYP enzymes of the Graminicola s.c. share redundant functions in secondary metabolite biosynthesis and xenobiotic metabolism. Hence, this current work suggests that the presence of a broad CYPome in the genus Colletotrichum plays a critical role in the optimization of the colonization capability and virulence.
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Affiliation(s)
- Jossue Ortiz-Álvarez
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
- Present Address: Programa "Investigadoras e Investigadores por México" Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Mexico City, México
| | - Sioly Becerra
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
| | - Riccardo Baroncelli
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, México
| | - Serenella A Sukno
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain.
| | - Michael R Thon
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain.
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Sahu N, Indic B, Wong-Bajracharya J, Merényi Z, Ke HM, Ahrendt S, Monk TL, Kocsubé S, Drula E, Lipzen A, Bálint B, Henrissat B, Andreopoulos B, Martin FM, Bugge Harder C, Rigling D, Ford KL, Foster GD, Pangilinan J, Papanicolaou A, Barry K, LaButti K, Virágh M, Koriabine M, Yan M, Riley R, Champramary S, Plett KL, Grigoriev IV, Tsai IJ, Slot J, Sipos G, Plett J, Nagy LG. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria. Nat Microbiol 2023; 8:1668-1681. [PMID: 37550506 PMCID: PMC7615209 DOI: 10.1038/s41564-023-01448-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.
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Affiliation(s)
- Neha Sahu
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Zsolt Merényi
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tori-Lee Monk
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, Szeged, Hungary
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Balázs Bálint
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 'Interactions Arbres/Microorganismes', Centre INRAE Grand Est - Nancy, Champenoux, France
| | - Christoffer Bugge Harder
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, København Ø, Denmark
- Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kathryn L Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Gary D Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Máté Virágh
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Maxim Koriabine
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simang Champramary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Krista L Plett
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Jonathan Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - László G Nagy
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary.
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Feyereisen R, Urban JM, Nelson DR. Aliens in the CYPome of the black fungus gnat, Bradysia coprophila. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 159:103965. [PMID: 37271423 DOI: 10.1016/j.ibmb.2023.103965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.
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Affiliation(s)
- René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium.
| | - John M Urban
- Carnegie Institution for Science, Department of Embryology, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
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5
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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6
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Permana D, Kitaoka T, Ichinose H. Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review. Biotechnol Bioeng 2023. [PMID: 37139574 DOI: 10.1002/bit.28411] [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: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia (Badan Riset dan Inovasi Nasional (BRIN)), Bandung Advanced Science and Creative Engineering Space (BASICS), Kawasan Sains dan Teknologi (KST) Prof. Dr. Samaun Samadikun, Bandung, Indonesia
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Khan MF, Murphy CD. Cytochrome P450 5208A3 is a promiscuous xenobiotic biotransforming enzyme in Cunninghamella elegans. Enzyme Microb Technol 2022; 161:110102. [DOI: 10.1016/j.enzmictec.2022.110102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 11/28/2022]
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8
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Nguyen TLA, Dao ATN, Dang HTC, Koekkoek J, Brouwer A, de Boer TE, van Spanning RJM. Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) by fungi originating from Vietnam. Biodegradation 2022; 33:301-316. [PMID: 35499742 PMCID: PMC9106640 DOI: 10.1007/s10532-022-09982-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Three different fungi were tested for their ability to degrade 2,4-dichlorophenoxyacetic acid and 2,4,5-trichlorophenoxyacetic acid and for the role of laccases and cytochromes P450-type in this process. We studied a white-rot fungus Rigidoporus sp. FMD21, which has a high laccase activity, for its efficiency to degrade these herbicides. A positive correlation was found between its laccase activity and the corresponding herbicide degradation rate. Even more, the doubling of the enzyme activity in this phase corresponded with a doubling of the herbicide degradation rate. It is, therefore, tempting to speculate that laccase is the most dominant enzyme in the degradation of 2,4-D and 2,4,5-T under these conditions. In addition, it was shown that Rigidoporus sp. FMD21 partly relies on cytochromes P450-type for the breakdown of the herbicides as well. Two filamentous fungi were isolated from soil contaminated with herbicides and dioxins located at Bien Hoa airbase. They belong to genera Fusarium and Verticillium of the phylum Ascomycota as judged by their 18S rRNA gene sequences. Both isolated fungi were able to degrade the herbicides but with different rates. Their laccase activity, however, was very low and did not correlate with the rate of breakdown of the herbicides. These data indicate that the white-rot fungus most likely synthesizes laccase and cytochromes P450-type for the breakdown of the herbicides, while the types of enzyme used for the breakdown of the herbicides by the two Ascomycota remain unclear.
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Affiliation(s)
- Thi Lan Anh Nguyen
- Department of Molecular Cell Biology, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
| | - Anh Thi Ngoc Dao
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- MicroLife Solutions, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Ha Thi Cam Dang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Jacco Koekkoek
- Department of Environment and Health, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Abraham Brouwer
- BioDetection Systems, Science Park 406, 1098 XH, Amsterdam, The Netherlands
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Tjalf E de Boer
- MicroLife Solutions, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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Khan MF, Murphy CD. Nitroreduction of flutamide by Cunninghamella elegans NADPH: Cytochrome P450 reductase. Biochem Biophys Rep 2022; 29:101209. [PMID: 35097225 PMCID: PMC8783101 DOI: 10.1016/j.bbrep.2022.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
The microbial model of mammalian drug metabolism, Cunninghamella elegans, has three cytochrome P450 reductase genes in its genome: g1631 (CPR_A), g4301 (CPR_B), and g7609 (CPR_C). The nitroreductase activity of the encoded enzymes was investigated via expression of the genes in the yeast Pichia pastoris X33. Whole cell assays with the recombinant yeast demonstrated that the reductases converted the anticancer drug flutamide to the nitroreduced metabolite that was also produced from the same substrate when incubated with human NADPH: cytochrome P450 reductase. The nitroreductase activity extended to other substrates such as the related drug nilutamide and the environmental contaminants 1-nitronaphthalene and 1,3-dinitronaphthalene. Comparative experiments with cell lysates of recombinant yeast were conducted under aerobic and reduced oxygen conditions and demonstrated that the reductases are oxygen sensitive. Three cytochrome P450 reductase genes from Cunninghamella elegans were heterologously expressed in Pichia pastoris. TThe enzymes displayed nitroreductase activity towards flutamide, which is analogous to human cytochrome P450 reductase. The enzymes are oxygen sensitive, which is also a property shared with the human enzyme. Other nitro-containing substrates can be reduced by the fungal enzymes.
