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Kim S, Sumner W, Miyauchi S, Jones RN, Mell LK, Sharabi A. Characterization of Antibody Repertoires in Patients with HPV-Related HNSCC Undergoing Definitive Radiation with Immunotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e593. [PMID: 37785792 DOI: 10.1016/j.ijrobp.2023.06.1945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Integrating immune checkpoint inhibitor (ICI) immunotherapy agents into the definitive treatment of head and neck squamous cell carcinoma (HNSCC) has been challenging. It is apparent that understanding how these therapies affect specific components of the immune response is critical to improve outcomes. The role of B cells has been increasingly recognized, especially in HPV+ HNSCC. As antibodies are one of the chief downstream products of B cells, we sought to evaluate the antibody repertoires of patients with HPV+ HNSCC undergoing definitive radiation therapy (RT) and ICI (RT-ICI). MATERIALS/METHODS Serum samples from patients with p16+ HNSCC undergoing RT-ICI were collected for the KEYCHAIN clinical trial (NCT03383094). We analyzed 8 samples from 4 patients collected pre-treatment and 3 months following treatment using the HuProt Human Proteome Microarray, which samples >20,000 human proteins. Genes encoding surface proteins (GESPs) were obtained from The Cancer Surfaceome Atlas. Mutational data were obtained from AACR Project GENIE. For murine studies, C3H mice were injected with 5x105 cells of AT-84-E7-OVA syngeneic SCC into the right flank. Anti-PD-L1 ICI (aPD-L1) was given via intraperitoneal injection every 3 days for 3 doses. RT was 12 Gy in 1 fraction. Cell surface markers in lymph nodes (LNs) were analyzed by flow cytometry. RESULTS In total, we detected antibodies against 10959 unique antigens in the pre-treatment serum, of which 14% and 11% were shared by 3 and 4 patients, respectively. Following completion of RT-ICI, we detected antibodies against 11019 unique antigens, of which 20% and 18% were shared by 3 and 4 patients, respectively. Of these, 5824 (53%) antigens were not detected in the pre-treatment serum, and therefore represent antibodies against "newly detected" antigens. We found 777 antigens that were newly detected and shared by at least 2 patients. Analysis of these antigens revealed enrichment in pathways such as, "response to oxygen levels." We next found that 114 (14.7%) of these represented GESPs. We integrated mutational analysis of the most frequently mutated genes in >1,800 HNSCC samples and found 2/114 GESPs were shared. Using a murine model of HPV+ HNSCC, we found that treatment with RT and aPD-L1 led to the greatest frequency of germinal center (GC) B cells in tumor-draining and non-tumor-draining LNs. CONCLUSION In patients with p16-positive HNSCC, proteomic analysis of antibody repertoires revealed many antigens against which antibodies were formed during RT-ICI that are shared between patients. Intriguingly, GC formation, which is the nidus for B cell responses, in locoregional LNs was greatest with RT-ICI. These findings support the further investigation of B-cell mediated responses in HPV+ HNSCC.
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Affiliation(s)
- S Kim
- UC San Diego, Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, La Jolla, CA
| | - W Sumner
- UC San Diego, Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, La Jolla, CA
| | - S Miyauchi
- UC San Diego, Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, La Jolla, CA
| | | | - L K Mell
- University of California San Diego, La Jolla, CA
| | - A Sharabi
- UC San Diego, Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, La Jolla, CA
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Yotsui I, Matsui H, Miyauchi S, Iwakawa H, Melkonian K, Schlüter T, Michavila S, Kanazawa T, Nomura Y, Stolze SC, Jeon HW, Yan Y, Harzen A, Sugano SS, Shirakawa M, Nishihama R, Ichihashi Y, Ibanez SG, Shirasu K, Ueda T, Kohchi T, Nakagami H. LysM-mediated signaling in Marchantia polymorpha highlights the conservation of pattern-triggered immunity in land plants. Curr Biol 2023; 33:3732-3746.e8. [PMID: 37619565 DOI: 10.1016/j.cub.2023.07.068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Pattern-recognition receptor (PRR)-triggered immunity (PTI) wards off a wide range of pathogenic microbes, playing a pivotal role in angiosperms. The model liverwort Marchantia polymorpha triggers defense-related gene expression upon sensing components of bacterial and fungal extracts, suggesting the existence of PTI in this plant model. However, the molecular components of the putative PTI in M. polymorpha and the significance of PTI in bryophytes have not yet been described. We here show that M. polymorpha has four lysin motif (LysM)-domain-containing receptor homologs, two of which, LysM-receptor-like kinase (LYK) MpLYK1 and LYK-related (LYR) MpLYR, are responsible for sensing chitin and peptidoglycan fragments, triggering a series of characteristic immune responses. Comprehensive phosphoproteomic analysis of M. polymorpha in response to chitin treatment identified regulatory proteins that potentially shape LysM-mediated PTI. The identified proteins included homologs of well-described PTI components in angiosperms as well as proteins whose roles in PTI are not yet determined, including the blue-light receptor phototropin MpPHOT. We revealed that MpPHOT is required for negative feedback of defense-related gene expression during PTI. Taken together, this study outlines the basic framework of LysM-mediated PTI in M. polymorpha and highlights conserved elements and new aspects of pattern-triggered immunity in land plants.
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Affiliation(s)
- Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Department of BioScience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hidenori Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Okinawa, Japan
| | - Hidekazu Iwakawa
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan
| | | | - Titus Schlüter
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Santiago Michavila
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | | | - Hyung-Woo Jeon
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yijia Yan
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Anne Harzen
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shigeo S Sugano
- Bioproduction Research Institute, The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Nara, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510, Chiba, Japan
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
| | - Selena Gimenez Ibanez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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3
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Getzke F, Hassani MA, Crüsemann M, Malisic M, Zhang P, Ishigaki Y, Böhringer N, Jiménez Fernández A, Wang L, Ordon J, Ma KW, Thiergart T, Harbort CJ, Wesseler H, Miyauchi S, Garrido-Oter R, Shirasu K, Schäberle TF, Hacquard S, Schulze-Lefert P. Cofunctioning of bacterial exometabolites drives root microbiota establishment. Proc Natl Acad Sci U S A 2023; 120:e2221508120. [PMID: 37018204 PMCID: PMC10104540 DOI: 10.1073/pnas.2221508120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Soil-dwelling microbes are the principal inoculum for the root microbiota, but our understanding of microbe-microbe interactions in microbiota establishment remains fragmentary. We tested 39,204 binary interbacterial interactions for inhibitory activities in vitro, allowing us to identify taxonomic signatures in bacterial inhibition profiles. Using genetic and metabolomic approaches, we identified the antimicrobial 2,4-diacetylphloroglucinol (DAPG) and the iron chelator pyoverdine as exometabolites whose combined functions explain most of the inhibitory activity of the strongly antagonistic Pseudomonas brassicacearum R401. Microbiota reconstitution with a core of Arabidopsis thaliana root commensals in the presence of wild-type or mutant strains revealed a root niche-specific cofunction of these exometabolites as root competence determinants and drivers of predictable changes in the root-associated community. In natural environments, both the corresponding biosynthetic operons are enriched in roots, a pattern likely linked to their role as iron sinks, indicating that these cofunctioning exometabolites are adaptive traits contributing to pseudomonad pervasiveness throughout the root microbiota.
