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Zhang S, Wang S, Fang Z, Lang BF, Zhang YJ. Characterization of the mitogenome of Gongronella sp. w5 reveals substantial variation in Mucoromycota. Appl Microbiol Biotechnol 2022; 106:2587-2601. [PMID: 35318523 DOI: 10.1007/s00253-022-11880-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 03/06/2022] [Indexed: 11/02/2022]
Abstract
Gongronella is a genus of fungi in Mucorales (Mucoromycota). Some of its members have important biotechnological applications, but until now, not a single mitogenome has been characterized in Gongronella. Here, we present the complete mitogenome assembly of Gongronella sp. w5, a soil isolate known to interact with plants and several fungi. Its 36,593-bp circular mitogenome encodes the large and small subunit rRNAs, 14 standard mitochondrial proteins, 24 tRNAs, three free-standing ORF proteins, and the RNA subunit of RNase P (rnpB). These genes arrange in an order novel to known fungal mitogenomes. Three group I introns are present in the cob, cox1, and nad5 genes, respectively, and they are probably acquired by horizontal gene transfer. Phylogenetic analysis based on mitochondrion-encoded proteins supports the grouping of Gongronella sp. w5 with Absidia glauca, forming the Cunninghamellaceae clade within Mucoromycota. Gongronella and most other Mucoromycota species are predicted to use the standard genetic code in mitochondrial translation, rather than code 4 assigned by GenBank. A comparison among seven publicly available mitogenomes in Mucoromycota reveals the presence of the same 14 typical protein-coding genes plus rnpB, yet substantial variation in mitogenome size, intron number, gene order, and orientation. In this comparison, the uniqueness of Gongronella is evident from similarly large differences to its closest phylogenetic neighbor, A. glauca. This study promotes our understanding of fungal evolution in Mucoromycota. KEY POINTS: • This study reports the first mitogenome in Gongronella, which presents a novel gene order. • Different Mucoromycota mitogenomes show substantial variation of gene organizations. • Most Mucoromycota species use the standard genetic code to translate mitochondrial genes.
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Affiliation(s)
- Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shuang Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - B Franz Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Montreal, Québec, H3T 1J4, Canada.
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
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Nie Y, Wang L, Cai Y, Tao W, Zhang YJ, Huang B. Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi. Appl Microbiol Biotechnol 2018; 103:1379-1391. [PMID: 30569217 DOI: 10.1007/s00253-018-9549-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Entomophthoroid fungi represent an ecologically important group of fungal pathogens on insects. Here, the whole mitogenome of Conidiobolus heterosporus, one of the entomophthoroid fungi, was described and compared to those early branching fungi with available mitogenomes. The 53,364-bp circular mitogenome of C. heterosporus contained two rRNA genes, 14 standard protein-coding genes, 26 tRNA genes, and three free-standing ORFs. Thirty introns interrupted nine mitochondrial genes. Phylogenetic analysis based on mitochondrion-encoded proteins revealed that C. heterosporus was most close to Zancudomyces culisetae in the Zoopagomycota of basal fungi. Comparison on mitogenomes of 23 basal fungi revealed great variabilities in terms of mitogenome conformation (circular or linear), genetic code (codes 1, 4, or 16), AT contents (53.3-85.5%), etc. These mitogenomes varied from 12.0 to 97.3 kb in sizes, mainly due to different numbers of genes and introns. They showed frequent DNA rearrangement events and a high variability of gene order, although high synteny and conserved gene order were also present between closely related species. By reporting the first mitogenome in Entomophthoromycotina and the second in Zoopagomycota, this study greatly enhanced our understanding on evolution of basal fungi.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, 243002, China
| | - Lin Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Yue Cai
- Department of Biological and Environmental Engineering, Hefei University, Hefei, 230601, China
| | - Wei Tao
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.
