1
|
Vanzolini T, Magnani M. Old and new strategies in therapy and diagnosis against fungal infections. Appl Microbiol Biotechnol 2024; 108:147. [PMID: 38240822 PMCID: PMC10799149 DOI: 10.1007/s00253-023-12884-8] [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: 06/26/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024]
Abstract
Fungal infections represent a serious global health threat. The new emerging pathogens and the spread of different forms of resistance are now hardly challenging the tools available in therapy and diagnostics. With the commonly used diagnoses, fungal identification is often slow and inaccurate, and, on the other hand, some drugs currently used as treatments are significantly affected by the decrease in susceptibility. Herein, the antifungal arsenal is critically summarized. Besides describing the old approaches and their mechanisms, advantages, and limitations, the focus is dedicated to innovative strategies which are designed, identified, and developed to take advantage of the discrepancies between fungal and host cells. Relevant pathways and their role in survival and virulence are discussed as their suitability as sources of antifungal targets. In a similar way, molecules with antifungal activity are reported as potential agents/precursors of the next generation of antimycotics. Particular attention was devoted to biotechnological entities, to their novelty and reliability, to drug repurposing and restoration, and to combinatorial applications yielding significant improvements in efficacy. KEY POINTS: • New antifungal agents and targets are needed to limit fungal morbidity and mortality. • Therapeutics and diagnostics suffer of delays in innovation and lack of targets. • Biologics, drug repurposing and combinations are the future of antifungal treatments.
Collapse
Affiliation(s)
- Tania Vanzolini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy.
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| |
Collapse
|
2
|
Kulik T, van Diepeningen AD, Hausner G. Editorial: The significance of mitogenomics in mycology, volume II. Front Microbiol 2023; 14:1344877. [PMID: 38192293 PMCID: PMC10773717 DOI: 10.3389/fmicb.2023.1344877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne D. van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
3
|
Li ZC, Xie TC, Feng XL, Wang ZX, Lin C, Li GM, Li XZ, Qi J. The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales. Int J Mol Sci 2023; 24:12599. [PMID: 37628782 PMCID: PMC10454537 DOI: 10.3390/ijms241612599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.
Collapse
Affiliation(s)
- Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Guo-ming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| |
Collapse
|
4
|
Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
Collapse
|
5
|
Zhang Z, Deng Z, Zhu L, Zeng J, Cai XM, Qiu Z, Zhao Z, Tang BZ. Aggregation-induced emission biomaterials for anti-pathogen medical applications: detecting, imaging and killing. Regen Biomater 2023; 10:rbad044. [PMID: 37265605 PMCID: PMC10229374 DOI: 10.1093/rb/rbad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 06/03/2023] Open
Abstract
Microbial pathogens, including bacteria, fungi and viruses, greatly threaten the global public health. For pathogen infections, early diagnosis and precise treatment are essential to cut the mortality rate. The emergence of aggregation-induced emission (AIE) biomaterials provides an effective and promising tool for the theranostics of pathogen infections. In this review, the recent advances about AIE biomaterials for anti-pathogen theranostics are summarized. With the excellent sensitivity and photostability, AIE biomaterials have been widely applied for precise diagnosis of pathogens. Besides, different types of anti-pathogen methods based on AIE biomaterials will be presented in detail, including chemotherapy and phototherapy. Finally, the existing deficiencies and future development of AIE biomaterials for anti-pathogen applications will be discussed.
Collapse
Affiliation(s)
- Zicong Zhang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ziwei Deng
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Lixun Zhu
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Jialin Zeng
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Xu Min Cai
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Rescources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zijie Qiu
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Zheng Zhao
- Correspondence address. E-mail: (Z.Z.); (B.Z.T.)
| | | |
Collapse
|
6
|
Li Q, Luo Y, Sha A, Xiao W, Xiong Z, Chen X, He J, Peng L, Zou L. Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species. Front Microbiol 2023; 14:1134228. [PMID: 36970689 PMCID: PMC10030801 DOI: 10.3389/fmicb.2023.1134228] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
IntroductionCodon basis is a common and complex natural phenomenon observed in many kinds of organisms.MethodsIn the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.ResultsThe results showed that the codons of all Amanita species tended to end in A/T, demonstrating the preference of mitochondrial codons of Amanita species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of Amanita is 30.81, which is <35, demonstrating the strong codon preference of mitochondrial core PCGs of Amanita. The neutrality plot analysis and PR2-Bias plot analysis further demonstrated that natural selection plays an important role in Amanita codon bias. In addition, we obtained 5–10 optimal codons (ΔRSCU > 0.08 and RSCU > 1) in nine Amanita species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different Amanita species and found large variations between them.DiscussionThis study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.
Collapse
|
7
|
Hugaboom M, Hatmaker EA, LaBella AL, Rokas A. Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. G3 (BETHESDA, MD.) 2022; 13:6777267. [PMID: 36305682 PMCID: PMC9836360 DOI: 10.1093/g3journal/jkac285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.