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Affiliation(s)
- Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn 53115 Bonn, Germany
| | - Milena Malisic
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Pengfan Zhang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Yuji Ishigaki
- Riken Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen 35392 Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen 35392 Giessen, Germany
| | - Alicia Jiménez Fernández
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Lei Wang
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen 35392 Giessen, Germany
| | - Jana Ordon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Ka-Wai Ma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Thorsten Thiergart
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Christopher J Harbort
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Hidde Wesseler
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Shingo Miyauchi
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo 113-8657 Tokyo, Japan
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen 35392 Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources 35392 Giessen, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research 50829 Cologne, Germany
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4
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Maillard F, Kohler A, Morin E, Hossann C, Miyauchi S, Ziegler-Devin I, Gérant D, Angeli N, Lipzen A, Keymanesh K, Johnson J, Barry K, Grigoriev IV, Martin FM, Buée M. Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. New Phytol 2023; 238:845-858. [PMID: 36702619 DOI: 10.1111/nph.18773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire 15 N from 15 N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.
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Affiliation(s)
- François Maillard
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Christian Hossann
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | | | - Dominique Gérant
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, 54000, Nancy, France
| | - Nicolas Angeli
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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5
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Plett JM, Miyauchi S, Morin E, Plett K, Wong-Bajracharya J, de Freitas Pereira M, Kuo A, Henrissat B, Drula E, Wojtalewicz D, Riley R, Pangilinan J, Andreopoulos W, LaButti K, Daum C, Yoshinaga Y, Fauchery L, Ng V, Lipzen A, Barry K, Singan V, Guo J, Lebel T, Costa MD, Grigoriev IV, Martin F, Anderson IC, Kohler A. Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus. Mol Biol Evol 2023; 40:7051143. [PMID: 36811946 PMCID: PMC10066745 DOI: 10.1093/molbev/msad045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 12/01/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
The mutualistic ectomycorrhizal (ECM) fungal genus Pisolithus comprises 19 species defined to date which colonize the roots of >50 hosts worldwide suggesting that substantial genomic and functional evolution occurred during speciation. To better understand this intra-genus variation, we undertook a comparative multi-omic study of nine Pisolithus species sampled from North America, South America, Asia, and Australasia. We found that there was a small core set of genes common to all species (13%), and that these genes were more likely to be significantly regulated during symbiosis with a host than accessory or species-specific genes. Thus, the genetic "toolbox" foundational to the symbiotic lifestyle in this genus is small. Transposable elements were located significantly closer to gene classes including effector-like small secreted proteins (SSPs). Poorly conserved SSPs were more likely to be induced by symbiosis, suggesting that they may be a class of protein that tune host specificity. The Pisolithus gene repertoire is characterized by divergent CAZyme profiles when compared with other fungi, both symbiotic and saprotrophic. This was driven by differences in enzymes associated with symbiotic sugar processing, although metabolomic analysis suggest that neither copy number nor expression of these genes is sufficient to predict sugar capture from a host plant or its metabolism in fungal hyphae. Our results demonstrate that intra-genus genomic and functional diversity within ECM fungi is greater than previously thought, underlining the importance of continued comparative studies within the fungal tree of life to refine our focus on pathways and evolutionary processes foundational to this symbiotic lifestyle.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France.,Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany.,Evolution and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Krista Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia.,Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, Australia
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia.,Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, Australia
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France.,INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Dominika Wojtalewicz
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Laure Fauchery
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jie Guo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Teresa Lebel
- Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, Australia
| | - Mauricio Dutra Costa
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil.,Laboratório de Associações Micorrízicas, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Av. P. H. Rolfs, s/n, Campus UFV. Bolsista Pesquisador do Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil, Viçosa, Brazil
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA.,Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA
| | - Francis Martin
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Annegret Kohler
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
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6
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Kim S, Sumner W, Miyauchi S, Mell L, Califano J, Sharabi A. Combination Radiation Therapy and Selective TLR9 Agonist Improves Local Control in a Murine Model of HPV-Related HNSCC. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Lebreton A, Tang N, Kuo A, LaButti K, Andreopoulos W, Drula E, Miyauchi S, Barry K, Clum A, Lipzen A, Mousain D, Ng V, Wang R, Dai Y, Henrissat B, Grigoriev IV, Guerin-Laguette A, Yu F, Martin FM. Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap (Lactarius) mushrooms. New Phytol 2022; 235:306-319. [PMID: 35383395 DOI: 10.1111/nph.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
| | - Nianwu Tang
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Elodie Drula
- CNRS, Aix-Marseille Université, Marseille, 13288, France
- USC1408 AFMB, INRAE, Marseille, 13288, France
| | - Shingo Miyauchi
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | | | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Ran Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexis Guerin-Laguette
- Mycotree C/- Southern Woods Nursery, 1002 Robinsons Road, RD8, Christchurch, 7678, New Zealand
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
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8
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Sun YF, Lebreton A, Xing JH, Fang YX, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, Lipzen A, Koriabine M, Riley R, Kohler A, Barry K, Henrissat B, Grigoriev IV, Martin FM, Cui BK. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J Fungi (Basel) 2022; 8:jof8030311. [PMID: 35330313 PMCID: PMC8955403 DOI: 10.3390/jof8030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.