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11
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Antibacterial, Antifungal, and Antioxidant Activities of Silver Nanoparticles Biosynthesized from Bauhinia tomentosa Linn. Antioxidants (Basel) 2021; 10:antiox10121959. [PMID: 34943062 PMCID: PMC8749995 DOI: 10.3390/antiox10121959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/04/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023] Open
Abstract
The biogenic synthesis of silver nanoparticles (AgNPs) has a wide range of applications in the pharmaceutical industry. Here, we synthesized AgNPs using the aqueous flower extract of Bauhinia tomentosa Linn. Formation of AgNPs was observed using ultraviolet-visible light spectrophotometry at different time intervals. Maximum absorption was observed after 4 h at 420 nm due to the reduction of Ag+ to Ag0. The stabilizing activity of functional groups was identified by Fourier-transform infrared spectroscopy. Size and surface morphology were also analyzed using scanning electron microscopy. The present study revealed the AgNPs were spherical in form with a diameter of 32 nm. The face-centered cubic structure of AgNPs was indexed using X-ray powder diffraction with peaks at 2θ = 37°, 49°, 63°, and 76° (corresponding to the planes of silver 111, 200, 220, 311), respectively. Energy-dispersive X-ray spectroscopy revealed that pure reduced silver (Ag0) was the major constituent (59.08%). Antimicrobial analyses showed that the biosynthesized AgNPs possess increased antibacterial activity (against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative), with larger zone formation against S. aureus (9.25 mm) compared with that of E. coli (6.75 mm)) and antifungal activity (against Aspergillus flavus and Candida albican (with superior inhibition against A. flavus (zone of inhibition: 7 mm) compared with C. albicans (zone of inhibition: 5.75 mm)). Inhibition of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity was found to be dose-dependent with half-maximal inhibitory concentration (IC50) values of 56.77 μg/mL and 43.03 μg/mL for AgNPs and ascorbic acid (control), respectively, thus confirming that silver nanoparticles have greater antioxidant activity than ascorbic acid. Molecular docking was used to determine the mode of antimicrobial interaction of our biosynthesized B. tomentosa Linn flower-powder extract-derived AgNPs. The biogenic AgNPs preferred hydrophobic contacts to inhibit bacterial and fungal sustainability with reducing antioxidant properties, suggesting that biogenic AgNPs can serve as effective medicinal agents.
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Fischer MS, Stark FG, Berry TD, Zeba N, Whitman T, Traxler MF. Pyrolyzed Substrates Induce Aromatic Compound Metabolism in the Post-fire Fungus, Pyronema domesticum. Front Microbiol 2021; 12:729289. [PMID: 34777277 PMCID: PMC8579045 DOI: 10.3389/fmicb.2021.729289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/22/2021] [Indexed: 11/25/2022] Open
Abstract
Wildfires represent a fundamental and profound disturbance in many ecosystems, and their frequency and severity are increasing in many regions of the world. Fire affects soil by removing carbon in the form of CO2 and transforming remaining surface carbon into pyrolyzed organic matter (PyOM). Fires also generate substantial necromass at depths where the heat kills soil organisms but does not catalyze the formation of PyOM. Pyronema species strongly dominate soil fungal communities within weeks to months after fire. However, the carbon pool (i.e., necromass or PyOM) that fuels their rise in abundance is unknown. We used a Pyronema domesticum isolate from the catastrophic 2013 Rim Fire (CA, United States) to ask whether P. domesticum is capable of metabolizing PyOM. Pyronema domesticum grew readily on agar media where the sole carbon source was PyOM (specifically, pine wood PyOM produced at 750°C). Using RNAseq, we investigated the response of P. domesticum to PyOM and observed a comprehensive induction of genes involved in the metabolism and mineralization of aromatic compounds, typical of those found in PyOM. Lastly, we used 13C-labeled 750°C PyOM to demonstrate that P. domesticum is capable of mineralizing PyOM to CO2. Collectively, our results indicate a robust potential for P. domesticum to liberate carbon from PyOM in post-fire ecosystems and return it to the bioavailable carbon pool.
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Affiliation(s)
- Monika S. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Frances Grace Stark
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Timothy D. Berry
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Nayela Zeba
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Thea Whitman
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Matthew F. Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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13
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Abstract
Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.
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14
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Davolos D, Russo F, Canfora L, Malusà E, Tartanus M, Furmanczyk EM, Ceci A, Maggi O, Persiani AM. A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites. Microorganisms 2021; 9:microorganisms9081680. [PMID: 34442757 PMCID: PMC8401308 DOI: 10.3390/microorganisms9081680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 01/09/2023] Open
Abstract
Trichoderma hamatum FBL 587 isolated from DDT-contaminated agricultural soils stands out as a remarkable strain with DDT-resistance and the ability to enhance DDT degradation process in soil. Here, whole genome sequencing and RNA-Seq studies for T. hamatum FBL 587 under exposure to DDT were performed. In the 38.9 Mb-genome of T. hamatum FBL 587, 10,944 protein-coding genes were predicted and annotated, including those of relevance to mycoremediation such as production of secondary metabolites and siderophores. The genome-scale transcriptional responses of T. hamatum FBL 587 to DDT exposure showed 1706 upregulated genes, some of which were putatively involved in the cellular translocation and degradation of DDT. With regards to DDT removal capacity, it was found upregulation of metabolizing enzymes such as P450s, and potentially of downstream DDT-transforming enzymes such as epoxide hydrolases, FAD-dependent monooxygenases, glycosyl- and glutathione-transferases. Based on transcriptional responses, the DDT degradation pathway could include transmembrane transporters of DDT, antioxidant enzymes for oxidative stress due to DDT exposure, as well as lipases and biosurfactants for the enhanced solubility of DDT. Our study provides the first genomic and transcriptomic data on T. hamatum FBL 587 under exposure to DDT, which are a base for a better understanding of mycoremediation strategies for DDT-polluted sites.
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Affiliation(s)
- Domenico Davolos
- Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements (DIT), INAIL, Research Area, Via R. Ferruzzi 38/40, 00143 Rome, Italy
- Correspondence: ; Tel.: +39-0654876328
| | - Fabiana Russo
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.R.); (A.C.); (O.M.); (A.M.P.)
| | - Loredana Canfora
- Council of Agricultural Research and Economics, Centre for Agriculture and Environment, Via Della Navicella 2/4, 00184 Rome, Italy;
| | - Eligio Malusà
- The National Institute of Horticultural Research, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (E.M.); (M.T.); (E.M.F.)
| | - Małgorzata Tartanus
- The National Institute of Horticultural Research, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (E.M.); (M.T.); (E.M.F.)
| | - Ewa Maria Furmanczyk
- The National Institute of Horticultural Research, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (E.M.); (M.T.); (E.M.F.)
| | - Andrea Ceci
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.R.); (A.C.); (O.M.); (A.M.P.)
| | - Oriana Maggi
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.R.); (A.C.); (O.M.); (A.M.P.)
| | - Anna Maria Persiani
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.R.); (A.C.); (O.M.); (A.M.P.)
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15
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Cai E, Li L, Deng Y, Sun S, Jia H, Wu R, Zhang L, Jiang Z, Chang C. MAP kinase Hog1 mediates a cytochrome P450 oxidoreductase to promote the Sporisorium scitamineum cell survival under oxidative stress. Environ Microbiol 2021; 23:3306-3317. [PMID: 33973324 DOI: 10.1111/1462-2920.15565] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/16/2021] [Accepted: 05/06/2021] [Indexed: 01/11/2023]
Abstract
The MAP kinase high osmolarity glycerol 1 (Hog1) plays a central role in responding to external oxidative stress in budding yeast Saccchromyces cerevisiae. However, the downstream responsive elements regulated by Hog1 remain poorly understood. In this study, we report that a Sporisorium scitamineum orthologue of Hog1, named as SsHog1, induced transcriptional expression of a putative cytochrome P450 oxidoreductase encoding gene SsCPR1, to antagonize oxidative stress. We found that upon exposure to hydrogen peroxide (H2 O2 ), SsHog1 underwent strikingly phosphorylation, which was proved to be critical for transcriptional induction of SsCPR1. Loss of SsCPR1 led to hypersensitive to oxidative stress similar as the sshog1Δ mutant did, but was resistant to osmotic stress, which is different from the sshog1Δ mutant. On the other hand, overexpression of SsCPR1 in the sshog1Δ mutant could partially restore its ability of oxidative stress tolerance, which indicated that the Hog1 MAP kinase regulates the oxidative stress response specifically through cytochrome P450 (SsCpr1) pathway. Overall, our findings highlight a novel MAPK signalling pathway mediated by Hog1 in regulation of the oxidative stress response via the cytochrome P450 system, which plays an important role in host-fungus interaction.