Collapse
Affiliation(s)
- Miya Hugaboom
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Elizabeth Anne Hatmaker
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AH)
| | - Abigail L LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Antonis Rokas
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AR)
| |
Collapse
|
8
|
Morón-López J, Vergara K, Sato M, Gajardo G, Ueki S. Intraspecies variation of the mitochondrial genome: An evaluation for phylogenetic approaches based on the conventional choices of genes and segments on mitogenome. PLoS One 2022; 17:e0273330. [PMID: 35980990 PMCID: PMC9387813 DOI: 10.1371/journal.pone.0273330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 08/07/2022] [Indexed: 12/01/2022] Open
Abstract
Intraspecies nucleotide sequence variation is a key to understanding the evolutionary history of a species, such as the geographic distribution and population structure. To date, numerous phylogenetic and population genetics studies have been conducted based on the sequences of a gene or an intergenic region on the mitochondrial genome (mtDNA), such as cytochrome c oxidase subunits or the D-loop. To evaluate the credibility of the usage of such ‘classic’ markers, we compared the phylogenetic inferences based on the analyses of the partial and entire mtDNA sequences. Importantly, the phylogenetic reconstruction based on the short marker sequences did not necessarily reproduce the tree topologies based on the analyses of the entire mtDNA. In addition, analyses on the datasets of various organisms revealed that the analyses based on the classic markers yielded phylogenetic trees with poor confidence in all tested cases compared to the results based on full-length mtDNA. These results demonstrated that phylogenetic analyses based on complete mtDNA sequences yield more insightful results compared to those based on mitochondrial genes and segments. To ameliorate the shortcomings of the classic markers, we identified a segment of mtDNA that may be used as an ‘approximate marker’ to closely reproduce the phylogenetic inference obtained from the entire mtDNA in the case of mammalian species, which can be utilized to design amplicon-seq-based studies. Our study demonstrates the importance of the choice of mitochondrial markers for phylogenetic analyses and proposes a novel approach to choosing appropriate markers for mammalian mtDNA that reproduces the phylogenetic inferences obtained from full-length mtDNA.
Collapse
Affiliation(s)
- Jesús Morón-López
- Institute of Plant Science and Resources, Okayama University, Kurashiki city, Okayama, Japan
| | - Karen Vergara
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda, Osorno, Chile
| | - Masanao Sato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda, Osorno, Chile
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, Kurashiki city, Okayama, Japan
- * E-mail:
| |
Collapse
|
9
|
Ellena V, Steiger MG. The importance of complete and high-quality genome sequences in Aspergillus niger research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:935993. [PMID: 37746178 PMCID: PMC10512394 DOI: 10.3389/ffunb.2022.935993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/27/2022] [Indexed: 09/26/2023]
Abstract
The possibility to sequence the entire genome of an organism revolutionized the fields of biology and biotechnology. The first genome sequence of the important filamentous fungus Aspergillus niger was obtained in 2007, 11 years after the release of the first eukaryotic genome sequence. From that moment, genomics of A. niger has seen major progresses, facilitated by the advances in the sequencing technologies and in the methodologies for gene function prediction. However, there are still challenges to face when trying to obtain complete genomes, equipped with all the repetitive sequences that they contain and without omitting the mitochondrial sequences. The aim of this perspective article is to discuss the current status of A. niger genomics and draw attention to the open challenges that the fungal community should address to move research of this important fungus forward.
Collapse
Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
| | - Matthias G. Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
| |
Collapse
|
10
|
Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
Collapse
Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| |
Collapse
|
11
|
Li Q, Bao Z, Tang K, Feng H, Tu W, Li L, Han Y, Cao M, Zhao C. First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes. IMA Fungus 2022; 13:7. [PMID: 35501936 PMCID: PMC9059411 DOI: 10.1186/s43008-022-00094-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 04/22/2022] [Indexed: 02/03/2023] Open
Abstract
In the present study, two mitogenomes from the Filobasidium genus were assembled and compared with other Tremellomycetes mitogenomes. The mitogenomes of F. wieringae and F. globisporum both comprised circular DNA molecules, with sizes of 27,861 bp and 71,783 bp, respectively. Comparative mitogenomic analysis revealed that the genetic contents, tRNAs, and codon usages of the two Filobasidium species differed greatly. The sizes of the two Filobasidium mitogenomes varied greatly with the introns being the main factor contributing to mitogenome expansion in F. globisporum. Positive selection was observed in several protein-coding genes (PCGs) in the Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina species, including cob, cox2, nad2, and rps3 genes. Frequent intron loss/gain events were detected to have occurred during the evolution of the Tremellomycetes mitogenomes, and the mitogenomes of 17 species from Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina have undergone large-scale gene rearrangements. Phylogenetic analyses based on Bayesian inference and the maximum likelihood methods using a combined mitochondrial gene set generated identical and well-supported phylogenetic trees, wherein Filobasidium species had close relationships with Trichosporonales species. This study, which is the first report on mitogenomes from the order Filobasidiales, provides a basis for understanding the genomics, evolution, and taxonomy of this important fungal group.
Collapse
Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ke Tang
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Huiyu Feng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yunlei Han
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China. .,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China.