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Affiliation(s)
- Yi-Fei Sun
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Annie Lebreton
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jia-Hui Xing
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Yu-Xuan Fang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829 Cologne, Germany
| | - Elodie Drula
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France;
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Kelly Cobaugh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Department of Biological Sciences, King Abdulaziz University, Jeddah 999088, Saudi Arabia
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
- Department of Microbial and Plant Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
| | - Bao-Kai Cui
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
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9
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Looney B, Miyauchi S, Morin E, Drula E, Courty PE, Kohler A, Kuo A, LaButti K, Pangilinan J, Lipzen A, Riley R, Andreopoulos W, He G, Johnson J, Nolan M, Tritt A, Barry KW, Grigoriev IV, Nagy LG, Hibbett D, Henrissat B, Matheny PB, Labbé J, Martin FM. Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi. New Phytol 2022; 233:2294-2309. [PMID: 34861049 DOI: 10.1111/nph.17892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall-degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE 'nests', or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.
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Affiliation(s)
- Brian Looney
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Shingo Miyauchi
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Emmanuelle Morin
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Univ., Marseille, 13009, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), INRAE, Marseille, 13009, France
| | - Pierre Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Université de Bourgogne Franche- Comté, Dijon, 25000, France
| | - Annegret Kohler
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Guifen He
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Matt Nolan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Andrew Tritt
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1053, Hungary
| | - David Hibbett
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Univ., Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, TN, 37830, USA
| | - Francis M Martin
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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10
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Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Guan R, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. ISME J 2022; 16:876-889. [PMID: 34686763 PMCID: PMC8857181 DOI: 10.1038/s41396-021-01138-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/05/2022]
Abstract
Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
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Affiliation(s)
- Lisa K. Mahdi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Shingo Miyauchi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Charles Uhlmann
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Ruben Garrido-Oter
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gregor Langen
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Stephan Wawra
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Yulong Niu
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Rui Guan
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Senga Robertson-Albertyn
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Jane E. Parker
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Alga Zuccaro
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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11
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Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, Lipzen A, Daum C, Hundley H, Pangilinan J, Johnson J, Barry K, LaButti K, Ng V, Ahrendt S, Min B, Choi IG, Park H, Plett JM, Magnuson J, Spatafora JW, Nagy LG, Henrissat B, Grigoriev IV, Yang ZL, Xu J, Martin FM. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. New Phytol 2022; 233:1383-1400. [PMID: 34767630 DOI: 10.1111/nph.17858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Bang Feng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Yang Cao
- Yunnan Institute of Tropic Crops, Jinghong, Yunnan, 666100, China
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Christopher Daum
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Hope Hundley
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Byoungnam Min
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - Hongjae Park
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jon Magnuson
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhu-Liang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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12
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Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 2021; 12:7227. [PMID: 34893598 PMCID: PMC8664821 DOI: 10.1038/s41467-021-27479-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/11/2021] [Indexed: 02/03/2023] Open
Abstract
The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.
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Affiliation(s)
- Fantin Mesny
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Thorsten Thiergart
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Brigitte Pickel
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lea Atanasova
- Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
- Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elodie Drula
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, 13009, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Univ., 13009, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annegret Kohler
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Igor V Grigoriev
- U.S. 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
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Tsinghua East Road Haidian District, Beijing, China.
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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13
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Lebreton A, Zeng Q, Miyauchi S, Kohler A, Dai YC, Martin FM. Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems. Annu Rev Ecol Evol Syst 2021. [DOI: 10.1146/annurev-ecolsys-012021-114902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Qingchao Zeng
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Köln, Germany, D-50829
| | - Annegret Kohler
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Francis M. Martin
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
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14
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Kim S, Sumner W, Miyauchi S, Mell L, Califano J, Sharabi A. Radiation Therapy Activates Interferon-Responsive Genes in Follicular B-Cells in the Tumor-Draining Lymph Node. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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16
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Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
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17
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Marqués‐Gálvez JE, Miyauchi S, Paolocci F, Navarro‐Ródenas A, Arenas F, Pérez‐Gilabert M, Morin E, Auer L, Barry KW, Kuo A, Grigoriev IV, Martin FM, Kohler A, Morte A. Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle. New Phytol 2021; 229:2917-2932. [PMID: 33118170 PMCID: PMC7898904 DOI: 10.1111/nph.17044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.
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Affiliation(s)
- José Eduardo Marqués‐Gálvez
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Shingo Miyauchi
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Francesco Paolocci
- CNR‐IBBRIstituto di Bioscienze e BiorisorseUOS di PerugiaPerugia06128Italy
| | - Alfonso Navarro‐Ródenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Francisco Arenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Manuela Pérez‐Gilabert
- Departamento de Bioquímica y Biología Molecular‐AUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Emmanuelle Morin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Lucas Auer
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Kerrie W. Barry
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Alan Kuo
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCA94598USA
| | - Francis M. Martin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Annegret Kohler
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Asunción Morte
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
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18
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Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso MN. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay. Environ Microbiol 2021; 23:5716-5732. [PMID: 33538380 PMCID: PMC8596683 DOI: 10.1111/1462-2920.15423] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022]
Abstract