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Affiliation(s)
- Enping Cai
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Lingyu Li
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yizhen Deng
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Shuquan Sun
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huan Jia
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Rongrong Wu
- Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Lianhui Zhang
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Zide Jiang
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Changqing Chang
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Integrate Microbiology Research Center/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
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16
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Paparokidou C, Leake JR, Beerling DJ, Rolfe SA. Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. MYCORRHIZA 2021; 31:69-83. [PMID: 33200348 PMCID: PMC7782400 DOI: 10.1007/s00572-020-01001-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Many plant species form symbioses with ectomycorrhizal fungi, which help them forage for limiting nutrients in the soil such as inorganic phosphate (Pi). The transcriptional responses to symbiosis and nutrient-limiting conditions in ectomycorrhizal fungal hyphae, however, are largely unknown. An artificial system was developed to study ectomycorrhizal basidiomycete Paxillus involutus growth in symbiosis with its host tree Pinus sylvestris at different Pi concentrations. RNA-seq analysis was performed on P. involutus hyphae growing under Pi-limiting conditions, either in symbiosis or alone. We show that Pi starvation and ectomycorrhizal symbiosis have an independent effect on the P. involutus transcriptome. Notably, low Pi availability induces expression of newly identified putative high-affinity Pi transporter genes, while reducing the expression of putative organic acid transporters. Additionally, low Pi availability induces a close transcriptional interplay between P and N metabolism. GTP-related signalling was found to have a positive effect in the maintenance of ectomycorrhizal symbiosis, whereas multiple putative cytochrome P450 genes were found to be downregulated, unlike arbuscular mycorrhizal fungi. We provide the first evidence of global transcriptional changes induced by low Pi availability and ectomycorrhizal symbiosis in the hyphae of P. involutus, revealing both similarities and differences with better-characterized arbuscular mycorrhizal fungi.
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Affiliation(s)
| | - Jonathan R Leake
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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17
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Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å. The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce. Sci Rep 2020; 10:5884. [PMID: 32246017 PMCID: PMC7125170 DOI: 10.1038/s41598-020-62521-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.
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Affiliation(s)
- Yang Hu
- Zhejiang Academy of Forestry, Liuhe Road, 310023, Hangzhou, China.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden.
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18
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Omics Approaches to Pesticide Biodegradation. Curr Microbiol 2020; 77:545-563. [DOI: 10.1007/s00284-020-01916-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/08/2020] [Indexed: 02/08/2023]
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19
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The host generalist phytopathogenic fungus Sclerotinia sclerotiorum differentially expresses multiple metabolic enzymes on two different plant hosts. Sci Rep 2019; 9:19966. [PMID: 31882688 PMCID: PMC6934579 DOI: 10.1038/s41598-019-56396-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/11/2019] [Indexed: 01/06/2023] Open
Abstract
Sclerotinia sclerotiorum is a necrotrophic fungal pathogen that infects upwards of 400 plant species, including several economically important crops. The molecular processes that underpin broad host range necrotrophy are not fully understood. This study used RNA sequencing to assess whether S. sclerotiorum genes are differentially expressed in response to infection of the two different host crops canola (Brassica napus) and lupin (Lupinus angustifolius). A total of 10,864 of the 11,130 genes in the S. sclerotiorum genome were expressed. Of these, 628 were upregulated in planta relative to in vitro on at least one host, suggesting involvement in the broader infection process. Among these genes were predicted carbohydrate-active enzymes (CAZYmes) and secondary metabolites. A considerably smaller group of 53 genes were differentially expressed between the two plant hosts. Of these host-specific genes, only six were either CAZymes, secondary metabolites or putative effectors. The remaining genes represented a diverse range of functional categories, including several associated with the metabolism and efflux of xenobiotic compounds, such as cytochrome P450s, metal-beta-lactamases, tannases and major facilitator superfamily transporters. These results suggest that S. sclerotiorum may regulate the expression of detoxification-related genes in response to phytotoxins produced by the different host species. To date, this is the first comparative whole transcriptome analysis of S. sclerotiorum during infection of different hosts.
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20
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Theron CW, Labuschagné M, Albertyn J, Smit MS. Heterologous coexpression of the benzoate-para-hydroxylase CYP53B1 with different cytochrome P450 reductases in various yeasts. Microb Biotechnol 2019; 12:1126-1138. [PMID: 30341814 PMCID: PMC6801163 DOI: 10.1111/1751-7915.13321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450) are enzymes with high potential as biocatalysts for industrial applications. Their large-scale applications are, however, limited by instability and requirement for coproteins and/or expensive cofactors. These problems are largely overcome when whole cells are used as biocatalysts. We previously screened various yeast species heterologously expressing self-sufficient P450s for their potential as whole-cell biocatalysts. Most P450s are, however, not self-sufficient and consist of two or three protein component systems. Therefore, in the present study, we screened different yeast species for coexpression of P450 and P450-reductase (CPR) partners, using CYP53B1 from Rhodotorula minuta as an exemplary P450. The abilities of three different coexpressed CPR partners to support P450 activity were investigated, two from basidiomycetous origin and one from an ascomycete. The various P450-CPR combinations were cloned into strains of Saccharomyces cerevisiae, Kluyveromyces marxianus, Hansenula polymorpha, Yarrowia lipolytica and Arxula adeninivorans, using a broad-range yeast expression vector. The results obtained supported the previous finding that recombinant A. adeninivorans strains perform excellently as whole-cell biocatalysts. This study also demonstrated for the first time the P450 reductase activity of the CPRs from R. minuta and U. maydis. A very interesting observation was the variation in the supportive activity provided by the different reductase partners tested and demonstrated better P450 activity enhancement by a heterologous CPR compared to its natural partner CPR. This study highlights reductase selection as a critical variable for consideration in the pursuit of optimal P450-based catalytic systems. The usefulness of A. adeninivorans as both a host for recombinant P450s and whole-cell biocatalyst was emphasized, supporting earlier findings.
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Affiliation(s)
- Chrispian W. Theron
- Department of Microbial, Biochemical and Food BiotechnologyUniversity of the Free StateBloemfonteinSouth Africa
- South African DST‐NRF Centre of Excellence in Catalysis, c*changeUniversity of Cape TownCape TownSouth Africa
| | - Michel Labuschagné
- Department of Microbial, Biochemical and Food BiotechnologyUniversity of the Free StateBloemfonteinSouth Africa
| | - Jacobus Albertyn
- Department of Microbial, Biochemical and Food BiotechnologyUniversity of the Free StateBloemfonteinSouth Africa
| | - Martha S. Smit
- Department of Microbial, Biochemical and Food BiotechnologyUniversity of the Free StateBloemfonteinSouth Africa
- South African DST‐NRF Centre of Excellence in Catalysis, c*changeUniversity of Cape TownCape TownSouth Africa
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21
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Kowalczyk JE, Peng M, Pawlowski M, Lipzen A, Ng V, Singan V, Wang M, Grigoriev IV, Mäkelä MR. The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds. Front Bioeng Biotechnol 2019; 7:229. [PMID: 31616664 PMCID: PMC6763618 DOI: 10.3389/fbioe.2019.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/05/2019] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic plant biomass is an important feedstock for bio-based economy. In particular, it is an abundant renewable source of aromatic compounds, which are present as part of lignin, as side-groups of xylan and pectin, and in other forms, such as tannins. As filamentous fungi are the main organisms that modify and degrade lignocellulose, they have developed a versatile metabolism to convert the aromatic compounds that are toxic at relatively low concentrations to less toxic ones. During this process, fungi form metabolites some of which represent high-value platform chemicals or important chemical building blocks, such as benzoic, vanillic, and protocatechuic acid. Especially basidiomycete white-rot fungi with unique ability to degrade the recalcitrant lignin polymer are expected to perform highly efficient enzymatic conversions of aromatic compounds, thus having huge potential for biotechnological exploitation. However, the aromatic metabolism of basidiomycete fungi is poorly studied and knowledge on them is based on the combined results of studies in variety of species, leaving the overall picture in each organism unclear. Dichomitus squalens is an efficiently wood-degrading white-rot basidiomycete that produces a diverse set of extracellular enzymes targeted for lignocellulose degradation, including oxidative enzymes that act on lignin. Our recent study showed that several intra- and extracellular aromatic compounds were produced when D. squalens was cultivated on spruce wood, indicating also versatile aromatic metabolic abilities for this species. In order to provide the first molecular level systematic insight into the conversion of plant biomass derived aromatic compounds by basidiomycete fungi, we analyzed the transcriptomes of D. squalens when grown with 10 different lignocellulose-related aromatic monomers. Significant differences for example with respect to the expression of lignocellulose degradation related genes, but also putative genes encoding transporters and catabolic pathway genes were observed between the cultivations supplemented with the different aromatic compounds. The results demonstrate that the transcriptional response of D. squalens is highly dependent on the specific aromatic compounds present suggesting that instead of a common regulatory system, fine-tuned regulation is needed for aromatic metabolism.