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
| |
Collapse
|
12
|
Kouvelis VN, Hausner G. Editorial: Mitochondrial Genomes and Mitochondrion Related Gene Insights to Fungal Evolution. Front Microbiol 2022; 13:897981. [PMID: 35479620 PMCID: PMC9036184 DOI: 10.3389/fmicb.2022.897981] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Vassili N. Kouvelis
- Division of Genetics and Biotechnology, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
- *Correspondence: Vassili N. Kouvelis
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Lin R, Xia Y, Liu Y, Zhang D, Xiang X, Niu X, Jiang L, Wang X, Zheng A. Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups. Front Microbiol 2021; 12:707281. [PMID: 34616376 PMCID: PMC8488467 DOI: 10.3389/fmicb.2021.707281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. Rhizoctonia solani, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published Rhizoctonia mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five Rhizoctonia sp. mitogenomes). These mitogenomes encoded 15 typical proteins (cox1-3, cob, atp6, atp8-9, nad1-6, nad4L, and rps3) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (Rhizoctonia sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the rps3 gene in 10 Rhizoctonia mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven R. solani and other five Rhizoctonia sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of R. solani had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the R. solani clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of rps3-nad2 and nad1-m3g18/mag28 (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of R. solani mitogenomes.
Collapse
Affiliation(s)
- Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Xia
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Yao Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Danhua Zhang
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Xing Xiang
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Xianyu Niu
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Linjia Jiang
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Xiaolin Wang
- Agriculture College, Sichuan Agricultural University, Chengdu, China
| | - Aiping Zheng
- Agriculture College, Sichuan Agricultural University, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| |
Collapse
|
15
|
Zhang S, Bai X, Ren LY, Sun HH, Tang HP, Vaario LM, Xu J, Zhang YJ. Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake. Environ Microbiol 2021; 23:7214-7230. [PMID: 34587365 DOI: 10.1111/1462-2920.15792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/25/2021] [Indexed: 01/26/2023]
Abstract
Fungi, as eukaryotic organisms, contain two genomes, the mitochondrial genome and the nuclear genome, in their cells. How the two genomes evolve and correlate to each other is debated. Herein, taking the gourmet pine mushroom Tricholoma matsutake as an example, we performed comparative mitogenomic analysis using samples collected from diverse locations and compared the evolution of the two genomes. The T. matsutake mitogenome encodes 49 genes and is rich of repetitive and non-coding DNAs. Six genes were invaded by up to 11 group I introns, with one cox1 intron cox1P372 showing presence/absence dynamics among different samples. Bioinformatic analyses suggested limited or no evidence of mitochondrial heteroplasmy. Interestingly, hundreds of mitochondrial DNA fragments were found in the nuclear genome, with several larger than 500 nt confirmed by PCR assays and read count comparisons, indicating clear evidence of transfer of mitochondrial DNA into the nuclear genome. Nuclear DNA of T. matsutake showed a higher mutation rate than mitochondrial DNA. Furthermore, we found evidence of incongruence between phylogenetic trees derived from mitogenome and nuclear DNA sequences. Together, our results reveal the dynamic genome evolution of the gourmet pine mushroom.
Collapse
Affiliation(s)
- Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Xue Bai
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Li-Yuan Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Hui-Hui Sun
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Hui-Ping Tang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Lu-Min Vaario
- Department of Forest Science, University of Helsinki, Helsinki, FI-00014, Finland
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| |
Collapse
|
16
|
Liang G, Zhang M, Xu W, Wang X, Zheng H, Mei H, Liu W. Characterization of mitogenomes from four Mucorales species and insights into pathogenicity. Mycoses 2021; 65:45-56. [PMID: 34570921 DOI: 10.1111/myc.13374] [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: 04/08/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Mucorales, as one major order of Zygomycetes fungi, can infect human beings and cause serious consequence. We have noticed the pathogenicity of Mucorales is closely related to energy metabolism, while mitochondria play the role of energy factories in almost all biological activities. METHODS Virulence of M irregularis, M hiemalis, L corymbifera and R arrhizus were verified in Galleria mellonella larvae, as well as mitochondrial gene copies analysed with RT-qPCR. Mitogenomes of the four Mucorales species were sequenced based on illumina NovaSeq technology to study their characteristic features and functional regions. RESULTS Variant virulence of M irregularis, M hiemalis, L corymbifera and R arrhizu were verified by clinical retrospective data and our G mellonella infection models, also copies of mitochondrial genes indicated the significant associations with pathogenicity. A total of 274.18 clean reads were generated to be assembled; the complete mitogenomes of the four Mucorales species were obtained with totally different length. After the genomes annotated and compared, M irregularis was found more similar with M hiemalis than those of L corymbifera and R arrhizus, especially the small (rrns) and large (rrnl) subunits of mitochondrial ribosomal RNA (rRNA) genes. The GC content, ncRNAs and the distribution of the SNPs and InDels were also compared, and the GC content rate of fungi seems to be related to the fungal thermal adaptability. In addition, linear mitogenomes of these four Mucorales showed diverse arrangements of orf genes and directionality of some conserved gene elements. CONCLUSION This study uncovered the pathogenicity variances among the four Mucorales species and the relationship between their mitogenomic features and clinical pathogenicity. Further studies like spatial structure of mitochondrial genomes and the comprehensive analysis of transcription regulation are needed.