Because they comprise some of the most efficient wood‐decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin‐like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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Affiliation(s)
- Hayat Hage
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Shingo Miyauchi
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Köln, Germany
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Elodie Drula
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, USC1408, AFMB, Marseille, 13009, France
| | - Byoungnam Min
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Delphine Chaduli
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - David Navarro
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Anne Favel
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Manon Norest
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Laurence Lesage-Meessen
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Laura de Eugenio
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Cenek Novotny
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic.,University of Ostrava, Ostrava, 701 03, Czech Republic
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joey W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, 0316, Norway
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Willian Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hope Hundley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary.,Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
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Kim S, Sumner W, Miyauchi S, Sanders P, Mell L, Cohen E, Gutkind J, Califano J, Sharabi A. CD40 Agonist Combined with Radiation and PD-1 Blockade Enhances Development Of Systemic Tumor-Specific B-Cells And B-Cell Memory. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Sumner W, Kim S, Miyauchi S, Sanders P, Mell L, Cohen E, Gutkind J, Califano J, Sharabi A. Radiation Combined With CD40 Agonist And PD-1 Blockade Enhances B-cell Tumor Infiltration And Local Tumor Control. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Umekita K, Hashiba Y, Kudou R, Miyauchi S, Kimura M, Matsuda M, Iwao C, Kariya Y, Kawaguchi T, Takajo K, Iwao K, Rikitake Y, Takajo I, Hidaka T, Okayama A. AB0268 HUMAN T-CELL LEUKAEMIA VIRUS TYPE 1 MAY INVALIDATE T-SPOT.TB RESULTS AMONG RHEUMATOID ARTHRITIS PATIENTS: A RETROSPECTIVE OBSERVATIONAL STUDY. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.1588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:In clinical rheumatology, interferon-γ release assays (IGRAs) have been reported as a useful diagnostic test for latent tuberculosis infection (LTBI) before beginning the administration of biologics such as anti-TNF therapies (1). CD4-positive T cells are the main target in Human T-cell leukaemia virus type 1 (HTLV-1) infection. Several reports suggest that the reaction of tuberculin skin test (TST) is attenuated in HTLV-1-positive individuals compared with that in HTLV-1-negative individuals (2). However, it remains unclear whether IGRAs are reliable for detecting TB infection among HTLV-1-positive RA patients.Objectives:The present study aimed to investigate the usefulness of the T-SPOT.TBassay in HTLV-1-positive RA patients. In addition, the association between the existence of IFN-γ producing T cells and HTLV-1 proviral loads (PVLs) in HTLV-1-positive RA patients was analysed on the basis of the T-SPOT.TBassay results.Methods:We reviewed the medical records of 75 HTLV-1-negative and 29 HTLV-1-positive RA patients were suspected cases of LTBI and evaluated using the T-SPOT.TBassay as a clinical practice from April 2012 to July 2019. The results of T-SPOT.TBwere collected from medical records, retrospectively. Peripheral blood samples were obtained from HTLV-1-positive RA patients for the analysis of HTLV-1 PVLs values. The study protocol was approved by the research ethics committees of our hospitals.Results:Approximately 55% of the HTLV-1-positive RA patients showed invalid results for the T-SPOT.TBassay (p < 0.0001); the cause of invalid results was a spot-forming count of >10 spots in the negative controls of the T-SPOT.TBassay among HTLV-1-positive RA patients. Among HTLV-1-positive RA patients, HTLV-1 PVL values were significantly higher in 16 patients who showed invalid results than in 13 patients who did not (p = 0.003). There were no between-group differences in female patient ratio, age, RA disease activity and therapeutic regimens. IFN-γ producing cells were detected in the peripheral blood of HTLV-1-positive RA patients without stimulation with TB-specific antigens.Conclusion:The incidence of invalid results for the T-SPOT.TBassay has been reported to be as low as 0.6% (3). The results of this assay for screening of LTBI in HTLV-1-positive RA patients should be interpreted with caution. Furthermore, our results show that an increase in IFN-γ producing T cell numbers due to HTLV-1 infection in RA patients may affect the pathogenesis of RA.References:[1]Iannone, F., et al.J. Rheumatol. Suppl.91, 41-46 (2014).[2]Tachibana, N., et al.Int. J. Cancer42, 829-831 (1988).[3]Rego, K., et al.Tuberculosis (Edinb.)108, 178-185 (2018).Acknowledgments:We would like to thank Dr Yuki Hashikura and Ms Yuki Kaseda of the University of Miyazaki for their technical support in this work. We would also like to acknowledge Ms Yumiko Kai at the Institute of Rheumatology, Zenjinkai Shimin-no-Mori Hospital, for her help in data management.A part this work was supported by a grant from the Practical Research Project for Rare/Intractable Diseases of the Japan Agency for Medical Research and Development (Grant No. JP19ek0109356), a Health and Labor Sciences Research Grant on Rare and Intractable Diseases from the Ministry of Health, Labor and Welfare of Japan (Grant No. 19FC1007), and a Grant-in-Aid for Clinical Research from Miyazaki University Hospital.Disclosure of Interests:Kunihiko Umekita Paid instructor for: Astellas Pharma Inc. Chugai Pharma Inc. Tanabe-Mitsubishi Pharma Inc., Speakers bureau: Bristol-Myers Squibb, Yayoi Hashiba: None declared, Risa Kudou: None declared, Shunichi Miyauchi: None declared, Masatoshi Kimura: None declared, Motohiro Matsuda: None declared, Chihiro Iwao: None declared, Yumi Kariya: None declared, Takeshi Kawaguchi: None declared, Katoko Takajo: None declared, Koushou Iwao: None declared, Yuuki Rikitake: None declared, Ichiro Takajo: None declared, Toshihiko Hidaka Paid instructor for: Astellas Pharma Inc. Chugai Pharma Inc. Tanabe-Mitsubishi Pharma Inc., Speakers bureau: Astellas Pharma Inc. Chugai Pharma Inc. Tanabe-Mitsubishi Pharma Inc., Akihiko Okayama: None declared
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22
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Basso V, Kohler A, Miyauchi S, Singan V, Guinet F, Šimura J, Novák O, Barry KW, Amirebrahimi M, Block J, Daguerre Y, Na H, Grigoriev IV, Martin F, Veneault-Fourrey C. An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots. Plant Cell Environ 2020; 43:1047-1068. [PMID: 31834634 DOI: 10.1111/pce.13702] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.
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Affiliation(s)
- Veronica Basso
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Annegret Kohler
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Shingo Miyauchi
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Vasanth Singan
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Frédéric Guinet
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Jan Šimura
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Ondřej Novák
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Kerrie W Barry
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Mojgan Amirebrahimi
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Jonathan Block
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Yohann Daguerre
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Hyunsoo Na
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Igor V Grigoriev
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
| | - Francis Martin
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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23
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Araki K, Suzawa K, Miyauchi S, Miura A, Namba K, Otani S, Yamamoto H, Okazaki M, Sugimoto S, Yamane M, Toyooka S. EP1.01-18 Clinical Features of Locally Advanced Lung Cancer Patients with Radiation Pneumonitis After Induction Chemoradiotherapy. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Miki T, Miyoshi T, Ichikawa K, Miyauchi S, Soh J, Toyooka S, Nakamura K, Morita H, Ito H. P692Chemoradiation therapy to patients with lung cancer exacerbates thoracic aortic calcification. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz747.0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Development of chemoradiation therapy (CRT) has improved mortality in patients with cancer. Whereas, it is emerging problem that cancer-survivors suffer from cardiovascular diseases, and the association between modern CRT and the increase in future cardiovascular events is suggested. Meanwhile, previous studies showed that thoracic aortic calcification (TAC) detected by computed tomography (CT), a marker of atherosclerosis, was associated with all-cause mortality and cardiovascular events. However, the influence of CRT on TAC progression remains unclear.