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Affiliation(s)
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Megan Pawlowski
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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22
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Felpeto‐Santero C, Galán B, Luengo JM, Fernández‐Cañon JM, del Cerro C, Medrano FJ, García JL. Identification and expression of the 11β-steroid hydroxylase from Cochliobolus lunatus in Corynebacterium glutamicum. Microb Biotechnol 2019; 12:856-868. [PMID: 31197939 PMCID: PMC6680611 DOI: 10.1111/1751-7915.13428] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/01/2022] Open
Abstract
Hydroxylation of steroids has acquired special relevance for the pharmaceutical industries. Particularly, the 11β-hydroxylation of steroids is a reaction of biotechnological importance currently carried out at industrial scale by the fungus Cochliobolus lunatus. In this work, we have identified the genes encoding the cytochrome CYP103168 and the reductase CPR64795 of C. lunatus responsible for the 11β-hydroxylase activity in this fungus, which is the key step for the preparative synthesis of cortisol in industry. A recombinant Corynebacterium glutamicum strain harbouring a plasmid expressing both genes forming a synthetic bacterial operon was able to 11β-hydroxylate several steroids as substrates. This is a new example to show that the industrial strain C. glutamicum can be used as a suitable chassis to perform steroid biotransformation expressing eukaryotic cytochromes.
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Affiliation(s)
| | - Beatriz Galán
- Department of Environmental BiologyCentro de Investigaciones BiológicasCSICMadridSpain
| | - José M. Luengo
- Department of Molecular BiologyUniversity of LeónLeónSpain
| | | | - Carlos del Cerro
- Department of Environmental BiologyCentro de Investigaciones BiológicasCSICMadridSpain
| | - Francisco J. Medrano
- Department of Chemical and Physical BiologyCentro de Investigaciones BiológicasCSICMadridSpain
| | - José L. García
- Department of Environmental BiologyCentro de Investigaciones BiológicasCSICMadridSpain
- Department of Applied BiotechnologyInstitute for Integrative Systems Biology (I2SysBio)(Universidad de Valencia‐CSIC)ValenciaSpain
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23
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Martins TM, Martins C, Silva Pereira C. Multiple degrees of separation in the central pathways of the catabolism of aromatic compounds in fungi belonging to the Dikarya sub-Kingdom. Adv Microb Physiol 2019; 75:177-203. [PMID: 31655737 DOI: 10.1016/bs.ampbs.2019.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The diversity and abundance of aromatic compounds in nature is crucial for proper metabolism in all biological systems, and also impacts greatly the development of many industrial processes. Naturally, understanding their catabolism becomes fundamental for many scientific fields of research, from clinical and environmental to technological. The genetic basis of the central pathways for the catabolism of aromatic compounds in fungi, particularly of benzene derivatives, remains however poorly understood largely overlooking their significance. In some Dikarya species the genes of the central pathways are clustered in the genome, often in an array with peripheral pathway genes, even if the existence of a specific pathway does not necessarily mean that the composing genes are clustered. The current availability of many annotated fungal genomes in the postgenomic era creates conditions to reach a more holistic view of these processes through target analysis of the central pathways gene clusters. Inspired by this, we have critically analyzed the established biochemical and genetic data on the catabolism of aromatic compounds in Dikarya after dissecting the presence and distribution of central catabolic gene clusters (at times including also details on gene diversity, order and orientation) and of peripheral genes. Our methodological approach illustrates the multiple degrees of separation in these central pathways gene clusters across Dikarya. Surprisingly, they show a great degree of similarity irrespectively of the Dikarya division, emphasizing that knowledge established on either phyla can guide the identification of clusters of comparable composition (in-cluster plus peripheral genes) in uncharacterized species.
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Affiliation(s)
- Tiago M Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, Oeiras, Portugal
| | - Celso Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, Oeiras, Portugal
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24
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Chen J, Tang J, Xi Y, Dai Z, Bi C, Chen X, Fan F, Zhang X. Production of 14α-hydroxysteroids by a recombinant Saccharomyces cerevisiae biocatalyst expressing of a fungal steroid 14α-hydroxylation system. Appl Microbiol Biotechnol 2019; 103:8363-8374. [PMID: 31414163 DOI: 10.1007/s00253-019-10076-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/28/2019] [Accepted: 07/28/2019] [Indexed: 01/08/2023]
Abstract
The 14α-hydroxysteroids have specific anti-gonadotropic and carcinolytic biological activities and can be produced by microbial biotransformation. The steroid 11β-/14α-hydroxylase P-450lun from Cochliobolus lunatus is the only fungal cytochrome P450 enzyme identified to date with steroid C14 hydroxylation ability. Previous work has mainly revealed the 11β-hydroxylation activity of the P-450lun towards cortexolone (RSS) substrate; however, the potential steroid 14α-hydroxylation activity of this enzyme, especially for androstenedione (AD) substrate, has not yet conducted in-depth testing. In this work, we further tested the steroid 14α-hydroxylation activity of the P-450lun towards RSS and AD in the Saccharomyces cerevisiae system. We demonstrated that P-450lun functions as the specific 14α-hydroxylase towards the AD substrate (regiospecificity > 99%); however, it showed a poor C14-hydroxylation regiospecificity (around 40%) for the RSS substrate. In addition, through transcriptome analysis combined with gene functional characterizations, we also identified and cloned the gene for the P-450lun-associated redox partner CPRlun. Finally, through codon optimization, knockout of genes for the side reactions related enzymes GCY1 and YPR1, and increasing copies of the P-450lun and CPRlun, we developed a recombinant S. cerevisiae biocatalyst based on the C. lunatus steroid 14α-hydroxylation system to produce 14α-hydroxysteroids. Initial production of 14α-OH-AD (150 mg/L day productivity, 99% regioisomeric purity, and 60% w/w yield) and 14α-OH-RSS (64 mg/L day productivity, 40% regioisomeric purity, and 26% w/w yield) were separately achieved in shake flasks; these results represent the highest level of 14α-hydroxysteroid production in the current yeast system.