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Abstract
The pathogenic entomophthoralean fungi cause infection in insects and mammalian hosts. Basidiobolus and Conidiobolus species can be found in soil and insect, reptile, and amphibian droppings in tropical and subtropical areas. The life cycles of these fungi occur in these environments where infecting sticky conidia are developed. The infection is acquired by insect bite or contact with contaminated environments through open skin. Conidiobolus coronatus typically causes chronic rhinofacial disease in immunocompetent hosts, whereas some Conidiobolus species can be found in immunocompromised patients. Basidiobolus ranarum infection is restricted to subcutaneous tissues but may be involved in intestinal and disseminated infections. Its early diagnosis remains challenging due to clinical similarities to other intestinal diseases. Infected tissues characteristically display eosinophilic granulomas with the Splendore-Höeppli phenomenon. However, in immunocompromised patients, the above-mentioned inflammatory reaction is absent. Laboratory diagnosis includes wet mount, culture serological assays, and molecular methodologies. The management of entomophthoralean fungi relies on traditional antifungal therapies, such as potassium iodide (KI), amphotericin B, itraconazole, and ketoconazole, and surgery. These species are intrinsically resistant to some antifungals, prompting physicians to experiment with combinations of therapies. Research is needed to investigate the immunology of entomophthoralean fungi in infected hosts. The absence of an animal model and lack of funding severely limit research on these fungi.
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Affiliation(s)
- Raquel Vilela
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, Michigan, USA
- Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Leonel Mendoza
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, Michigan, USA
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Mbenoun M, Wingfield MJ, Letsoalo T, Bihon W, Wingfield BD, Roux J. Independent origins and incipient speciation among host-associated populations of Thielaviopsis ethacetica in Cameroon. Fungal Biol 2015; 119:957-972. [PMID: 26466872 DOI: 10.1016/j.funbio.2015.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/01/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
Thielaviopsis ethacetica was recently reinstated as a distinct taxon using DNA phylogenies. It is widespread affecting several crop plants of global economic importance. In this study, microsatellite markers were developed and used in conjunction with sequence data to investigate the genetic diversity and structure of Th. ethacetica in Cameroon. A collection of 71 isolates from cacao, oil palm, and pineapple, supplemented with nine isolates from other countries were analysed. Four genetic groups were identified. Two of these were associated with oil palm in Cameroon and showed high genetic diversity, suggesting that they might represent an indigenous population of the pathogen. In contrast, the remaining two groups, associated with cacao and pineapple, had low genetic diversity and, most likely, represent introduced populations. There was no evidence of gene flow between these groups. Phylogenetic analyses based on sequences of the tef1-α as well as the combined flanking regions of six microsatellite loci were consistent with population genetic analyses and suggested that Th. ethacetica is comprised of two divergent genetic lineages.
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Affiliation(s)
- Michael Mbenoun
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa
| | - Teboho Letsoalo
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa
| | - Wubetu Bihon
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa; Agricultural Research Council-Vegetable and Ornamental Plant Institute (ARC-VOPI), Private Bag X293, Pretoria 0001, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa
| | - Jolanda Roux
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa.
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Metagenomic Approach Yields Insights into Fungal Diversity and Functioning. SPRINGERBRIEFS IN BIOLOGY 2014. [DOI: 10.1007/978-4-431-54261-2_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.
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Affiliation(s)
- David S Hibbett
- Biology Department, Clark University, Worcester, Massachusetts 01610
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Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12073] [Citation(s) in RCA: 365] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Johan Bengtsson-Palme
- Department of Neuroscience and Physiology; The Sahlgrenska Academy; University of Gothenburg; Box 434; 40530; Göteborg; Sweden
| | - Martin Ryberg
- Department of Organismal Biology; Uppsala University; Norbyvägen 18D; Uppsala; 75236; Sweden
| | | | - Sara Branco
- Department of Plant and Microbial Biology; University of California; Berkeley; CA; 94720-3102; USA
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology; Yale University; New Haven; CT 06520-8106; USA
| | - Anna Godhe
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Pierre De Wit
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville; TN; 37996-1610; USA
| | - Ingo Ebersberger
- Department for Applied Bioinformatics; Institute for Cell Biology and Neuroscience, Goethe University; Max-von-Laue Str. 13; Frankfurt; D-60438; Germany
| | - Filipe de Sousa
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Anthony S. Amend
- Botany Department; University of Hawai'i at Manoa; 3190 Maile Way; Honolulu; HI; 96822; USA