Purpose
The purpose of this study was to evaluate whether CRT would exacerbate TAC.
Methods
A total of 68 patients who treated lung cancer at our hospital between 2011 and 2015 were retrospectively analyzed (mean 62 year-old, male 78%): 35 patients underwent surgical treatment after induction CRT (CRT group) and 33 patients underwent surgical treatment alone (control group), extracted by propensity score matching by age, sex, smoking status, and diseased side. The volume of TAC between 2nd and 12th thoracic vertebrae was quantitatively measured with CT imaging, at baseline and at 1 year follow-up. The annual percent change in TAC was compared between the CRT and the control group. Moreover, the independent relationship between implementation of CRT and the progression of TAC was assessed by multivariate logistic regression analysis, adjusting for age, gender, conventional atherosclerotic risk factors and baseline aortic calcification volume.
Results
Patients in the CRT group received radiation (mean 47.3±4.0 Gy) and chemotherapy: 2 courses of cisplatin with docetaxel (34 cases) or vinorelbine (1 case). The prevalence of dyslipidemia, taking statins and diabetes drugs were significantly higher in the control groups (17% vs. 39%; p=0.041, 11% vs. 33%; p=0.029, 3% vs. 18%; p=0.044, respectively). Baseline C-reactive protein level was significantly higher in the CRT group (0.255 vs. 0.115; p=0.034). In univariate analysis, the annual percent change in TAC volume was significantly increased in the CRT group compared with the control group (37.6% vs. 23.3%; p=0.006). Multivariate logistic regression analysis demonstrated that CRT was an independent factor associated with the progression of TAC volume, even after adjustment for baseline calcification volume and coronary risk factors (OR, 3.90; 95% CI, 1.32–11.47; p=0.014).
Conclusion
CRT to patients with lung cancer exacerbates thoracic aortic calcification, which may result in future cardiovascular events.
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Affiliation(s)
- T Miki
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
| | - T Miyoshi
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
| | - K Ichikawa
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
| | - S Miyauchi
- Okayama University Hospital, Department of General Thoracic Surgery, Okayama, Japan
| | - J Soh
- Okayama University Hospital, Department of General Thoracic Surgery, Okayama, Japan
| | - S Toyooka
- Okayama University Hospital, Department of General Thoracic Surgery, Okayama, Japan
| | - K Nakamura
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
| | - H Morita
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
| | - H Ito
- Okayama University Hospital, Cardiovascular Medicine, Okayama, Japan
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25
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Frandsen KEH, Tovborg M, Jørgensen CI, Spodsberg N, Rosso MN, Hemsworth GR, Garman EF, Grime GW, Poulsen JCN, Batth TS, Miyauchi S, Lipzen A, Daum C, Grigoriev IV, Johansen KS, Henrissat B, Berrin JG, Lo Leggio L. Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 2019; 294:17117-17130. [PMID: 31471321 DOI: 10.1074/jbc.ra119.009223] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/22/2019] [Indexed: 01/13/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
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Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark.,INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | | | | | | | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Glyn R Hemsworth
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Geoffrey W Grime
- The Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, United Kingdom
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shingo Miyauchi
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, 13009 Marseille, France.,INRA, USC 1408 AFMB, 13009 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, de la Providencia I, Ndikumana S, Beaudet D, Hainaut M, Drula E, Kuo A, Tang N, Roy S, Viala J, Henrissat B, Grigoriev IV, Corradi N, Roux C, Martin FM. Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina. New Phytol 2019; 222:1584-1598. [PMID: 30636349 DOI: 10.1111/nph.15687] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/28/2018] [Indexed: 05/21/2023]
Abstract
Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.
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Affiliation(s)
- Emmanuelle Morin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Shingo Miyauchi
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Adrian Pelin
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | | | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Mathieu Hainaut
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Elodie Drula
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nianwu Tang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Sébastien Roy
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Julie Viala
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13007, Marseille, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Francis M Martin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forest University, 100080, Beijing, China
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Jurak E, Suzuki H, van Erven G, Gandier JA, Wong P, Chan K, Ho CY, Gong Y, Tillier E, Rosso MN, Kabel MA, Miyauchi S, Master ER. Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. BMC Genomics 2018; 19:815. [PMID: 30424733 PMCID: PMC6234650 DOI: 10.1186/s12864-018-5210-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
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Affiliation(s)
- E Jurak
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Department of Aquatic Biotechnology and Bioproduct Engineering, Groningen, The Netherlands
| | - H Suzuki
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - G van Erven
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - J A Gandier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - P Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - K Chan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - C Y Ho
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Y Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - E Tillier
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - M-N Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - M A Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - S Miyauchi
- Laboratory of Excellence ARBRE, INRA, Nancy, Lorraine, France.,Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - E R Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
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Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Žifčáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nat Ecol Evol 2018; 2:1956-1965. [DOI: 10.1038/s41559-018-0710-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/04/2018] [Indexed: 11/09/2022]
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Sharabi A, Kim S, Proudfoot J, Kato S, Patel H, Nunez M, Sanders P, Guram K, Miyauchi S, Simpson D, Cohen E, Patel S, Weihe E, Mell L, Mundt A, Kurzrock R. Interim Safety and Toxicity Analysis of a Prospective Phase II Randomized Trial of Checkpoint Blockade Immunotherapy Combined with Stereotactic Body Radiation Therapy in Advanced Metastatic Disease. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Guram K, Sanders P, Miyauchi S, Kim S, Venuti A, Cohen E, Gutkind J, Mell L, Sharabi A. Analysis of Anti-Tumor Immune Responses with Radiation Combined with Anti-PD-L1 Immunotherapy in an HPV Specific Head & Neck Cancer Model. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Takahashi Y, Soh J, Miyauchi S, Araki K, Miura A, Kurihara E, Ogoshi Y, Shien K, Yamamoto H, Sugimoto S, Yamane M, Kiura K, Kanazawa S, Toyooka S. P1.17-17 The Impact of Induction Chemoradiotherapy Followed by Surgery for N1 Involved Non-Small Cell Lung Cancer. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Soh J, Miyauchi S, Araki K, Miura A, Takahashi Y, Kurihara E, Ogoshi Y, Shien K, Yamamoto H, Sugimoto S, Yamane M, Kiura K, Kanazawa S, Toyooka S. P1.17-15 Perioperative Prognostic Nutrition Index for Induction Chemoradiotherapy Followed by Surgery in Locally Advanced Non-Small Lung Cancers. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Miyauchi S, Rancon A, Drula E, Hage H, Chaduli D, Favel A, Grisel S, Henrissat B, Herpoël-Gimbert I, Ruiz-Dueñas FJ, Chevret D, Hainaut M, Lin J, Wang M, Pangilinan J, Lipzen A, Lesage-Meessen L, Navarro D, Riley R, Grigoriev IV, Zhou S, Raouche S, Rosso MN. Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass. Biotechnol Biofuels 2018; 11:201. [PMID: 30061923 PMCID: PMC6055342 DOI: 10.1186/s13068-018-1198-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. RESULTS We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. CONCLUSION As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Affiliation(s)
