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Navarro-Mendoza MI, Pérez-Arques C, Parker J, Xu Z, Kelly S, Heitman J. Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex. mBio 2024; 15:e0166124. [PMID: 38980037 PMCID: PMC11323496 DOI: 10.1128/mbio.01661-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and, consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis. IMPORTANCE The Mucor species complex comprises a variety of opportunistic pathogens known to cause mucormycosis, a potentially lethal fungal infection with limited therapeutic options. The only effective first-line treatments against mucormycosis consist of liposomal formulations of amphotericin B and the triazoles posaconazole and isavuconazole, all of which target components within the ergosterol biosynthetic pathway. This study uncovered M. circinelloides Erg3 and Erg6a as key enzymes to produce ergosterol, a vital constituent of fungal membranes. Absence of any of those enzymes leads to decreased ergosterol and consequently, resistance to ergosterol-binding polyenes such as amphotericin B. Particularly, losing Erg6a function poses a higher threat as the ergosterol pathway is channeled into alternative sterols similar to cholesterol, which maintain membrane permeability. As a result, erg6a mutants survive within the host and disseminate the infection, indicating that Erg6a deficiency may arise during human infections and confer resistance to the most effective treatment against mucormycoses.
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Affiliation(s)
- María Isabel Navarro-Mendoza
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Carlos Pérez-Arques
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Josie Parker
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ziyan Xu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Steven Kelly
- Institute of Life Science, Swansea University Medical School, Swansea, Wales, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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Navarro-Mendoza MI, Pérez-Arques C, Parker J, Xu Z, Kelly S, Heitman J. Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.01.569667. [PMID: 38076934 PMCID: PMC10705545 DOI: 10.1101/2023.12.01.569667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis.
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3
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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Nguyen TTT, Santiago ALCMDA, Kirk PM, Lee HB. Discovery of a New Lichtheimia (Lichtheimiaceae, Mucorales) from Invertebrate Niche and Its Phylogenetic Status and Physiological Characteristics. J Fungi (Basel) 2023; 9:jof9030317. [PMID: 36983485 PMCID: PMC10056009 DOI: 10.3390/jof9030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Species of Lichtheimia are important opportunistic fungal pathogens in the order Mucorales that are isolated from various sources such as soil, indoor air, food products, feces, and decaying vegetables. In recent years, species of Lichtheimia have become an emerging causative agent of invasive mucormycosis. In Europe and USA, Lichtheimia are the second and third most common causal fungus of mucormycosis, respectively. Thus, the aim of this study was to survey the diversity of species of Lichtheimia hidden in poorly studied hosts, such as invertebrates, in Korea. Eight Lichtheimia strains were isolated from invertebrate samples. Based on morphology, physiology, and phylogenetic analyses of ITS and LSU rDNA sequence data, the strains were identified as L. hyalospora, L. ornata, L. ramosa, and a novel species, L. koreana sp. nov. Lichtheimia koreana is characterized by a variable columellae, sporangiophores arising solitarily or up to three at one place from stolons, and slow growth on MEA and PDA at all temperatures tested. The new species grows best at 30 and 35 °C and has a maximum growth temperature of 40 °C. Detailed descriptions, illustrations, and a phylogenetic tree are provided.
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Affiliation(s)
- Thuong T. T. Nguyen
- Environmental Microbiology Laboratory, Department of Agricultural Biological Chemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | | | - Paul M. Kirk
- Biodiversity Informatics and Spatial Analysis, Jodrell Laboratory, Royal Botanic Gardens Kew, Surrey TW9 3DS, UK
| | - Hyang Burm Lee
- Departamento de Micologia, Universidade Federal de Pernambuco, Av. da Engenharia, s/n, Recife 50740-4600, PE, Brazil
- Correspondence:
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Zhao H, Nie Y, Jiang Y, Wang S, Zhang TY, Liu XY. Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase. J Fungi (Basel) 2022; 8:jof8090891. [PMID: 36135616 PMCID: PMC9503022 DOI: 10.3390/jof8090891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and β comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.