| | - Ari Jumpponen
- Division of Biology; Kansas State University; Manhattan; KS; 66506; USA
| | - Martin Unterseher
- Institute of Botany and Landscape Ecology; Ernst-Moritz-Arndt University Greifswald; Grimmer Str. 88; Greifswald; D-17487; Germany
| | - Erik Kristiansson
- Department of Mathematical Statistics; Chalmers University of Technology; Göteborg; 41296; Sweden
| | - Kessy Abarenkov
- Natural History Museum; University of Tartu; 46 Vanemuise Str.; Tartu; 51014; Estonia
| | - Yann J. K. Bertrand
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Kemal Sanli
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - K. Martin Eriksson
- Department of Shipping and Marine Technology; Chalmers University of Technology; Göteborg; 41296; Sweden
| | - Unni Vik
- Department of Biosciences; University of Oslo; PO Box 1066, Blindern; Oslo; N-0316; Norway
| | | | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
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Gryganskyi A, Humber R, Smith M, Hodge K, Huang B, Voigt K, Vilgalys R. Phylogenetic lineages in Entomophthoromycota. PERSOONIA 2013; 30:94-105. [PMID: 24027349 PMCID: PMC3734969 DOI: 10.3767/003158513x666330] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 01/02/2013] [Indexed: 12/01/2022]
Abstract
Entomophthoromycota is one of six major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular studies have shown the monophyly of Entomophthoromycota, thus justifying raising the taxonomic status of these fungi to a phylum. Multi-gene phylogenies have identified five major lineages of Entomophthoromycota. In this review we provide a detailed discussion about the biology and taxonomy of these lineages: I) Basidiobolus (Basidiobolomycetes: Basidiobolaceae; primarily saprobic); II) Conidiobolus (Entomophthoromycetes, Ancylistaceae; several clades of saprobes and invertebrate pathogens), as well as three rapidly evolving entomopathogenic lineages in the family Entomophthoraceae centering around; III) Batkoa; IV) Entomophthora and allied genera; and V) the subfamily Erynioideae which includes Zoophthora and allied genera. Molecular phylogenic analysis has recently determined the relationships of several taxa that were previously unresolved based on morphology alone: Eryniopsis, Macrobiotophthora, Massospora, Strongwellsea and two as yet undescribed genera of Basidiobolaceae.
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Affiliation(s)
- A.P. Gryganskyi
- Duke University, Department of Biology, Durham, NC 27708-90338, USA
| | - R.A. Humber
- USDA-ARS BioIPM Research, RW Holley Center for Agriculture & Health, 538 Tower Rd, Ithaca, NY 14853, USA
| | - M.E. Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - K. Hodge
- Department of Plant Pathology & Plant-Microbe Biology, Cornell University, 334 Plant Science Bldg, Ithaca, NY 14853, USA
| | - B. Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, 130 West Changjiang Rd, Hefei, Anhui 230036, China
| | - K. Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology and University of Jena, 11a Beutenbergstr., Jena 07745, Germany
| | - R. Vilgalys
- Duke University, Department of Biology, Durham, NC 27708-90338, USA
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Lee CM, Cho EM, Yang SI, Ganbold EO, Jun J, Cho KH. Raman Spectroscopy and Density Functional Theory Calculations of β-Glucans and Chitins in Fungal Cell Walls. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.3.943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Glass DJ, Takebayashi N, Olson LE, Taylor DL. Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling. Mol Phylogenet Evol 2013; 67:234-45. [PMID: 23403224 DOI: 10.1016/j.ympev.2013.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/09/2013] [Accepted: 01/29/2013] [Indexed: 01/31/2023]
Abstract
The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts, such as PCR chimeras, and biological artifacts such as pseudogenes or other paralogous sequences. Sequences that fall in basal positions in phylogenetic trees and appear distant from known sequences are particularly suspect. Phylogenetic analyses suggest that a novel sequence type (NS1) found in two boreal forest soil clone libraries belongs to the fungal kingdom but does not fall unambiguously within any known phylum. We have evaluated this sequence type using an array of secondary-structure analyses. To our knowledge, such analyses have never been used on environmental ribosomal sequences. Ribosomal secondary structure was modeled for four rRNA loci (ITS1, 5.8S, ITS2, 5' LSU). These models were analyzed for the presence of conserved domains, conserved nucleotide motifs, and compensatory base changes. Minimal free energy (MFE) foldings and GC contents of sequences representing the major fungal clades, as well as NS1, were also compared. NS1 displays secondary rRNA structures consistent with other fungi and many, but not all, conserved nucleotide motifs found across eukaryotes. However, our analyses show that many other authentic sequences from basal fungi lack more of these conserved motifs than does NS1. Together our findings suggest that NS1 represents an authentic gene copy. The methods described here can be used on any rRNA-coding sequence, not just environmental fungal sequences. As new-generation sequencing methods that yield shorter sequences become more widely implemented, methods that evaluate sequence authenticity should also be more widely implemented. For fungi, the adjacent 5.8S and ITS2 loci should be prioritized. This region is not only suited to distinguishing between closely related species, but it is also more informative in terms of expected secondary structure.