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Affiliation(s)
- Jing Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Jinlei Tang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Yongyan Xi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Zhubo Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Xi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
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25
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Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol Adv 2019; 37:107396. [PMID: 31075306 DOI: 10.1016/j.biotechadv.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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26
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Rosero-Hernández ED, Moraga J, Collado IG, Echeverri F. Natural Compounds That Modulate the Development of the Fungus Botrytis cinerea and Protect Solanum lycopersicum. PLANTS (BASEL, SWITZERLAND) 2019; 8:E111. [PMID: 31027383 PMCID: PMC6571876 DOI: 10.3390/plants8050111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 11/30/2022]
Abstract
Botrytis cinerea is the causal agent of gray mold disease and is responsible for the loss of millions of dollars in crops in worldwide. Currently, this pathogen exhibits increasing resistance to conventional fungicides; therefore, better control methods and novel compounds with a more specific mechanism of action but without biocidal effects, are required. In this work, several natural compounds to control B. cinerea were analyzed in vitro. Detected effects were dependent on the stage of fungus development, and 3-phenyl-1-propanol displayed the most potent inhibition of in vitro germination, germ tube development, and sporulation. However, it had lower protection of leaves and postharvest fruit in plant infection. Isoeugenol and 1-phenylethanol exhibited lower inhibition of in vitro germination and sporulation, but at the highest concentrations, they inhibited germ tube elongation. Although the lowest rates of foliage infection were recorded using isoeugenol and 3-phenyl-1-propanol, 1-phenylethanol significantly decreased the disease in postharvest tomato fruit, with an efficacy like Mancozeb, but at 18 times lower micromolar concentration. All compounds resulted in high cell viability after spores were removed from the treatment solution exhibited high cell viability, suggesting a non-biocidal effect. The diversity of in vitro and in-plant effects seems to indicate a different mechanism of action.
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Affiliation(s)
- Esteban D Rosero-Hernández
- Química Orgánica de Productos Naturales, Instituto de Química, Universidad de Antioquia, Cl. 62 #52⁻59, Medellín, Colombia.
| | - Javier Moraga
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
| | - Fernando Echeverri
- Química Orgánica de Productos Naturales, Instituto de Química, Universidad de Antioquia, Cl. 62 #52⁻59, Medellín, Colombia.
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27
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ud Din Z, de Medeiros L, Abreu L, Pfenning LH, Lopes Jymeni D, Rodrigues-Filho E. Differential metabolism of diastereoisomeric diterpenes by Preussia minima, found as endophytic fungus in Cupressus lusitanica. Bioorg Chem 2018; 78:436-443. [DOI: 10.1016/j.bioorg.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 01/02/2023]
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28
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Kassotaki E, Pijuan M, Joss A, Borrego CM, Rodriguez-Roda I, Buttiglieri G. Unraveling the potential of a combined nitritation-anammox biomass towards the biodegradation of pharmaceutically active compounds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:722-731. [PMID: 29272841 DOI: 10.1016/j.scitotenv.2017.12.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
In the past few years, anaerobic ammonium oxidation-based processes have attracted a lot of attention for their implementation at the mainstream line of wastewater treatment plants, due to the possibility of leading to energy autarky if combined with anaerobic digestion. However, little is known about the potential degradation of micropollutants by the microbial groups responsible of these processes and the few results available are inconclusive. This study aimed to assess the degradation capability of biomass withdrawn from a combined nitritation/anaerobic ammonium oxidation (combined N/A) pilot plant towards five pharmaceutically active compounds (ibuprofen, sulfamethoxazole, metoprolol, venlafaxine and carbamazepine). Batch experiments were performed under different conditions by selectively activating or inhibiting different microbial groups: i) regular combined N/A operation, ii) aerobic (optimal for nitrifying bacteria), iii) aerobic with allylthiourea (an inhibitor of ammonia monooxygenase, enzyme of ammonia oxidizing bacteria), iv) anoxic (optimal for anaerobic ammonium oxidizing bacteria), v) aerobic with acetate (optimal for heterotrophic bacteria) and vi) anoxic with acetate (optimal for heterotrophic denitrifying bacteria). Ibuprofen was the most biodegradable compound being significantly degraded (49-100%) under any condition except heterotrophic denitrification. Sulfamethoxazole, exhibited the highest removal (70%) under optimal conditions for nitrifying bacteria but in the rest of the experiments anoxic conditions were found to be slightly more favorable (up to 58%). For metoprolol the highest performance was obtained under anoxic conditions favoring anammox bacteria (62%). Finally, carbamazepine and venlafaxine were hardly removed (≤10% in the majority of cases). Taken together, these results suggest the specificity of different microbial groups that in combination with alternating operational parameters can lead to enhanced removal of some micropollutants.
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Affiliation(s)
- Elissavet Kassotaki
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
| | - Maite Pijuan
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
| | - Adriano Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, 8600 Dübendorf, Switzerland.
| | - Carles M Borrego
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain.
| | - Ignasi Rodriguez-Roda
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain; LEQUiA, Laboratory of Chemical and Environmental Engineering, University of Girona, Campus Montilivi, 17071 Girona, Spain.
| | - Gianluigi Buttiglieri
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
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29
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Specialized plant biochemistry drives gene clustering in fungi. ISME JOURNAL 2018; 12:1694-1705. [PMID: 29463891 DOI: 10.1038/s41396-018-0075-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 01/31/2023]
Abstract
The fitness and evolution of prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of genes can coordinate gene expression and can prevent the breakup of co-adapted alleles. Although clustering may thus result from selection for phenotype optimization and persistence, the impact of environmental selection pressures on eukaryotic genome organization has rarely been systematically explored. Here, we investigated the organization of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified 1110 gene clusters and many conserved combinations of clusters in a diverse set of fungi. We demonstrate that congruence in genome organization over small spatial scales is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules into a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between genome organization and ecological evolution in this ancient eukaryotic lineage.
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30
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Singh DK, Kumar J, Sharma VK, Verma SK, Singh A, Kumari P, Kharwar RN. Mycosynthesis of bactericidal silver and polymorphic gold nanoparticles: physicochemical variation effects and mechanism. Nanomedicine (Lond) 2017; 13:191-207. [PMID: 29199886 DOI: 10.2217/nnm-2017-0235] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Extracellular synthesis of silver and gold nanoparticles using aqueous cell-free filtrate (CFF) of endophytic Chaetomium globosum and characterization of its bioactive proteins. METHODS Temperature and pH gradients were used to assess their effects on dimensions of NPs. NPs were tested in vivo for antibacterial activity. MALDI-TOF-MS/MS was used for characterization of CFF proteins. RESULTS Fungal CFF fabricated nanoparticles of various shape under varied physicochemical conditions. Silver nanoparticles showed significantly (p ≤ 0.5) enhanced antibacterial activity against Staphylococcus aureus and Klebsiella pneumoniae compared with AgNO3. Two prominent CFF proteins showed homology with benzoate 4-monooxygenase cytochrome P450 and ubiquinol-cytochrome c reductase. CONCLUSION The study achieved controlled mycosynthesis of NPs and explains the hitherto poorly known mechanism of reduction, stabilization and antibacterial activity of nanoparticles.