Collapse
Affiliation(s)
- Guanzhao Liang
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Meijie Zhang
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Wenqi Xu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Xiaowen Wang
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, China
| | - Hailin Zheng
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Huan Mei
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Weida Liu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China.,CAMS Collection Center of Pathogen Microorganisms-D (CAMS-CCPM-D), Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| |
Collapse
|
17
|
Zhou C, Peng C, Shi C, Jiang M, Chau JHC, Liu Z, Bai H, Kwok RTK, Lam JWY, Shi Y, Tang BZ. Mitochondria-Specific Aggregation-Induced Emission Luminogens for Selective Photodynamic Killing of Fungi and Efficacious Treatment of Keratitis. ACS NANO 2021; 15:12129-12139. [PMID: 34181408 DOI: 10.1021/acsnano.1c03508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The development of effective antifungal agents remains a big challenge in view of the close evolutionary relationship between mammalian cells and fungi. Moreover, rapid mutations of fungal receptors at the molecular level result in the emergence of drug resistance. Here, with low tendency to develop drug-resistance, the subcellular organelle mitochondrion is exploited as an alternative target for efficient fungal killing by photodynamic therapy (PDT) of mitochondrial-targeting luminogens with aggregation-induced emission characteristics (AIEgens). With cationic isoquinolinium (IQ) moiety and proper hydrophobicity, three AIEgens, namely, IQ-TPE-2O, IQ-Cm, and IQ-TPA, can preferentially accumulate at the mitochondria of fungi over the mammalian cells. Upon white light irradiation, these AIEgens efficiently generate reactive 1O2, which causes irreversible damage to fungal mitochondria and further triggers the fungal death. Among them, IQ-TPA shows the highest PDT efficiency against fungi and negligible toxicity to mammalian cells, achieving the selective and highly efficient killing of fungi. Furthermore, we tested the clinical utility of this PDT strategy by treating fungal keratitis on a fungus-infected rabbit model. It was demonstrated that IQ-TPA presents obviously better therapeutic effects as compared with the clinically used rose bengal, suggesting the success of this PDT strategy and its great potential for clinical treatment of fungal infections.
Collapse
Affiliation(s)
- Chengcheng Zhou
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Chen Peng
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Chunzi Shi
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Meijuan Jiang
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Joe H C Chau
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Zhiyang Liu
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Haotian Bai
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Ryan T K Kwok
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Jacky W Y Lam
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
| | - Yuxin Shi
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Ben Zhong Tang
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and SCUT-HKUST Joint Research Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong China
- Shenzhen Institute of Aggregate Science and Technology, School of Science & Engineering, The Chinese University of Hong Kong, Shenzhen, Longgang, Shenzhen, Guangdong 518172, China
- AIE Institute, Guangzhou Development District, Huangpu, Guangzhou 510530, China
| |
Collapse
|
18
|
Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A. Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion 2021; 58:1-13. [PMID: 33582235 DOI: 10.1016/j.mito.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.
Collapse
Affiliation(s)
- Daniel S Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luiz M R Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Paula L C Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
19
|
The Future of Antifungal Drug Therapy: Novel Compounds and Targets. Antimicrob Agents Chemother 2021; 65:AAC.01719-20. [PMID: 33229427 DOI: 10.1128/aac.01719-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fungal infections are a universal problem and are routinely associated with high morbidity and mortality rates in immunocompromised patients. Existing therapies comprise five different classes of antifungal agents, four of which target the synthesis of ergosterol and cell wall glucans. However, the currently available antifungals have many limitations, including poor oral bioavailability, narrow therapeutic indices, and emerging drug resistance resulting from their use, thus making it essential to investigate the development of novel drugs which can overcome these limitations and add to the antifungal armamentarium. Advances have been made in antifungal drug discovery research and development over the past few years as evidenced by the presence of several new compounds currently in various stages of development. In the following minireview, we provide a comprehensive summary of compounds aimed at one or more novel molecular targets. We also briefly describe potential pathways relevant for fungal pathogenesis that can be considered for drug development in the near future.
Collapse
|
20
|
Oren-Young L, Llorens E, Bi K, Zhang M, Sharon A. Botrytis cinerea methyl isocitrate lyase mediates oxidative stress tolerance and programmed cell death by modulating cellular succinate levels. Fungal Genet Biol 2020; 146:103484. [PMID: 33220429 DOI: 10.1016/j.fgb.2020.103484] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/25/2020] [Accepted: 11/10/2020] [Indexed: 12/21/2022]
Abstract
Fungi lack the entire animal core apoptotic machinery. Nevertheless, regulated cell death with apoptotic markers occurs in multicellular as well as in unicellular fungi and is essential for proper fungal development and stress adaptation. The discrepancy between appearance of an apoptotic-like regulated cell death (RCD) in the absence of core apoptotic machinery is further complicated by the fact that heterologous expression of animal apoptotic genes in fungi affects fungal RCD. Here we describe the role of BcMcl, a methyl isocitrate lyase from the plant pathogenic fungus Botrytis cinerea, in succinate metabolism, and the connection of succinate with stress responses and cell death. Over expression of bcmcl resulted in elevated tolerance to oxidative stress and reduced levels of RCD, which were associated with accumulation of elevated levels of succinate. Deletion of bcmcl had almost no effect on fungal development or stress sensitivity, and succinate levels were unchanged in the deletion strain. Gene expression experiments showed co-regulation of bcmcl and bcicl (isocitrate lyase); expression of the bcicl gene was enhanced in bcmcl deletion and suppressed in bcmcl over expression strains. External addition of succinate reproduced the phenotypes of the bcmcl over expression strains, including developmental defects, reduced virulence, and improved oxidative stress tolerance. Collectively, our results implicate mitochondria metabolic pathways, and in particular succinate metabolism, in regulation of fungal stress tolerance, and highlight the role of this onco-metabolite as potential mediator of fungal RCD.