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Affiliation(s)
- Daniel J Glass
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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Ironside JE. Diversity and recombination of dispersed ribosomal DNA and protein coding genes in microsporidia. PLoS One 2013; 8:e55878. [PMID: 23405227 PMCID: PMC3566094 DOI: 10.1371/journal.pone.0055878] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 01/04/2013] [Indexed: 01/26/2023] Open
Abstract
Microsporidian strains are usually classified on the basis of their ribosomal DNA (rDNA) sequences. Although rDNA occurs as multiple copies, in most non-microsporidian species copies within a genome occur as tandem arrays and are homogenised by concerted evolution. In contrast, microsporidian rDNA units are dispersed throughout the genome in some species, and on this basis are predicted to undergo reduced concerted evolution. Furthermore many microsporidian species appear to be asexual and should therefore exhibit reduced genetic diversity due to a lack of recombination. Here, DNA sequences are compared between microsporidia with different life cycles in order to determine the effects of concerted evolution and sexual reproduction upon the diversity of rDNA and protein coding genes. Comparisons of cloned rDNA sequences between microsporidia of the genus Nosema with different life cycles provide evidence of intragenomic variability coupled with strong purifying selection. This suggests a birth and death process of evolution. However, some concerted evolution is suggested by clustering of rDNA sequences within species. Variability of protein-coding sequences indicates that considerable intergenomic variation also occurs between microsporidian cells within a single host. Patterns of variation in microsporidian DNA sequences indicate that additional diversity is generated by intragenomic and/or intergenomic recombination between sequence variants. The discovery of intragenomic variability coupled with strong purifying selection in microsporidian rRNA sequences supports the hypothesis that concerted evolution is reduced when copies of a gene are dispersed rather than repeated tandemly. The presence of intragenomic variability also renders the use of rDNA sequences for barcoding microsporidia questionable. Evidence of recombination in the single-copy genes of putatively asexual microsporidia suggests that these species may undergo cryptic sexual reproduction, a possibility with profound implications for the evolution of virulence, host range and drug resistance in these species.
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Affiliation(s)
- Joseph Edward Ironside
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom.
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14
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Abstract
Parasitism, aptly defined as one of the 'living-together' strategies (Trager, 1986), presents a dynamic system in which the parasite and its host are under evolutionary pressure to evolve new and specific adaptations, thus enabling the coexistence of the two closely interacting partners. Microsporidia are very frequently encountered obligatory intracellular protistan parasites that can infect both animals and some protists and are a consummate example of various aspects of the 'living-together' strategy. Microsporidia, relatives of fungi in the superkingdom Opisthokonta, belong to the relatively small group of parasites for which the host cell cytoplasm is the site of both reproduction and maturation. The structural and physiological reduction of their vegetative stage, together with the manipulation of host cell physiology, enables microsporidia to live in the cytosolic environment for most of their life cycle in a way resembling endocytobionts. The ability to form structurally complex spores and the invention and assembly of a unique injection mechanism enable microsporidia to disperse within host tissues and between host organisms, resulting in long-lasting infections. Microsporidia have adapted their genomes to the intracellular way of life, evolved strategies how to obtain nutrients directly from the host and how to manipulate not only the infected cells, but also the hosts themselves. The enormous variability of host organisms and their tissues provide microsporidian parasites a virtually limitless terrain for diversification and ecological expansion. This review attempts to present a general overview of microsporidia, emphasising some less known and/or more recently discovered facets of their biology.