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Affiliation(s)
- Dheeraj Kumar Singh
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Jitendra Kumar
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Vijay Kumar Sharma
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Satish Kumar Verma
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arti Singh
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Puja Kumari
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ravindra Nath Kharwar
- Mycopathology & Microbial Technology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Lin H, Wang J, Qi M, Guo J, Rong Q, Tang J, Wu Y, Ma X, Huang L. Molecular cloning and functional characterization of multiple NADPH-cytochrome P450 reductases from Andrographis paniculata. Int J Biol Macromol 2017; 102:208-217. [DOI: 10.1016/j.ijbiomac.2017.04.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 01/07/2023]
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32
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Martins I, Varela A, Frija LMT, Estevão MAS, Planchon S, Renaut J, Afonso CAM, Silva Pereira C. Proteomic Insights on the Metabolism of Penicillium janczewskii during the Biotransformation of the Plant Terpenoid Labdanolic Acid. Front Bioeng Biotechnol 2017; 5:45. [PMID: 28824907 PMCID: PMC5534450 DOI: 10.3389/fbioe.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 07/10/2017] [Indexed: 01/24/2023] Open
Abstract
Plant terpenoids compose a natural source of chemodiversity of exceptional value. Many of these compounds own biological/pharmacological activity, others are regarded as unique chemical skeletons for the synthesis of derivatives with improved properties. Functional chemical modification of terpenoids through biotransformation frequently relies on the use of Ascomycota strains, but information on major cellular responses is still largely lacking. Penicillium janczewskii mediates a stereo-selective hydroxylation of labdanolic acid (LA)-terpenoid found abundantly in Cistus ladanifer-producing 3β-hydroxy-labdanolic acid with yields >90%. Herein, combined analyses of mycelial and extracellular differential proteomes demonstrated that the plant terpenoid increased stress responses, especially against oxidative stress (e.g., accumulation of superoxide dismutase) and apparently altered mitochondria functioning. One putative cytochrome P450 monooxygenase differentially accumulated in the secretome and the terpenoid bioconversion was inhibited in vivo in the presence of a P450 inhibitor. The stereo-selective hydroxylation of the plant terpenoid is likely mediated by P450 enzymes, yet its unequivocal identity remains unclear. To the best of our knowledge, this is the first time that proteomics was used to investigate how a plant terpenoid impacts the metabolism of a filamentous fungus during its efficiently biotransformation. Our findings may encourage the development of new strategies for the valorization of plant natural resources through biotechnology.
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Affiliation(s)
- Isabel Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Adélia Varela
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Instituto Nacional Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Luís M. T. Frija
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica A. S. Estevão
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Sébastien Planchon
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Carlos A. M. Afonso
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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Chen J, Zhang N, Wen J, Zhang Z. Silencing TAK1 alters gene expression signatures in bladder cancer cells. Oncol Lett 2017; 13:2975-2981. [PMID: 28521404 PMCID: PMC5431247 DOI: 10.3892/ol.2017.5819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2016] [Indexed: 02/06/2023] Open
Abstract
The aim of the present study was to identify the differentially expressed genes (DEGs) that are induced by the silencing of transforming growth factor-β-activated kinase 1 (TAK1) in bladder cancer cells and to analyze the potential biological effects. Dataset GSE52452 from mutant fibroblast growth factor receptor 3 (FGFR3) bladder cancer cells transfected with control siRNA or TAK1-specific siRNA was downloaded from Gene Expression Omnibus. The DEGs between the two groups were identified using Limma package following data pre-processing by Affy in Bioconductor. Enrichment analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, followed by functional annotation using TRANSFAC, TSGene and TAG databases. Integrated networks were constructed by Cytoscape and sub-networks were extracted employing BioNet, followed by enrichment analysis of DEGs in the sub-network. A total of 43 downregulated and 21 upregulated genes were obtained. The downregulated genes were enriched in five pathways, including NOD-like receptor signaling pathway and functions related to cellular response. The upregulated genes were associated with cellular developmental processes. Transcription factor EGR1 and 9 tumor-associated genes were screened from the DEGs. Among the DEGs, 10 hub nodes may represent important roles in the complex metabolic network, including EGFR, CYP3A5, MAP3K7, GSTA1, PTHLH, ALDH1A1, KCND2, EGR1, ARRB1 and ITPR1. Additionally, EGFR was correlated with ERBB2, GRB2 and PIK3R1, and these were enriched in ErbB signaling pathway and various cancer-associated pathways. Silencing TAK1 may decrease cellular response to chemical stimulus via downregulating CYP3A5, MAP3K7, GSTA1, ALDH1A1, ARRB1 and ITPR1; increase cancer cell development via upregulating EGFR, EGR1 and PTHLH; and regulate cancer metastasis through EGFR, ERBB2, GRB2 and PIK3R1.
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Affiliation(s)
- Jimin Chen
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Nan Zhang
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Jiaming Wen
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Zhewei Zhang
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
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Durairaj P, Hur JS, Yun H. Versatile biocatalysis of fungal cytochrome P450 monooxygenases. Microb Cell Fact 2016; 15:125. [PMID: 27431996 PMCID: PMC4950769 DOI: 10.1186/s12934-016-0523-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/10/2016] [Indexed: 11/19/2022] Open
Abstract
Cytochrome P450 (CYP) monooxygenases, the nature’s most versatile biological catalysts have unique ability to catalyse regio-, chemo-, and stereospecific oxidation of a wide range of substrates under mild reaction conditions, thereby addressing a significant challenge in chemocatalysis. Though CYP enzymes are ubiquitous in all biological kingdoms, the divergence of CYPs in fungal kingdom is manifold. The CYP enzymes play pivotal roles in various fungal metabolisms starting from housekeeping biochemical reactions, detoxification of chemicals, and adaptation to hostile surroundings. Considering the versatile catalytic potentials, fungal CYPs has gained wide range of attraction among researchers and various remarkable strategies have been accomplished to enhance their biocatalytic properties. Numerous fungal CYPs with multispecialty features have been identified and the number of characterized fungal CYPs is constantly increasing. Literature reveals ample reviews on mammalian, plant and bacterial CYPs, however, modest reports on fungal CYPs urges a comprehensive review highlighting their novel catalytic potentials and functional significances. In this review, we focus on the diversification and functional diversity of fungal CYPs and recapitulate their unique and versatile biocatalytic properties. As such, this review emphasizes the crucial issues of fungal CYP systems, and the factors influencing efficient biocatalysis.
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Affiliation(s)
- Pradeepraj Durairaj
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
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Cytochrome P450 complement (CYPome) of Candida oregonensis, a gut-associated yeast of bark beetle, Dendroctonus rhizophagus. Fungal Biol 2016; 120:1077-89. [PMID: 27567714 DOI: 10.1016/j.funbio.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/01/2016] [Accepted: 06/08/2016] [Indexed: 01/20/2023]
Abstract
Bark beetles (Curculionidae: Scolytinae) and associated microorganisms must overcome a complex tree's defence system, which includes toxic monoterpenes, to successfully complete their life cycle. A number of studies have suggested these microorganisms could have ecological roles related with the nutrition, detoxification, and semiochemical production. In particular, in filamentous fungi symbionts, cytochrome P450 (CYP) have been involved with terpenoid detoxification and biotransformation processes. Candida oregonensis has been isolated from the gut, ovaries, and frass of different bark beetle species, and it is a dominant species in the Dendroctonus rhizophagus gut. In this study, we identify, characterise, and infer the phylogenetic relationships of C. oregonensis CYP genes. The results indicate that the cytochrome P450 complement (CYPome) is composed of nine genes (CYP51F1, CYP61A1, CYP56D1, CYP52A59, CYP52A60, CYP52A61, CYP52A62, CYP5217A8, and CYP5217B1), which might participate in primary metabolic reactions such as sterol biosynthesis, biodegradation of xenobiotic, and resistance to environmental stress. The prediction of the cellular location suggests that these CYPs to be anchored to the plasma membrane, membranes of the endoplasmic reticulum, mitochondria, and peroxisomes. These findings lay the foundation for future studies about the functional role of P450s, not only for yeasts, but also for the insects with which they interact.
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Perez-Garcia O, Lear G, Singhal N. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol 2016; 7:673. [PMID: 27242701 PMCID: PMC4870247 DOI: 10.3389/fmicb.2016.00673] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022] Open
Abstract
We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.