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Affiliation(s)
- Heng Zhao
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan 243002, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Shi Wang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Tian-Yu Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence:
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He GQ, Xiao L, Pan Z, Wu JR, Liang DN, Guo X, Jiang MY, Gao J. Case report: A rare case of pulmonary mucormycosis caused by Lichtheimia ramosa in pediatric acute lymphoblastic leukemia and review of Lichtheimia infections in leukemia. Front Oncol 2022; 12:949910. [PMID: 36046038 PMCID: PMC9421258 DOI: 10.3389/fonc.2022.949910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Mucormycosis caused by Lichtheimia ramosa is an emerging and uncommon opportunistic infection in patients with hematological malignancies, with high mortality rates. Herein, we first report a case of pulmonary mucormycosis with Lichtheimia ramosa in a 3-year-old girl recently diagnosed with B-cell acute lymphoblastic leukemia. The diagnosis was made using computerized tomography of the lung, metagenomic next-generation sequencing (mNGS) of blood and sputum specimens, and microscopic examination to detect the development of Lichtheimia ramosa on the surgical specimen. She was effectively treated after receiving prompt treatment with amphotericin B and posaconazole, followed by aggressive surgical debridement. In our case, the fungal isolates were identified as Lichtheimia ramosa using mNGS, which assisted clinicians in quickly and accurately diagnosing and initiating early intensive treatment. This case also indicated the importance of strong clinical suspicion, as well as aggressive antifungal therapy combined with surgical debridement of affected tissues.
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Affiliation(s)
- Guo-qian He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | | | - Zhen Pan
- Sichuan University, Chengdu, China
| | - Jian-rong Wu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Dong-ni Liang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xia Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ming-yan Jiang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ming-yan Jiang,
| | - Ju Gao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
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Stanford FA, Matthies N, Cseresnyés Z, Figge MT, Hassan MIA, Voigt K. Expression Patterns in Reductive Iron Assimilation and Functional Consequences during Phagocytosis of Lichtheimia corymbifera, an Emerging Cause of Mucormycosis. J Fungi (Basel) 2021; 7:jof7040272. [PMID: 33916756 PMCID: PMC8065604 DOI: 10.3390/jof7040272] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 12/30/2022] Open
Abstract
Iron is an essential micronutrient for most organisms and fungi are no exception. Iron uptake by fungi is facilitated by receptor-mediated internalization of siderophores, heme and reductive iron assimilation (RIA). The RIA employs three protein groups: (i) the ferric reductases (Fre5 proteins), (ii) the multicopper ferroxidases (Fet3) and (iii) the high-affinity iron permeases (Ftr1). Phenotyping under different iron concentrations revealed detrimental effects on spore swelling and hyphal formation under iron depletion, but yeast-like morphology under iron excess. Since access to iron is limited during pathogenesis, pathogens are placed under stress due to nutrient limitations. To combat this, gene duplication and differential gene expression of key iron uptake genes are utilized to acquire iron against the deleterious effects of iron depletion. In the genome of the human pathogenic fungus L. corymbifera, three, four and three copies were identified for FRE5, FTR1 and FET3 genes, respectively. As in other fungi, FET3 and FTR1 are syntenic and co-expressed in L. corymbifera. Expression of FRE5, FTR1 and FET3 genes is highly up-regulated during iron limitation (Fe-), but lower during iron excess (Fe+). Fe- dependent upregulation of gene expression takes place in LcFRE5 II and III, LcFTR1 I and II, as well as LcFET3 I and II suggesting a functional role in pathogenesis. The syntenic LcFTR1 I–LcFET3 I gene pair is co-expressed during germination, whereas LcFTR1 II- LcFET3 II is co-expressed during hyphal proliferation. LcFTR1 I, II and IV were overexpressed in Saccharomyces cerevisiae to represent high and moderate expression of intracellular transport of Fe3+, respectively. Challenge of macrophages with the yeast mutants revealed no obvious role for LcFTR1 I, but possible functions of LcFTR1 II and IVs in recognition by macrophages. RIA expression pattern was used for a new model of interaction between L. corymbifera and macrophages.