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Gryganskyi AP, Humber RA, Smith ME, Miadlikowska J, Miadlikovska J, Wu S, Voigt K, Walther G, Anishchenko IM, Vilgalys R. Molecular phylogeny of the Entomophthoromycota. Mol Phylogenet Evol 2012; 65:682-94. [PMID: 22877646 DOI: 10.1016/j.ympev.2012.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 07/03/2012] [Accepted: 07/23/2012] [Indexed: 01/19/2023]
Abstract
The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90 million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 2012; 109:6241-6. [PMID: 22454494 DOI: 10.1073/pnas.1117018109] [Citation(s) in RCA: 2813] [Impact Index Per Article: 234.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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Morgenstern I, Powlowski J, Ishmael N, Darmond C, Marqueteau S, Moisan MC, Quenneville G, Tsang A. A molecular phylogeny of thermophilic fungi. Fungal Biol 2012; 116:489-502. [PMID: 22483047 DOI: 10.1016/j.funbio.2012.01.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/30/2012] [Indexed: 11/29/2022]
Abstract
Sequences from 86 fungal genomes and from the two outgroup genomes Arabidopsis thaliana and Drosophila melanogaster were analyzed to construct a robust molecular phylogeny of thermophilic fungi, which are potentially rich sources of industrial enzymes. To provide experimental reference points, growth characteristics of 22 reported thermophilic or thermotolerant fungi, together with eight mesophilic species, were examined at four temperatures: 22 °C, 34 °C, 45 °C, and 55 °C. Based on the relative growth performances, species with a faster growth rate at 45 °C than at 34 °C were classified as thermophilic, and species with better or equally good growth at 34 °C compared to 45 °C as thermotolerant. We examined the phylogenetic relationships of a diverse range of fungi, including thermophilic and thermotolerant species, using concatenated amino acid sequences of marker genes mcm7, rpb1, and rpb2 obtained from genome sequencing projects. To further elucidate the phylogenetic relationships in the thermophile-rich orders Sordariales and Eurotiales, we used nucleotide sequences from the nuclear ribosomal small subunit (SSU), the 5.8S gene with internal transcribed spacers 1 and 2 (ITS 1 and 2), and the ribosomal large subunit (LSU) to include additional species for analysis. These phylogenetic analyses clarified the position of several thermophilic taxa. Thus, Myriococcum thermophilum and Scytalidium thermophilum fall into the Sordariales as members of the Chaetomiaceae, Thermomyces lanuginosus belongs to the Eurotiales, Malbranchea cinnamomea is a member of the Onygenales, and Calcarisporiella thermophila is assigned to the basal fungi close to the Mucorales. The mesophilic alkalophile Acremonium alcalophilum clusters with Verticillium albo-atrum and Verticillium dahliae, placing them in the recently established order Glomerellales. Taken together, these data indicate that the known thermophilic fungi are limited to the Sordariales, Eurotiales, and Onygenales in the Ascomycota and the Mucorales with possibly an additional order harbouring C. thermophila in the basal fungi. No supporting evidence was found for thermophilic species belonging to the Basidiomycota.
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Affiliation(s)
- Ingo Morgenstern
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
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Proteomics shows new faces for the old penicillin producer Penicillium chrysogenum. J Biomed Biotechnol 2012; 2012:105109. [PMID: 22318718 PMCID: PMC3270403 DOI: 10.1155/2012/105109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/30/2011] [Accepted: 10/14/2011] [Indexed: 12/14/2022] Open
Abstract
Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new “omics” era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.
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Abstract
The purpose of this paper was to analyse the causes, pathogenesis, diagnostic modalities and treatment outcomes of microsporidial keratoconjunctivitis (MKC). Microsporidia are increasingly recognized as opportunistic infectious pathogens in immunocompromized patients causing keratoconjunctivitis. In the recent years, there has been a surge in reports of MKC in immunocompetent individuals presenting with stromal keratitis. A detailed literature search was done using Medline, OVID, Cochrane Library, UptoDate and Google Scholar databases with the terms microsporidia, keratitis, conjunctivitis, immunocompromized and immunocompetent. The articles were reviewed to determine the spectrum of clinical presentation, disease course, investigations, treatment modalities and outcome. Thirty-six publications were reviewed, and 151 cases of MKC were included for this review. The main presenting features included pain, redness, photophobia, epiphora and blurring of vision. Duration of the symptoms lasted between 4 days and 18 months. Light microscopy with modified trichrome stain was most commonly used to diagnose MKC. Resolution of symptoms was most commonly achieved with oral albendazole and/or topical fumidil B. Topical fluoroquinolones are also effective as a monotherapy as suggested by recent studies. Clinical outcome was good (visual acuity ≤ 6/12) for the patients who presented earlier (≤1 month) (75% of cases with documented final best-corrected visual acuity). MKC occurs more commonly in immunocompetent individuals than expected and can be diagnosed in earlier stages. From our review, we conclude that the patients, who were diagnosed early and treated, had complete resolution of symptoms with a better clinical outcome.
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Affiliation(s)
- Alex Chengyao Tham
- Department of Ophthalmology and Visual Sciences, Khoo Teck Puat Hospital, Yishun, Singapore
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