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Affiliation(s)
- Octavio Perez-Garcia
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland Auckland, New Zealand
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
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37
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Mazzaferro LS, Hüttel W, Fries A, Müller M. Cytochrome P450-Catalyzed Regio- and Stereoselective Phenol Coupling of Fungal Natural Products. J Am Chem Soc 2015; 137:12289-95. [DOI: 10.1021/jacs.5b06776] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Laura S. Mazzaferro
- Institute of Pharmaceutical
Sciences, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical
Sciences, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Alexander Fries
- Institute of Pharmaceutical
Sciences, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical
Sciences, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
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Homologues of xenobiotic metabolizing N-acetyltransferases in plant-associated fungi: Novel functions for an old enzyme family. Sci Rep 2015; 5:12900. [PMID: 26245863 PMCID: PMC4542470 DOI: 10.1038/srep12900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/06/2015] [Indexed: 12/23/2022] Open
Abstract
Plant-pathogenic fungi and their hosts engage in chemical warfare, attacking each other with toxic products of secondary metabolism and defending themselves via an arsenal of xenobiotic metabolizing enzymes. One such enzyme is homologous to arylamine N-acetyltransferase (NAT) and has been identified in Fusarium infecting cereal plants as responsible for detoxification of host defence compound 2-benzoxazolinone. Here we investigate functional diversification of NAT enzymes in crop-compromising species of Fusarium and Aspergillus, identifying three groups of homologues: Isoenzymes of the first group are found in all species and catalyse reactions with acetyl-CoA or propionyl-CoA. The second group is restricted to the plant pathogens and is active with malonyl-CoA in Fusarium species infecting cereals. The third group generates minimal activity with acyl-CoA compounds that bind non-selectively to the proteins. We propose that fungal NAT isoenzymes may have evolved to perform diverse functions, potentially relevant to pathogen fitness, acetyl-CoA/propionyl-CoA intracellular balance and secondary metabolism.
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Novak M, Lah L, Šala M, Stojan J, Bohlmann J, Komel R. Oleic acid metabolism via a conserved cytochrome P450 system-mediated ω-hydroxylation in the bark beetle-associated fungus Grosmannia clavigera. PLoS One 2015; 10:e0120119. [PMID: 25794012 PMCID: PMC4368105 DOI: 10.1371/journal.pone.0120119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 01/22/2015] [Indexed: 12/27/2022] Open
Abstract
The bark beetle-associated fungus Grosmannia clavigera participates in the large-scale destruction of pine forests. In the tree, it must tolerate saturating levels of toxic conifer defense chemicals (e.g. monoterpenes). The fungus can metabolize some of these compounds through the ß-oxidation pathway and use them as a source of carbon. It also uses carbon from pine triglycerides, where oleic acid is the most common fatty acid. High levels of free fatty acids, however, are toxic and can cause additional stress during host colonization. Fatty acids induce expression of neighboring genes encoding a cytochrome P450 (CYP630B18) and its redox partner, cytochrome P450 reductase (CPR2). The aim of this work was to study the function of this novel P450 system. Using LC/MS, we biochemically characterized CYP630 as a highly specific oleic acid ω-hydroxylase. We explain oleic acid specificity using protein interaction modeling. Our results underscore the importance of ω-oxidation when the main ß-oxidation pathway may be overwhelmed by other substrates such as host terpenoid compounds. Because this CYP-CPR gene cluster is evolutionarily conserved, our work has implications for metabolism studies in other fungi.
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Affiliation(s)
- Metka Novak
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ljerka Lah
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- * E-mail: (LL); (RK)
| | - Martin Šala
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Jure Stojan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Radovan Komel
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- * E-mail: (LL); (RK)
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Martins TM, Hartmann DO, Planchon S, Martins I, Renaut J, Silva Pereira C. The old 3-oxoadipate pathway revisited: New insights in the catabolism of aromatics in the saprophytic fungus Aspergillus nidulans. Fungal Genet Biol 2015; 74:32-44. [DOI: 10.1016/j.fgb.2014.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/06/2014] [Accepted: 11/23/2014] [Indexed: 10/24/2022]
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41
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Comparative functional characterization of a novel benzoate hydroxylase cytochrome P450 of Fusarium oxysporum. Enzyme Microb Technol 2014; 70:58-65. [PMID: 25659633 DOI: 10.1016/j.enzmictec.2014.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 01/13/2023]
Abstract
FoCYP53A19, a novel cytochrome P450 capable of performing benzoate hydroxylation, was identified and characterized from the ascomycete Fusarium oxysporum f.sp. lycopersici. Comparative functional analysis of FoCYP53A19 with the heterologous and homologous cytochrome P450 reductases (CPR) such as Saccharomyces cerevisiae (ScCPR), Candida albicans (CaCPR) and F. oxysporum (FoCPR) revealed novel catalytic properties. The catalytic efficiency and substrate specificity of FoCYP53A19 were significantly influenced and altered by the source of the reductase employed. The yeast reconstitution system of FoCYP53A19 with ScCPR performed the hydroxylation of benzoic acid (BA) and demethylation of 3-methoxybenzoic acid (3-MBA); but when reconstituted with CaCPR, FoCYP53A19 performed only the essential hydroxylation of fungal benzoate catabolism. Remarkably, FoCYP53A19 with its homologous reductase FoCPR, not only demonstrated the improved conversion rates of BA and 3-MBA, but also exhibited activity toward the hydroxylation of 3-hydroxybenzoic acid. The electron transfer compatibility and the coupling efficiency between the homologous FoCYP-FoCPR system are significant and it favored enhanced monooxygenase activity with broader substrate specificity.
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42
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Lucas JA, Hawkins NJ, Fraaije BA. The evolution of fungicide resistance. ADVANCES IN APPLIED MICROBIOLOGY 2014; 90:29-92. [PMID: 25596029 DOI: 10.1016/bs.aambs.2014.09.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fungicides are widely used in developed agricultural systems to control disease and safeguard crop yield and quality. Over time, however, resistance to many of the most effective fungicides has emerged and spread in pathogen populations, compromising disease control. This review describes the development of resistance using case histories based on four important diseases of temperate cereal crops: eyespot (Oculimacula yallundae and Oculimacula acuformis), Septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), and Fusarium ear blight (a complex of Fusarium and Microdochium spp). The sequential emergence of variant genotypes of these pathogens with reduced sensitivity to the most active single-site fungicides, methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, and succinate dehydrogenase inhibitors illustrates an ongoing evolutionary process in response to the introduction and use of different chemical classes. Analysis of the molecular mechanisms and genetic basis of resistance has provided more rapid and precise methods for detecting and monitoring the incidence of resistance in field populations, but when or where resistance will occur remains difficult to predict. The extent to which the predictability of resistance evolution can be improved by laboratory mutagenesis studies and fitness measurements, comparison between pathogens, and reconstruction of evolutionary pathways is discussed. Risk models based on fungal life cycles, fungicide properties, and exposure to the fungicide are now being refined to take account of additional traits associated with the rate of pathogen evolution. Experimental data on the selection of specific mutations or resistant genotypes in pathogen populations in response to fungicide treatments can be used in models evaluating the most effective strategies for reducing or preventing resistance. Resistance management based on robust scientific evidence is vital to prolong the effective life of fungicides and safeguard their future use in crop protection.