Collapse
Affiliation(s)
- Liat Oren-Young
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Eugenio Llorens
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kai Bi
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mingzhe Zhang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
21
|
Chen C, Wang J, Li Q, Fu R, Jin X, Huang W, Lu D. Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny. Front Microbiol 2020; 11:573064. [PMID: 33193177 PMCID: PMC7644776 DOI: 10.3389/fmicb.2020.573064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.
Collapse
Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| |
Collapse
|
22
|
Chen M, Chen N, Wu T, Bian Y, Deng Y, Xu Z. Characterization of Two Mitochondrial Genomes and Gene Expression Analysis Reveal Clues for Variations, Evolution, and Large-Sclerotium Formation in Medical Fungus Wolfiporia cocos. Front Microbiol 2020; 11:1804. [PMID: 32849413 PMCID: PMC7417453 DOI: 10.3389/fmicb.2020.01804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/09/2020] [Indexed: 12/05/2022] Open
Abstract
Wolfiporia cocos, a precious mushroom with a long history as an edible food and Asian traditional medicine, remains unclear in the genetic mechanism underlying the formation of large sclerotia. Here, two complete circular mitogenomes (BL16, 135,686 bp and MD-104 SS10, 124,842 bp, respectively) were presented in detail first. The salient features in the mitogenomes of W. cocos include an intron in the tRNA (trnQ-UUG2), and an obvious gene rearrangement identified between the two mitogenomes from the widely geographically separated W. cocos strains. Genome comparison and phylogenetic analyses reveal some variations and evolutional characteristics in W. cocos. Whether the mitochondrion is functional in W. cocos sclerotium development was investigated by analyzing the mitogenome synteny of 10 sclerotium-forming fungi and mitochondrial gene expression patterns in different W. cocos sclerotium-developmental stages. Three common homologous genes identified across ten sclerotium-forming fungi were also found to exhibit significant differential expression levels during W. cocos sclerotium development. Most of the mitogenomic genes are not expressed in the mycelial stage but highly expressed in the sclerotium initial or developmental stage. These results indicate that some of mitochondrial genes may play a role in the development of sclerotium in W. cocos, which needs to be further elucidated in future studies. This study will stimulate new ideas on cytoplasmic inheritance of W. cocos and facilitate the research on the role of mitochondria in large sclerotium formation.
Collapse
Affiliation(s)
- Mengting Chen
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Naiyao Chen
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Wu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhangyi Xu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
23
|
The Novel J-Domain Protein Mrj1 Is Required for Mitochondrial Respiration and Virulence in Cryptococcus neoformans. mBio 2020; 11:mBio.01127-20. [PMID: 32518190 PMCID: PMC7373193 DOI: 10.1128/mbio.01127-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cryptococcus neoformans is the causative agent of cryptococcal meningitis, a disease responsible for ∼15% of all HIV-related deaths. Unfortunately, development of antifungal drugs is challenging because potential targets are conserved between humans and C. neoformans. In this context, we characterized a unique J-domain protein, Mrj1, which lacks orthologs in humans. We showed that Mrj1 was required for normal mitochondrial respiration and that mutants lacking Mrj1 were deficient in growth, capsule elaboration, and virulence. Furthermore, we were able to phenocopy the defects in growth and capsule elaboration by inhibiting respiration. This result suggests that the role of Mrj1 in mitochondrial function was responsible for the observed virulence defects and reinforces the importance of mitochondria to fungal pathogenesis. Mitochondria are difficult to target, as their function is also key to human cells; however, Mrj1 presents an opportunity to target a unique fungal protein required for mitochondrial function and virulence in C. neoformans. The opportunistic fungal pathogen Cryptococcus neoformans must adapt to the mammalian environment to establish an infection. Proteins facilitating adaptation to novel environments, such as chaperones, may be required for virulence. In this study, we identified a novel mitochondrial co-chaperone, Mrj1 (mitochondrial respiration J-domain protein 1), necessary for virulence in C. neoformans. The mrj1Δ and J-domain-inactivated mutants had general growth defects at both routine laboratory and human body temperatures and were deficient in the major virulence factor of capsule elaboration. The latter phenotype was associated with cell wall changes and increased capsular polysaccharide shedding. Accordingly, the mrj1Δ mutant was avirulent in a murine model of cryptococcosis. Mrj1 has a mitochondrial localization and co-immunoprecipitated with Qcr2, a core component of complex III of the electron transport chain. The mrj1 mutants were deficient in mitochondrial functions, including growth on alternative carbon sources, growth without iron, and mitochondrial polarization. They were also insensitive to complex III inhibitors and hypersensitive to an alternative oxidase (AOX) inhibitor, suggesting that Mrj1 functions in respiration. In support of this conclusion, mrj1 mutants also had elevated basal oxygen consumption rates which were completely abolished by the addition of the AOX inhibitor, confirming that Mrj1 is required for mitochondrial respiration through complexes III and IV. Furthermore, inhibition of complex III phenocopied the capsule and cell wall defects of the mrj1 mutants. Taken together, these results indicate that Mrj1 is required for normal mitochondrial respiration, a key aspect of adaptation to the host environment and virulence.