- Shingo Miyauchi
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Laboratoire d’Excellence ARBRE, UMR 1136, INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Champenoux, France
| | - Anaïs Rancon
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Elodie Drula
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Hayat Hage
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Delphine Chaduli
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Anne Favel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Sacha Grisel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Bernard Henrissat
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isabelle Herpoël-Gimbert
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | | | - Didier Chevret
- INRA, UMR1319, Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Matthieu Hainaut
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
| | - Junyan Lin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Laurence Lesage-Meessen
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - David Navarro
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Simeng Zhou
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Institut des Sciences Moléculaires de Marseille, UMR 7313, CNRS, Aix-Marseille Université, Marseille, France
| | - Sana Raouche
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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Morozumi T, Yashima A, Gomi K, Ujiie Y, Izumi Y, Akizuki T, Mizutani K, Takamatsu H, Minabe M, Miyauchi S, Yoshino T, Tanaka M, Tanaka Y, Hokari T, Yoshie H. Increased systemic levels of inflammatory mediators following one-stage full-mouth scaling and root planing. J Periodontal Res 2018; 53:536-544. [DOI: 10.1111/jre.12543] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2018] [Indexed: 12/29/2022]
Affiliation(s)
- T. Morozumi
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - A. Yashima
- Department of Periodontology; School of Dental Medicine; Tsurumi University; Yokohama Japan
| | - K. Gomi
- Department of Periodontology; School of Dental Medicine; Tsurumi University; Yokohama Japan
| | - Y. Ujiie
- Department of Periodontology; School of Dental Medicine; Tsurumi University; Yokohama Japan
| | - Y. Izumi
- Department of Periodontology; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - T. Akizuki
- Department of Periodontology; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - K. Mizutani
- Department of Periodontology; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - H. Takamatsu
- Department of Periodontology; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - M. Minabe
- Bunkyo-Dori Dental Clinic; Chiba Japan
- Division of Periodontology; Department of Oral Interdisciplinary Medicine; School of Dentistry; Kanagawa Dental University; Yokosuka Japan
| | | | - T. Yoshino
- Seikeikai Hospital; Seikeikai Group; Yokohama Japan
| | - M. Tanaka
- Seikeikai Hospital; Seikeikai Group; Yokohama Japan
| | - Y. Tanaka
- Seikeikai Hospital; Seikeikai Group; Yokohama Japan
| | - T. Hokari
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - H. Yoshie
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
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Tabeta K, Hosojima M, Nakajima M, Miyauchi S, Miyazawa H, Takahashi N, Matsuda Y, Sugita N, Komatsu Y, Sato K, Ishikawa T, Akiishi K, Yamazaki K, Kato K, Saito A, Yoshie H. Increased serum PCSK9, a potential biomarker to screen for periodontitis, and decreased total bilirubin associated with probing depth in a Japanese community survey. J Periodontal Res 2018. [DOI: 10.1111/jre.12533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- K. Tabeta
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - M. Hosojima
- Department of Clinical Nutrition Science; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - M. Nakajima
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - S. Miyauchi
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - H. Miyazawa
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - N. Takahashi
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - Y. Matsuda
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - N. Sugita
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - Y. Komatsu
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - K. Sato
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
| | - T. Ishikawa
- Division of Clinical Nephrology and Rheumatology; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - K. Akiishi
- Reagent R&D Department; Denka Seiken Co., Ltd.; Niigata Japan
| | - K. Yamazaki
- Laboratory of Periodontology and Immunology; Department of Oral Health and Welfare; Faculty of Dentistry; Niigata University; Niigata Japan
| | - K. Kato
- Department of Laboratory Medicine and Clinical Epidemiology for Prevention of Noncommunicable Diseases; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - A. Saito
- Department of Applied Molecular Medicine; Niigata University Graduate School of Medical and Dental Sciences; Niigata Japan
| | - H. Yoshie
- Division of Periodontology; Department of Oral Biological Science; Niigata University Graduate School of Medical and Dental Science; Niigata Japan
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Masumoto R, Kitagaki J, Matsumoto M, Miyauchi S, Fujihara C, Yamashita M, Yamada S, Kitamura M, Murakami S. Effects of paraoxonase 1 on the cytodifferentiation and mineralization of periodontal ligament cells. J Periodontal Res 2017; 53:200-209. [DOI: 10.1111/jre.12507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2017] [Indexed: 11/29/2022]
Affiliation(s)
- R. Masumoto
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - J. Kitagaki
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - M. Matsumoto
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - S. Miyauchi
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - C. Fujihara
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - M. Yamashita
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - S. Yamada
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
- Department of Periodontology and Endodontology; Tohoku University Graduate School of Dentistry; Sendai Japan
| | - M. Kitamura
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
| | - S. Murakami
- Division of Oral Biology and Disease Control; Department of Periodontology; Osaka University Graduate School of Dentistry; Suita Japan
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Nagai M, Dote K, Kato M, Sasaki S, Oda N, Kagawa E, Nakano Y, Yamane A, Higashihara T, Miyauchi S, Tsuchiya A. P3442Cognitive impairment: a mediator for the relationship of visit-to-visit blood pressure variability and long sleep duration with cardiovascular death in the elderly. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx504.p3442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Miyauchi S, Nagai M, Dote K, Kato M, Sasaki S, Oda N, Kagawa E, Nakano Y. P3557In-hospital blood pressure variability and arterial stiffness: associations with coronary calcification in patients with acute myocardial infarction. Data from optical frequency domain imaging study. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx504.p3557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Higashihara T, Dote K, Kato M, Sasaki S, Oda N, Kagawa E, Nakano Y, Nagai M, Yamane A, Miyauchi S, Tsuchiya A. P4644Myocardial wash grade: a novel index for evaluating the quality of reperfusion therapy in acute myocardial infarction. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx504.p4644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Miyauchi S, Kato M, Dote K, Oda N, Kagawa E, Nakano Y, Nagai M. P5558Impact of coronary calcification at culprit lesion of STEMI: Optical coherence tomography study. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p5558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kagawa E, Dote K, Kato M, Sasaki S, Oda N, Nakano Y, Nagai M, Higashihara T, Miyauchi S, Tsuchiya A. P2777Resuscitation duration and initial recorded rhythms in extracorporeal cardiopulmonary resuscitation. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx502.p2777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Miyauchi S, Navarro D, Grisel S, Chevret D, Berrin JG, Rosso MN. The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PLoS One 2017; 12:e0175528. [PMID: 28394946 PMCID: PMC5386290 DOI: 10.1371/journal.pone.0175528] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/27/2017] [Indexed: 01/22/2023] Open
Abstract
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.