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Affiliation(s)
- John A Lucas
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Nichola J Hawkins
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Bart A Fraaije
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
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Feng L, Fu C, Yuan D, Miao W. A P450 gene associated with robust resistance to DDT in ciliated protozoan, Tetrahymena thermophila by efficient degradation. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 149:126-132. [PMID: 24607688 DOI: 10.1016/j.aquatox.2014.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 06/03/2023]
Abstract
Analysis of metabolic mechanisms of dichlorodiphenyltrichloroethane (DDT) accumulation and degradation in microorganisms, which could be used to reduce its hazard to higher organisms at the higher in the food chain, have not been investigated. Robust resistance to DDT (grows well in 256 mg/L DDT) and a surprising ability to degrade DDT (more than 70% DDT within 4h) were found in the ciliated protozoan Tetrahymena thermophila. A P450 gene (CYP5013C2) was found to respond specifically to DDT treatment. In the presence of 256 mg/L DDT, cells with overexpressing CYP5013C2 (p450-OE) grew faster and degraded DDT more efficiently than wild-type (WT) cells, while cells with CYP5013C2 partially knocked down (p450-KD) grew slower and exhibited reduced ability to degrade DDT compared to WT cells. Both dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DDD) were detected in cells after exposure to DDT, and the concentration of DDD in the p450-OE strain gradually decreased from 0.5 to 4h. Thus, we argue that this P450 gene (CYP5013C2), by efficiently degrading DDT to DDD, is associated with robust resistance to DDT in Tetrahymena, and that a strain overexpressing this gene has the potential to serve as bioreactor that degrades environmental DDT.
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Affiliation(s)
- Lifang Feng
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
| | - Chengjie Fu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongxia Yuan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Wawrzyn GT, Quin MB, Choudhary S, López-Gallego F, Schmidt-Dannert C. Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota. ACTA ACUST UNITED AC 2014; 19:772-83. [PMID: 22726691 DOI: 10.1016/j.chembiol.2012.05.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/08/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023]
Abstract
The secondary metabolome of Basidiomycota represents a largely uncharacterized source of pharmaceutically relevant natural products. Terpenoids are the primary class of bioactive compounds isolated from mushrooms. The Jack O'Lantern mushroom Omphalotus olearius was identified 50 years ago as a prolific producer of anticancer illudin sesquiterpenoids; however, to date there have been exceptionally few studies into the biosynthesis of these important compounds. Here, we report the draft genome sequence of O. olearius, which reveals a diverse network of sesquiterpene synthases and two metabolic gene clusters associated with illudin biosynthesis. Characterization of the sesquiterpene synthases enabled a comprehensive survey of all currently available Basidiomycota genomes, thereby creating a predictive resource for terpenoid natural product biosynthesis in these organisms. Our results will facilitate discovery and biosynthetic production of unique pharmaceutically relevant bioactive compounds from Basidiomycota.
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Affiliation(s)
- Grayson T Wawrzyn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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45
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Korošec B, Sova M, Turk S, Kraševec N, Novak M, Lah L, Stojan J, Podobnik B, Berne S, Zupanec N, Bunc M, Gobec S, Komel R. Antifungal activity of cinnamic acid derivatives involves inhibition of benzoate 4-hydroxylase (CYP53). J Appl Microbiol 2014; 116:955-66. [PMID: 24314266 DOI: 10.1111/jam.12417] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 11/06/2013] [Accepted: 11/25/2013] [Indexed: 11/27/2022]
Abstract
AIMS CYP53A15, from the sorghum pathogen Cochliobolus lunatus, is involved in detoxification of benzoate, a key intermediate in aromatic compound metabolism in fungi. Because this enzyme is unique to fungi, it is a promising drug target in fungal pathogens of other eukaryotes. METHODS AND RESULTS In our work, we showed high antifungal activity of seven cinnamic acid derivatives against C. lunatus and two other fungi, Aspergillus niger and Pleurotus ostreatus. To elucidate the mechanism of action of cinnamic acid derivatives with the most potent antifungal properties, we studied the interactions between these compounds and the active site of C. lunatus cytochrome P450, CYP53A15. CONCLUSION We demonstrated that cinnamic acid and at least four of the 42 tested derivatives inhibit CYP53A15 enzymatic activity. SIGNIFICANCE AND IMPACT OF THE STUDY By identifying selected derivatives of cinnamic acid as possible antifungal drugs, and CYP53 family enzymes as their targets, we revealed a potential inhibitor-target system for antifungal drug development.
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Affiliation(s)
- B Korošec
- National Institute of Chemistry, Ljubljana, Slovenia
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46
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Fungal microsomes in a biotransformation perspective: protein nature of membrane-associated reactions. Appl Microbiol Biotechnol 2013; 97:10263-73. [DOI: 10.1007/s00253-013-5347-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/27/2022]
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Kelly SL, Kelly DE. Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? Philos Trans R Soc Lond B Biol Sci 2013; 368:20120476. [PMID: 23297358 DOI: 10.1098/rstb.2012.0476] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The first eukaryote genome revealed three yeast cytochromes P450 (CYPs), hence the subsequent realization that some microbial fungal genomes encode these proteins in 1 per cent or more of all genes (greater than 100) has been surprising. They are unique biocatalysts undertaking a wide array of stereo- and regio-specific reactions and so hold promise in many applications. Based on ancestral activities that included 14α-demethylation during sterol biosynthesis, it is now seen that CYPs are part of the genes and metabolism of most eukaryotes. In contrast, Archaea and Eubacteria often do not contain CYPs, while those that do are frequently interesting as producers of natural products undertaking their oxidative tailoring. Apart from roles in primary and secondary metabolism, microbial CYPs are actual/potential targets of drugs/agrochemicals and CYP51 in sterol biosynthesis is exhibiting evolution to resistance in the clinic and the field. Other CYP applications include the first industrial biotransformation for corticosteroid production in the 1950s, the diversion into penicillin synthesis in early mutations in fungal strain improvement and bioremediation using bacteria and fungi. The vast untapped resource of orphan CYPs in numerous genomes is being probed and new methods for discovering function and for discovering desired activities are being investigated.
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Affiliation(s)
- Steven L Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science and College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK.
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Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:205-20. [DOI: 10.1016/j.bbapap.2012.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/11/2023]
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49
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Steffen-Munsberg F, Vickers C, Thontowi A, Schätzle S, Meinhardt T, Svedendahl Humble M, Land H, Berglund P, Bornscheuer UT, Höhne M. Revealing the Structural Basis of Promiscuous Amine Transaminase Activity. ChemCatChem 2012. [DOI: 10.1002/cctc.201200545] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Lah L, Haridas S, Bohlmann J, Breuil C. The cytochromes P450 of Grosmannia clavigera: Genome organization, phylogeny, and expression in response to pine host chemicals. Fungal Genet Biol 2012; 50:72-81. [PMID: 23111002 DOI: 10.1016/j.fgb.2012.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/29/2012] [Accepted: 10/16/2012] [Indexed: 01/04/2023]
Abstract
Grosmannia clavigera is a fungal associate of the mountain pine beetle (Dendroctonus ponderosae) and a pathogen of lodgepole pine (Pinus contorta) that must overcome terpenoid oleoresin and phenolic defenses of host trees. G. clavigera responds to monoterpene influx with complementary mechanisms that include export and the use of these compounds as a carbon source. Cytochromes P450 (CYPs) may also be involved in the metabolism of host defense compounds. We have identified and phylogenetically classified G. clavigera CYPs (CYPome). We show that although the G. clavigera CYPome has contracted in evolution, certain CYP families have expanded by duplication. We analyzed RNA-seq data for CYP expression following treatment with terpenes and pine phloem extracts to identify CYPs potentially involved in detoxification of these pine defense compounds. We also used transcriptome analysis of G. clavigera grown on monoterpenes, triglycerides or oleic acid as a carbon source to identify up-regulated CYPs that may be involved in the utilization of these compounds to support fungal growth. Finally, we identify secondary metabolite biosynthetic gene clusters that contain CYPs, and CYPs in clusters that may be involved in conversion of host chemicals.
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Affiliation(s)
- Ljerka Lah
- Department of Wood Sciences, University of British Columbia, Vancouver, BC, Canada
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