Collapse
|
24
|
Kulik T, Brankovics B, van Diepeningen AD, Bilska K, Żelechowski M, Myszczyński K, Molcan T, Stakheev A, Stenglein S, Beyer M, Pasquali M, Sawicki J, Wyrȩbek J, Baturo-Cieśniewska A. Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes. Front Microbiol 2020; 11:1002. [PMID: 32528440 PMCID: PMC7263005 DOI: 10.3389/fmicb.2020.01002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
Collapse
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Balazs Brankovics
- Biointeractions & Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina.,Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
| | - Marco Beyer
- Department of Environmental Research and Innovation, Agro-Environmental Systems, Luxembourg Institute of Science and Technology, Belval, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Joanna Wyrȩbek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Baturo-Cieśniewska
- Laboratory of Phytopathology and Molecular Mycology, Department of Biology and Plant Protection, UTP University of Science and Technology, Bydgoszcz, Poland
| |
Collapse
|
25
|
Wang Y, Xu J. Mitochondrial Genome Polymorphisms in the Human Pathogenic Fungus Cryptococcus neoformans. Front Microbiol 2020; 11:706. [PMID: 32373103 PMCID: PMC7186387 DOI: 10.3389/fmicb.2020.00706] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
The Cryptococcus complex consists of at least seven evolutionary divergent lineages and causes ∼200,000 fatal human infections each year worldwide. The dominant lineage is Cryptococcus neoformans which consists of three haploid clades VNI, VNII, and VNB, their haploid hybrids, and various diploids derived from intra- and inter-clade mating events. In this study, we analyzed the mitogenomes of 184 strains of C. neoformans. Our analyses revealed that all 184 mitogenomes contained the same 15 protein-coding genes in the same gene order. However, their mitogenome sizes varied between 24,740 and 31,327 bp, primarily due to differences in the number and size of mitochondrial introns. Twelve nucleotide sites within five mitochondrial genes were found to contain introns in at least one of the 184 strains, ranging from 2 to 7 introns within each mitogenome. The concatenated mitochondrial exon sequences of the 15 protein-coding genes and two rRNA genes showed that VNI, VNII, and VNB strains were separated into distinct clades or sub-clades, largely consistent with results based on nuclear genome SNPs. However, several novel findings were observed. First, one strain of the VNB clade contained mitogenome exon sequences identical to the main VNI mitogenome type but was distant to other VNB mitogenomes. Second, hybrids among clades VNI, VNII, and VNB identified based on their nuclear genome SNPs contained mitogenomes from different clades, with evidence of their mitogenomes inherited from either the MAT a or the MAT α parents. Third, the eight diploid VNB (C. neoformans) × VNIV (C. deneoformans) hybrids contained recombinant mitogenomes. Fourth, analyses of intron distribution and the paired exon-intron phylogenies for each of the 12 exon-intron pairs suggested frequent gains and losses of mitochondrial introns during the evolution of C. neoformans. The combined mitogenome exon-based phylogeny and intron distributions suggested that clades VNI, VNII and VNB could be further divided into sub-clades. Together, our results revealed a dynamic evolution of mitochondrial genomes in this important human fungal pathogen.
Collapse
Affiliation(s)
- Yue Wang
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| |
Collapse
|
26
|
Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.
Collapse
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| |
Collapse
|
27
|
Tian F, Lee SY, Woo SY, Chun HS. Alternative Oxidase: A Potential Target for Controlling Aflatoxin Contamination and Propagation of Aspergillus flavus. Front Microbiol 2020; 11:419. [PMID: 32256475 PMCID: PMC7092633 DOI: 10.3389/fmicb.2020.00419] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/27/2020] [Indexed: 12/16/2022] Open
Abstract
Aflatoxins are among the most hazardous natural cereal contaminants. These mycotoxins are produced by Aspergillus spp. as polyketide secondary metabolites. Aflatoxigenic fungi including A. flavus express the alternative oxidase (AOX), which introduces a branch in the cytochrome-based electron transfer chain by coupling ubiquinol oxidation directly with the reduction of O2 to H2O. AOX is closely associated with fungal pathogenesis, morphogenesis, stress signaling, and drug resistance and, as recently reported, affects the production of mycotoxins such as sterigmatocystin, the penultimate intermediate in aflatoxin B1 biosynthesis. Thus, AOX might be considered a target for controlling the propagation of and aflatoxin contamination by A. flavus. Hence, this review summarizes the current understanding of fungal AOX and the alternative respiration pathway and the development and potential applications of AOX inhibitors. This review indicates that AOX inhibitors, either alone or in combination with current antifungal agents, are potentially applicable for developing novel, effective antifungal strategies. However, considering the conservation of AOX in fungal and plant cells, a deeper understanding of fungal alternative respiration and fungal AOX structure is needed, along with effective fungal-specific AOX inhibitors.