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Affiliation(s)
- Shingo Miyauchi
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - David Navarro
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Sacha Grisel
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Didier Chevret
- PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Guy Berrin
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noelle Rosso
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- * E-mail:
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Miyauchi S, Kitagaki J, Masumoto R, Imai A, Kobayashi K, Nakaya A, Kawai S, Fujihara C, Asano Y, Yamashita M, Yanagita M, Yamada S, Kitamura M, Murakami S. Sphingomyelin Phosphodiesterase 3 Enhances Cytodifferentiation of Periodontal Ligament Cells. J Dent Res 2016; 96:339-346. [DOI: 10.1177/0022034516677938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Sphingomyelin phosphodiesterase 3 ( Smpd3), which encodes neutral sphingomyelinase 2 (nSMase2), is a key molecule for skeletal development as well as for the cytodifferentiation of odontoblasts and alveolar bone. However, the effects of nSMase2 on the cytodifferentiation of periodontal ligament (PDL) cells are still unclear. In this study, the authors analyzed the effects of Smpd3 on the cytodifferentiation of human PDL (HPDL) cells. The authors found that Smpd3 increases the mRNA expression of calcification-related genes, such as alkaline phosphatase (ALPase), type I collagen, osteopontin, Osterix (Osx), and runt-related transcription factor (Runx)-2 in HPDL cells. In contrast, GW4869, an inhibitor of nSMase2, clearly decreased the mRNA expression of ALPase, type I collagen, and osteocalcin in HPDL cells, suggesting that Smpd3 enhances HPDL cytodifferentiation. Next, the authors used exome sequencing to evaluate the genetic variants of Smpd3 in a Japanese population with aggressive periodontitis (AgP). Among 44 unrelated subjects, the authors identified a single nucleotide polymorphism (SNP), rs145616324, in Smpd3 as a putative genetic variant for AgP among Japanese people. Moreover, Smpd3 harboring this SNP did not increase the sphingomyelinase activity or mRNA expression of ALPase, type I collagen, osteopontin, Osx, or Runx2, suggesting that this SNP inhibits Smpd3 such that it has no effect on the cytodifferentiation of HPDL cells. These data suggest that Smpd3 plays a crucial role in maintaining the homeostasis of PDL tissue.
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Affiliation(s)
- S. Miyauchi
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - J. Kitagaki
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - R. Masumoto
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - A. Imai
- Department of Genome Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - K. Kobayashi
- Department of Genome Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Medical Solutions Division, NEC Corporation, Minato-ku, Tokyo, Japan
| | - A. Nakaya
- Department of Genome Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - S. Kawai
- Challenge to Intractable Oral Disease, Center for Frontier Oral Science, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - C. Fujihara
- Challenge to Intractable Oral Disease, Center for Translational Dental Research, Osaka University Dental Hospital, Suita, Osaka, Japan
| | - Y. Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - M. Yamashita
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - M. Yanagita
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - S. Yamada
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - M. Kitamura
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - S. Murakami
- Department of Periodontology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
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Miyauchi S, Navarro D, Grigoriev IV, Lipzen A, Riley R, Chevret D, Grisel S, Berrin JG, Henrissat B, Rosso MN. Visual Comparative Omics of Fungi for Plant Biomass Deconstruction. Front Microbiol 2016; 7:1335. [PMID: 27605927 PMCID: PMC4996036 DOI: 10.3389/fmicb.2016.01335] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/12/2016] [Indexed: 11/13/2022] Open
Abstract
Wood-decay fungi contain the cellular mechanisms to decompose such plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant plant biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.
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Affiliation(s)
- Shingo Miyauchi
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France
| | - David Navarro
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie FongiquesMarseille, France; CIRM-CF, UMR1163 Biodiversité et Biotechnologie FongiquesMarseille, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Didier Chevret
- Plateforme d'Analyse Protéomique de Paris Sud-Ouest, UMR1319 Micalis, INRA Jouy-en-Josas, France
| | - Sacha Grisel
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Jean-Guy Berrin
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille UniversitéMarseille, France; INRA, USC 1408 AFMBMarseille, France; Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Marie-Noëlle Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France
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Kawano A, Umekita K, Matsuda M, Kubo K, Miyauchi S, Komura M, Takajo I, Nagatomo Y, Okayama A. AB0589 Hypercoagulable State Might Be Induced by Alveolar-Endothelial Damages in Interstitial Lung Disease Associated with Polymyositis/dermatomyositis. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.2857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Umekita K, Miyauchi S, Matsuda M, Kubo K, Komura M, Nomura H, Kawano A, Umeki K, Takajo I, Nagatomo Y, Frank-Bertoncelj M, Gay R, Gay S, Okayama A. AB0027 A Novel Transcription Factor NFAT5 Plays An Important Role as Critical Regulator in The Inflammatory Response of Rheumatoid Arthritis Fibroblasts Mediated via Toll-Like Receptor 4 Signaling Pathways. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.1676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Lawson JS, Glenn WK, Salyakina D, Clay R, Delprado W, Cheerala B, Tran DD, Ngan CC, Miyauchi S, Karim M, Antonsson A, Whitaker NJ. Human Papilloma Virus Identification in Breast Cancer Patients with Previous Cervical Neoplasia. Front Oncol 2016; 5:298. [PMID: 26779441 PMCID: PMC4705232 DOI: 10.3389/fonc.2015.00298] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/14/2015] [Indexed: 11/13/2022] Open
Abstract