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Affiliation(s)
- Felicia Adelina Stanford
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute (HKI), 07745 Jena, Germany; (F.A.S.); (N.M.); (M.I.A.H.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Nina Matthies
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute (HKI), 07745 Jena, Germany; (F.A.S.); (N.M.); (M.I.A.H.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Zoltán Cseresnyés
- Applied Systems Biology, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute, 12622 Jena, Germany;
| | - Marc Thilo Figge
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Applied Systems Biology, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute, 12622 Jena, Germany;
| | - Mohamed I. Abdelwahab Hassan
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute (HKI), 07745 Jena, Germany; (F.A.S.); (N.M.); (M.I.A.H.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany;
- National Research Centre, Pests & Plant Protection Department, 33rd El Buhouth St., Dokki, Giza 12622, Egypt
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research, and Infection Biology—Hans Knöll Institute (HKI), 07745 Jena, Germany; (F.A.S.); (N.M.); (M.I.A.H.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Correspondence: or ; Tel.: +49-3641-532-1395
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8
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Muszewska A, Okrasińska A, Steczkiewicz K, Drgas O, Orłowska M, Perlińska-Lenart U, Aleksandrzak-Piekarczyk T, Szatraj K, Zielenkiewicz U, Piłsyk S, Malc E, Mieczkowski P, Kruszewska JS, Bernat P, Pawłowska J. Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina. Front Microbiol 2021; 12:636986. [PMID: 33679672 PMCID: PMC7928374 DOI: 10.3389/fmicb.2021.636986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.
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Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Alicja Okrasińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Olga Drgas
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Katarzyna Szatraj
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ewa Malc
- High Throughput Sequencing Facility of UNC, Chapel Hill, NC, United States
| | - Piotr Mieczkowski
- High Throughput Sequencing Facility of UNC, Chapel Hill, NC, United States
| | - Joanna S. Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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9
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A thermophilic fungal GH36 α-galactosidase from Lichtheimia ramosa and its synergistic hydrolysis of locust bean gum. Carbohydr Res 2020; 491:107911. [PMID: 32217360 DOI: 10.1016/j.carres.2020.107911] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 01/07/2023]
Abstract
A novel GH36 α-galactosidase gene (LrAgal36A) from Lichtheimia ramosa was synthesized and highly expressed in Pichia pastoris. The enzyme titer and protein yield for high-density fermentation in a 5 L fermentor were up to 953.6 U mL-1 and 4.36 g L-1. Purified recombinant LrAgal36A showed the maximum activity at pH 6.0 and 65 °C and was thermostable with a half-life of 70 min at 60 °C. LrAgal36A displayed the highest specific activity (353.17 ± 4.19 U mg-1) toward p-nitrophenyl-α-d-galactopyranoside (pNPGal) followed by galacto-oligosaccharides and could act slightly on galactomannans. The Km and catalytic efficiency (kcat/Km) of LrAgal36A for pNPGal were 0.33 mM and 1569.50 mM-1 s-1, respectively. LrAgal36A and GH5 β-mannanase from L. ramosa showed a significant synergistic effect on the degradation of locust bean gum (LBG), resulting in release more reducing sugars (1.56 folds) and galactose (7.6 folds) by simultaneous or sequential reactions. Due to its hydrolysis properties, LrAgal36A might have potential applications in the area of pulp biobleaching, feed and food processing.
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10
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de Almeida ÂB, Corrêa IP, Furuie JL, de Farias Pires T, do Rocio Dalzoto P, Pimentel IC. Inhibition of growth and ochratoxin A production in Aspergillus species by fungi isolated from coffee beans. Braz J Microbiol 2019; 50:1091-1098. [PMID: 31515726 DOI: 10.1007/s42770-019-00152-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/04/2019] [Indexed: 11/24/2022] Open
Abstract
Ochratoxin A (OTA) is a mycotoxin found in several agricultural commodities. Produced by Aspergillus spp., it is nephrotoxic and hepatotoxic and can be carcinogenic. Preventive measures are preventing fungal growth and OTA production. In this study, fungal strains (Rhizopus oryzae, Lichtheimia ramosa, Aspergillus westerdijkiae, Aspergillus niger, Aspergillus tamarii, Aspergillus sp., and Aspergillus fumigatus) isolated from coffee beans were identified for their abilities to inhibit the growth of Aspergillus ochraceus, Aspergillus westerdijkiae, Aspergillus carbonarius, and Aspergillus niger, and OTA production. All fungi strains tested were able to inhibit growth of the four Aspergillus species and OTA production, where A. niger showed the best results in both tests. L. ramosa showed the lowest growth-reducing potential, while the other fungal strains had a growth-reducing potential higher than 70% against all Aspergillus species tested. Regarding OTA production, L. ramosa and Aspergillus sp. completely inhibited the mycotoxin production by A. ochraceus and non-toxigenic strain A. niger completely inhibited OTA production by A. niger. Our findings indicate that the strains tested can be used as an alternative means to control growth of OTA-producing fungi and production of the mycotoxin in coffee beans.