Collapse
Affiliation(s)
- Fei Tian
- Food Toxicology Laboratory, Advanced Food Safety Research Group, BK21 Plus, School of Food Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Sang Yoo Lee
- Food Toxicology Laboratory, Advanced Food Safety Research Group, BK21 Plus, School of Food Science and Technology, Chung-Ang University, Anseong, South Korea
| | - So Young Woo
- Food Toxicology Laboratory, Advanced Food Safety Research Group, BK21 Plus, School of Food Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Hyang Sook Chun
- Food Toxicology Laboratory, Advanced Food Safety Research Group, BK21 Plus, School of Food Science and Technology, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
28
|
Chen C, Li Q, Fu R, Wang J, Xiong C, Fan Z, Hu R, Zhang H, Lu D. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Sci Rep 2019; 9:17447. [PMID: 31768013 PMCID: PMC6877775 DOI: 10.1038/s41598-019-53941-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
Collapse
Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, 610066, Sichuan, P.R. China
| | - Qiang Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Jian Wang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhonghan Fan
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Rongping Hu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, P.R. China.
| |
Collapse
|
29
|
Aeration, Agitation and Cell Immobilization on Corncobs and Oak Wood Chips Effects on Balsamic-Styled Vinegar Production. Foods 2019; 8:foods8080303. [PMID: 31374870 PMCID: PMC6723862 DOI: 10.3390/foods8080303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 11/16/2022] Open
Abstract
Optimum fermentor conditions are essential for desired microbial growth and activity in fermentations. In balsamic vinegar fermentation systems, the microorganisms used must endure several stressful conditions including high sugar concentration, low water activity, high osmotic pressure and high acetic acid concentration. Consequently, the present study was aimed at improving the performance of a microbial consortium of non-Saccharomyces yeast and acetic acid bacteria during balsamic-styled vinegar fermentation. Cell immobilization via adsorption on corncobs and oak wood chips in combination with aeration and agitation effects, have never been tested during balsamic-styled vinegar fermentation. Therefore, fermentations were initially conducted under static conditions without aeration with successive fermentations also being subjected to low (0.15 vvm min-1) and high (0.3 vvm min-1) aeration. The results showed improved acetification rates when cells were immobilized on corncobs under static conditions. Low aeration showed better acetification rates (1.45-1.56 g·L·day-1), while only free-floating cells were able to complete fermentations (1.2 g·L·day-1) under high aeration conditions. Overall, cells immobilized on corncobs showed higher acetification rates of 1.56 and 2.7 g·L·day-1 under low aeration and static fermentations, respectively. Oak wood chips were determined to be less efficient adsorbents due to their relatively smooth surface, while the rough surface and porosity of corncobs led to improved adsorption and, therefore, enhanced acetification rates.
Collapse
|
30
|
Inhibition of Classical and Alternative Modes of Respiration in Candida albicans Leads to Cell Wall Remodeling and Increased Macrophage Recognition. mBio 2019; 10:mBio.02535-18. [PMID: 30696734 PMCID: PMC6355986 DOI: 10.1128/mbio.02535-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human fungal pathogen Candida albicans requires respiratory function for normal growth, morphogenesis, and virulence. Mitochondria therefore represent an enticing target for the development of new antifungal strategies. This possibility is bolstered by the presence of characteristics specific to fungi. However, respiration in C. albicans, as in many fungal organisms, is facilitated by redundant electron transport mechanisms, making direct inhibition a challenge. In addition, many chemicals known to target the electron transport chain are highly toxic. Here we made use of chemicals with low toxicity to efficiently inhibit respiration in C. albicans We found that use of the nitric oxide donor sodium nitroprusside (SNP) and of the alternative oxidase inhibitor salicylhydroxamic acid (SHAM) prevents respiration and leads to a loss of viability and to cell wall rearrangements that increase the rate of uptake by macrophages in vitro and in vivo We propose that treatment with SNP plus SHAM (SNP+SHAM) leads to transcriptional changes that drive cell wall rearrangement but which also prime cells to activate the transition to hyphal growth. In line with this, we found that pretreatment of C. albicans with SNP+SHAM led to an increase in virulence. Our data reveal strong links between respiration, cell wall remodeling, and activation of virulence factors. Our findings demonstrate that respiration in C. albicans can be efficiently inhibited with chemicals that are not damaging to the mammalian host but that we need to develop a deeper understanding of the roles of mitochondria in cellular signaling if they are to be developed successfully as a target for new antifungals.IMPORTANCE Current approaches to tackling fungal infections are limited, and new targets must be identified to protect against the emergence of resistant strains. We investigated the potential of targeting mitochondria, which are organelles required for energy production, growth, and virulence, in the human fungal pathogen Candida albicans Our findings suggest that mitochondria can be targeted using drugs that can be tolerated by humans and that this treatment enhances their recognition by immune cells. However, release of C. albicans cells from respiratory inhibition appears to activate a stress response that increases the levels of traits associated with virulence. Our results make it clear that mitochondria represent a valid target for the development of antifungal strategies but that we must determine the mechanisms by which they regulate stress signaling and virulence ahead of successful therapeutic advance.