Purpose Women with human papilloma virus (HPV)-associated cervical neoplasia have a higher risk of developing breast cancer than the general female population. The purpose of this study was to (i) identify high-risk HPVs in cervical neoplasia and subsequent HPV positive breast cancers which developed in the same patients and (ii) determine if these HPVs were biologically active. Methods A range of polymerase chain reaction and immunohistochemical techniques were used to conduct a retrospective cohort study of cervical precancers and subsequent breast cancers in the same patients. Results The same high-risk HPV types were identified in both the cervical and breast specimens in 13 (46%) of 28 patients. HPV type 18 was the most prevalent. HPVs appeared to be biologically active as demonstrated by the expression of HPV E7 proteins and the presence of HPV-associated koilocytes. The average age of these patients diagnosed with breast cancer following prior cervical precancer was 51 years, as compared to 60 years for all women with breast cancer (p for difference = 0.001). Conclusion These findings indicate that high-risk HPVs can be associated with cervical neoplasia and subsequent young age breast cancer. However, these associations are unusual and are a very small proportion of breast cancers. These outcomes confirm and extend the observations of two similar previous studies and offer one explanation for the increased prevalence of serious invasive breast cancer among young women.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Daria Salyakina
- Center for Computational Science, University of Miami , Miami, FL , USA
| | - Rosemary Clay
- Douglass Hanly Moir - Pathology , Macquarie Park, NSW , Australia
| | - Warick Delprado
- Douglass Hanly Moir - Pathology , Macquarie Park, NSW , Australia
| | | | - Dinh D Tran
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Christopher C Ngan
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Shingo Miyauchi
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Martha Karim
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Annika Antonsson
- QIMR Berghofer Medical Research Institute , Brisbane, QLD , Australia
| | - Noel J Whitaker
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
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Lawson JS, Glenn WK, Salyakina D, Delprado W, Clay R, Antonsson A, Heng B, Miyauchi S, Tran DD, Ngan CC, Lutze-Mann L, Whitaker NJ. Human Papilloma Viruses and Breast Cancer. Front Oncol 2015; 5:277. [PMID: 26734565 PMCID: PMC4679879 DOI: 10.3389/fonc.2015.00277] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/26/2015] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Human papillomaviruses (HPV) may have a role in some breast cancers. The purpose of this study is to fill important gaps in the evidence. These gaps are: (i) confirmation of the presence of high risk for cancer HPVs in breast cancers, (ii) evidence of HPV infections in benign breast tissues prior to the development of HPV-positive breast cancer in the same patients, (iii) evidence that HPVs are biologically active and not harmless passengers in breast cancer. METHODS RNA-seq data from The Cancer Genome Atlas (TCGA) was used to identify HPV RNA sequences in breast cancers. We also conducted a retrospective cohort study based on polymerase chain reaction (PCR) analyses to identify HPVs in archival specimens from Australian women with benign breast biopsies who later developed breast cancer. To assess whether HPVs in breast cancer were biologically active, the expression of the oncogenic protein HPV E7 was assessed by immunohistochemistry (IHC). RESULTS Thirty (3.5%) low-risk and 20 (2.3%) high-risk HPV types were identified in 855 breast cancers from the TCGA database. The high risk types were HPV 18 (48%), HPV 113 (24%), HPV 16 (10%), HPV 52 (10%). Data from the PCR cohort study indicated that HPV type 18 was the most common type identified in breast cancer specimens (55% of 40 breast cancer specimens) followed by HPV 16 (13%). The same HPV type was identified in both the benign and subsequent breast cancer in 15 patients. HPV E7 proteins were identified in 72% of benign breast specimens and 59% of invasive breast cancer specimens. CONCLUSION There were four observations of particular interest: (i) confirmation by both NGS and PCR of the presence of high-risk HPV gene sequences in breast cancers, (ii) a correlation between high-risk HPV in benign breast specimens and subsequent HPV-positive breast cancer in the same patient, (iii) HPVs in breast cancer are likely to be biologically active (as shown by transcription of HPV DNA to RNA plus the expression of HPV E7 proteins), (iv) HPV oncogenic influences may occur early in the development of breast cancer.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Daria Salyakina
- Center for Computational Science, University of Miami , Miami, FL , USA
| | - Warick Delprado
- Douglass Hanly Moir Pathology , Macquarie Park, NSW , Australia
| | - Rosemary Clay
- Douglass Hanly Moir Pathology , Macquarie Park, NSW , Australia
| | - Annika Antonsson
- QIMR Berghofer Medical Research Institute , Brisbane, QLD , Australia
| | - Benjamin Heng
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Shingo Miyauchi
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Dinh D Tran
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Christopher C Ngan
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Louise Lutze-Mann
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
| | - Noel J Whitaker
- School of Biotechnology and Biomolecular Science, University of New South Wales , Sydney, NSW , Australia
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Umekita K, Hidaka T, Miyauchi S, Kubo K, Hashiba Y, Okayama A. AB0124 Tocilizumab is Clinically Effective and Safe for Human T-Lymphotropic Virus Type 1 Positive Patients with Rheumatoid Arthritis Who Are Not Responsive to Anti-TNF Treatment. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.1629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ono M, Miyauchi S, Edzuki Y, Saiki K, Fukuda H, Tonai M, Magilvy J, Murashima S. J
apanese nurse practitioner practice and outcomes in a nursing home. Int Nurs Rev 2014; 62:275-9. [DOI: 10.1111/inr.12158] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Ono
- Division of General and Gerontological Nursing Department of Specialized Nursing Oita University of Nursing and Health Sciences Oita Japan
| | - S. Miyauchi
- Division of Linguistics Oita University of Nursing and Health Sciences Oita Japan
| | - Y. Edzuki
- Division of General and Gerontological Nursing Department of Specialized Nursing Oita University of Nursing and Health Sciences Oita Japan
| | - K. Saiki
- Division of Health Informatics and Biostatistics Department of Human Sciences Oita University of Nursing and Health Sciences Oita Japan
| | - H. Fukuda
- The Center for Nursing Education, Research and Collaboration Oita University of Nursing and Health Sciences Oita Japan
| | - M. Tonai
- Division of Nursing Assessment Department of Basic Nursing Sciences Oita University of Nursing and Health Sciences Oita Japan
| | - J.K. Magilvy
- College of Nursing University of Colorado Aurora CO USA
| | - S. Murashima
- Oita University of Nursing and Health Sciences Oita Japan
- Department of Community Health Nursing University of Tokyo Tokyo Japan
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