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Affiliation(s)
- Ângela Bozza de Almeida
- Departamento de Patologia Básica, Laboratório de Microbiologia e Biologia Molecular, Universidade Federal do Paraná, Setor de Ciências Biológicas, Paraná, Brazil
| | - Isabela Pauluk Corrêa
- Departamento de Patologia Básica, Laboratório de Microbiologia e Biologia Molecular, Universidade Federal do Paraná, Setor de Ciências Biológicas, Paraná, Brazil
| | - Jason Lee Furuie
- Departamento de Patologia Básica, Laboratório de Microbiologia e Biologia Molecular, Universidade Federal do Paraná, Setor de Ciências Biológicas, Paraná, Brazil.
| | - Thiago de Farias Pires
- Laboratório de Genética e Cardiologia Molecular, Universidade de São Paulo, Instituto do Coração, São Paulo, Brazil
| | - Patrícia do Rocio Dalzoto
- Departamento de Patologia Básica, Laboratório de Microbiologia e Biologia Molecular, Universidade Federal do Paraná, Setor de Ciências Biológicas, Paraná, Brazil
| | - Ida Chapaval Pimentel
- Departamento de Patologia Básica, Laboratório de Microbiologia e Biologia Molecular, Universidade Federal do Paraná, Setor de Ciências Biológicas, Paraná, Brazil
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11
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Nian HJ, Li S, Wang J, Yang XX, Ji XL, Lin LB, Wei YL, Zhang Q. Expression, Purification and Functional Characterization of Two Recombinant Malate Dehydrogenases from Mortierella isabellina. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819030098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Lacombe-Harvey MÈ, Brzezinski R, Beaulieu C. Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution. Appl Microbiol Biotechnol 2018; 102:7219-7230. [PMID: 29931600 PMCID: PMC6097792 DOI: 10.1007/s00253-018-9149-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022]
Abstract
Actinobacteria, a large group of Gram-positive bacteria, secrete a wide range of extracellular enzymes involved in the degradation of organic compounds and biopolymers including the ubiquitous aminopolysaccharides chitin and chitosan. While chitinolytic enzymes are distributed in all kingdoms of life, actinobacteria are recognized as particularly good decomposers of chitinous material and several members of this taxon carry impressive sets of genes dedicated to chitin and chitosan degradation. Degradation of these polymers in actinobacteria is dependent on endo- and exo-acting hydrolases as well as lytic polysaccharide monooxygenases. Actinobacterial chitinases and chitosanases belong to nine major families of glycosyl hydrolases that share no sequence similarity. In this paper, the distribution of chitinolytic actinobacteria within different ecosystems is examined and their chitinolytic machinery is described and compared to those of other chitinolytic organisms.
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Affiliation(s)
| | - Ryszard Brzezinski
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Carole Beaulieu
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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14
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Hüttner S, Granchi Z, Nguyen TT, van Pelt S, Larsbrink J, Thanh VN, Olsson L. Genome sequence of Rhizomucor pusillus FCH 5.7, a thermophilic zygomycete involved in plant biomass degradation harbouring putative GH9 endoglucanases. ACTA ACUST UNITED AC 2018; 20:e00279. [PMID: 30211016 PMCID: PMC6132078 DOI: 10.1016/j.btre.2018.e00279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 11/12/2022]
Abstract
R. pusillus encodes cellulose-, xylan- and chitin-degrading proteins. Two putative GH9 endoglucanases were identified. Enzyme system of R. pusillus is suited to consume easily accessible sugars. Endoglucanase and xylanase activity detected when the fungus was grown on wheat bran and xylan.
We report here the annotated draft genome sequence of the thermophilic zygomycete Rhizomucor pusillus strain FCH 5.7, isolated from compost soil in Vietnam. The genome assembly contains 25.59 Mb with an overall GC content of 44.95%, and comprises 10,898 protein coding genes. Genes encoding putative cellulose-, xylan- and chitin-degrading proteins were identified, including two putative endoglucanases (EC 3.2.1.4) from glycoside hydrolase family 9, which have so far been mostly assigned to bacteria and plants.
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Affiliation(s)
- Silvia Hüttner
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Thanh Thuy Nguyen
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Viet Nam
| | - Sake van Pelt
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Johan Larsbrink
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Vu Nguyen Thanh
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Viet Nam
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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15
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Diversity of mucoralean fungi in soils of papaya (Carica papaya L.) producing regions in Mexico. Fungal Biol 2018; 122:810-816. [PMID: 30007431 DOI: 10.1016/j.funbio.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 11/22/2022]
Abstract
Mexico is the fifth largest producer of papaya worldwide and has recently reported problems with mucoralean fungi in this crop. These fungi are considered saprophytes in the soil and are ubiquitous in nature. In this work, they were isolated from soil in regions of intensive papaya cultivation in Mexico. Collections were made in the states of Colima, Oaxaca and Veracruz in Apr 2016. A total of 72 mucorales fungal isolates was obtained and morphologically characterized and then molecular characterization (28S ribosomal region) of 25 representative isolates was carried out. Phylogenetic analysis of the sequences confirmed the presence of the species Gilbertella persicaria, Rhizopus oryzae, Rhizopus stolonifer, Mucor circinelloides and Mucor hiemalis, which cause soft rot in papaya fruits, therefore, spores of these fungi found in the orchard soils can be considered as a constant source of contamination that affects healthy fruits. Additionally, Choanephora cucurbitarum, Mucor ellipsoideus, Rhizopus homothallicus, Rhizopus microsporus, Rhizopus schipperae, Lichteimia ramosa, Gongronella butleri, Cunninghamella bertholletiae and Cunninghamella blakesleeana were identified which are considered to have agricultural, biotechnological and medical importance.
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16
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Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun 2016; 7:12218. [PMID: 27447865 PMCID: PMC4961843 DOI: 10.1038/ncomms12218] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets.
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Affiliation(s)
- Marcus C. Chibucos
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sameh Soliman
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Teclegiorgis Gebremariam
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Hongkyu Lee
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Tracy H. Hazen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kizee A. Etienne
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David A. Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Shawn R. Lockhart
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher D. Skory
- National Center for Agriculture Utilization Research, USDA, Agricultural Research Service, Peoria, Illinois 61604, USA
| | - Ashraf S. Ibrahim
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Vincent M. Bruno
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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17
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Abstract
Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.
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18
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Chitosanases from Family 46 of Glycoside Hydrolases: From Proteins to Phenotypes. Mar Drugs 2015; 13:6566-87. [PMID: 26516868 PMCID: PMC4663542 DOI: 10.3390/md13116566] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Chitosanases, enzymes that catalyze the endo-hydrolysis of glycolytic links in chitosan, are the subject of numerous studies as biotechnological tools to generate low molecular weight chitosan (LMWC) or chitosan oligosaccharides (CHOS) from native, high molecular weight chitosan. Glycoside hydrolases belonging to family GH46 are among the best-studied chitosanases, with four crystallography-derived structures available and more than forty enzymes studied at the biochemical level. They were also subjected to numerous site-directed mutagenesis studies, unraveling the molecular mechanisms of hydrolysis. This review is focused on the taxonomic distribution of GH46 proteins, their multi-modular character, the structure-function relationships and their biological functions in the host organisms.
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19
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Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Brakhage AA, Valiante V. Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. GENOME ANNOUNCEMENTS 2015; 3:e00724-15. [PMID: 26337871 PMCID: PMC4559720 DOI: 10.1128/genomea.00724-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/24/2015] [Indexed: 02/02/2023]
Abstract
The genus Penicillium belongs to the phylum Ascomycota and includes a variety of fungal species important for food and drug production. We report the draft genome sequence of Penicillium brasilianum MG11. This strain was isolated from soil, and it was reported to produce different secondary metabolites.
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Affiliation(s)
- Fabian Horn
- Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Jörg Linde
- Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Grit Walther
- National Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Reinhard Guthke
- Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany Friedrich Schiller University, Institute for Microbiology, Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
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20
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Chibucos MC, Etienne KA, Orvis J, Lee H, Daugherty S, Lockhart SR, Ibrahim AS, Bruno VM. The genome sequence of four isolates from the family Lichtheimiaceae. Pathog Dis 2015; 73:ftv024. [PMID: 25857734 PMCID: PMC4467520 DOI: 10.1093/femspd/ftv024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/24/2015] [Accepted: 03/23/2015] [Indexed: 01/25/2023] Open
Abstract
This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi.
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Affiliation(s)
- Marcus C Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kizee A Etienne
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hongkyu Lee
- The Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles (UCLA) Medical Center, Torrance, CA 90502, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shawn R Lockhart
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Ashraf S Ibrahim
- The Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles (UCLA) Medical Center, Torrance, CA 90502, USA David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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21
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Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C. Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. GENOME ANNOUNCEMENTS 2015; 3:e01370-14. [PMID: 25614557 PMCID: PMC4319578 DOI: 10.1128/genomea.01370-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022]
Abstract
Specific Rhizopus microsporus pathovars harbor bacterial endosymbionts (Burkholderia rhizoxinica) for the production of a phytotoxin. Here, we present the draft genome sequences of two R. microsporus strains, one symbiotic (ATCC 62417), and one endosymbiont-free (CBS 344.29). The gene predictions were supported by RNA sequencing (RNA-seq) data. The functional annotation sets the basis for comparative analyses.
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Affiliation(s)
- Fabian Horn
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Zerrin Üzüm
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Nadine Möbius
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
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22
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Horn F, Habel A, Scharf DH, Dworschak J, Brakhage AA, Guthke R, Hertweck C, Linde J. Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. GENOME ANNOUNCEMENTS 2015; 3:e01439-14. [PMID: 25614560 PMCID: PMC4319583 DOI: 10.1128/genomea.01439-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
Verticillium hemipterigenum (anamorph Torrubiella hemipterigena) is an entomopathogenic fungus and produces a broad range of secondary metabolites. Here, we present the draft genome sequence of the fungus, including gene structure and functional annotation. Genes were predicted incorporating RNA-Seq data and functionally annotated to provide the basis for further genome studies.
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Affiliation(s)
- Fabian Horn
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Andreas Habel
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Daniel H Scharf
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Jan Dworschak
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Axel A Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
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23
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Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O. Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 2015; 43:1392-406. [PMID: 25586221 PMCID: PMC4330350 DOI: 10.1093/nar/gku1357] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host–pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.
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Affiliation(s)
- Jörg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Seána Duggan
- Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Michael Weber
- Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Fabian Horn
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Patricia Sieber
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany Department of Bioinformatics, Faculty of Biology and Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Daniela Hellwig
- Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Konstantin Riege
- Research Group Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Sciences, Friedrich Schiller University, Jena, Germany
| | - Manja Marz
- Research Group Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Sciences, Friedrich Schiller University, Jena, Germany
| | - Ronny Martin
- Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Oliver Kurzai
- Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany National Reference Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
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Priebe S, Kreisel C, Horn F, Guthke R, Linde J. FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 2014; 31:445-6. [PMID: 25294921 PMCID: PMC4308660 DOI: 10.1093/bioinformatics/btu627] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Summary: Systematically extracting biological meaning from omics data is a major challenge in systems biology. Enrichment analysis is often used to identify characteristic patterns in candidate lists. FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins. The novel tool FungiFun2 uses a completely revised data management system and thus allows enrichment analysis for 298 currently available fungal strains published in standard databases. FungiFun2 offers a modern Web interface and creates interactive tables, charts and figures, which users can directly manipulate to their needs. Availability and implementation: FungiFun2, examples and tutorials are publicly available at https://elbe.hki-jena.de/fungifun/. Contact: steffen.priebe@hki-jena.de or joerg.linde@hki-jena.de
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Affiliation(s)
- Steffen Priebe
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Kreisel
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Fabian Horn
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jörg Linde
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
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