Collapse
|
31
|
Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Liu Q, Huang W. Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol 2019; 121:249-260. [DOI: 10.1016/j.ijbiomac.2018.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
|
32
|
Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Zhao J, Huang W. Characterization and comparison of the mitochondrial genomes from two Lyophyllum fungal species and insights into phylogeny of Agaricomycetes. Int J Biol Macromol 2019; 121:364-372. [DOI: 10.1016/j.ijbiomac.2018.10.037] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/12/2018] [Accepted: 10/10/2018] [Indexed: 12/29/2022]
|
33
|
Maintenance of Mitochondrial Morphology in Cryptococcus neoformans Is Critical for Stress Resistance and Virulence. mBio 2018; 9:mBio.01375-18. [PMID: 30401774 PMCID: PMC6222134 DOI: 10.1128/mbio.01375-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
C. neoformans is a yeast that causes fatal brain infection in close to 200,000 people worldwide every year, mainly afflicting individuals with AIDS or others who are severely immunocompromised. One feature of this microbe that helps it cause disease is that it is able to withstand toxic molecules it encounters when host cells engulf it in their efforts to control the infection. Mitochondria are important organelles responsible for energy production and other key cellular processes. They typically exist in a complex network that changes morphology by fusing and dividing; these alterations also influence mitochondrial function. Using genetic approaches, we found that changes in mitochondrial morphology dramatically influence cryptococcal virulence. We showed that this occurs because the altered mitochondria are less able to eliminate the harmful molecules that host cells produce to kill invading microbes. These findings are important because they elucidate fundamental biology and virulence and may suggest avenues for therapy. Mitochondria are essential organelles that act in pathways including ATP production, β-oxidation, and clearance of reactive oxygen species. They occur as a complex reticular network that constantly undergoes fusion and fission, mediated by dynamin-related proteins (DRPs). DRPs include Fzo1, which mediates fusion, and Dnm1, Mdv1, and Fis1, which mediate fission. Mitochondrial morphology has been implicated in virulence in multiple fungi, as with the association between virulence and increased mitochondrial fusion in Cryptococcus gattii. This relationship, however, has not been studied in Cryptococcus neoformans, a related opportunistic pathogen. C. neoformans is an environmental yeast that can adapt to the human host environment, overcome the innate immune system, and eventually disseminate and cause lethal meningoencephalitis. We used gene deletion of key DRPs to study their role in mitochondrial morphology and pathogenesis of this yeast. Interestingly, increasing mitochondrial fusion did not increase resistance to oxidative stress, unlike in model yeast. Blocking mitochondrial fusion, however, yielded increased susceptibility to oxidative and nitrosative stresses as well as complete avirulence. This lack of virulence was not mediated by any effects of altered mitochondrial function on two major virulence factors, capsule and melanin. Instead, it was due to decreased survival within macrophages, which in turn was a consequence of increased susceptibility to oxidative and nitrosative stress. Supporting this conclusion, reactive oxygen species (ROS) scavengers rescued the ability of fusion mutants to survive intracellularly. These findings increase our understanding of cryptococcal biology and virulence and shed light on an important group of proteins and cellular processes in this pathogen.
Collapse
|
34
|
Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Zhao J, Huang W. The first complete mitochondrial genome from the family Hygrophoraceae (Hygrophorus russula) by next-generation sequencing and phylogenetic implications. Int J Biol Macromol 2018; 122:1313-1320. [PMID: 30227210 DOI: 10.1016/j.ijbiomac.2018.09.091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/08/2023]
Abstract
Hygrophorus russula (Schaeff.) Kauffman is an edible ectomycorrhizal fungus that is widely distributed in the world. In this study, the mitogenome of H. russula was sequenced and assembled. The mitogenome of H. russula is composed of circular DNA molecules, with a total size of 55,769 bp. Further analysis indicated that the frequent use of A and T in codons contributes to the high AT content (80.87%) in the H. russula mitogenome. Comparative analysis indicated that the length and base composition of the core protein-encoding genes, and the number of tRNA genes in the H. russula mitogenome varied from that of other Agaricales mitogenomes. Gene arrangement analysis revealed a novel gene order in the H. russula mitogenome. In addition, the expansion of the mitogenome in Agaricales was found to be closely related to the increase in the number of introns. Phylogenetic analysis of the combined mitochondrial gene set showed strong support for tree topologies, and H. russula was determined to be relatively distant from other Agaricales species. This study is the first report on the mitogenome of a member of genus Hygrophorus as well as family Hygrophoraceae, which improves our understanding of mitochondrial differentiation and evolution in the important ectomycorrhizal fungi Hygrophorus species.
Collapse
Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Qiangfeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Zuqin Chen
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Jian Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China.
| |
Collapse
|
35
|
Fungal mitochondrial genomes and genetic polymorphisms. Appl Microbiol Biotechnol 2018; 102:9433-9448. [PMID: 30209549 DOI: 10.1007/s00253-018-9350-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022]
Abstract
Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.
Collapse
|
36
|
Li Q, Yang M, Chen C, Xiong C, Jin X, Pu Z, Huang W. Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus. Sci Rep 2018; 8:9104. [PMID: 29904057 PMCID: PMC6002367 DOI: 10.1038/s41598-018-27489-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events. Both the GC and AT skews in the L. sulphureus mitogenome were negative, in contrast to the other seven Polyporales species tested. Of the 15 PCGs conserved across the seven species of Polyporales, the lengths of 11 were unique in the L. sulphureus mitogenome. The Ka/Ks of these 15 PCGs were all less than 1, indicating that PCGs were subject to purifying selection. Our phylogenetic analysis showed that three single genes (cox1, cob, and rnl) were potentially useful as molecular markers. This study is the first publication of a mitochondrial genome in the family Laetiporaceae, and will facilitate the study of population genetics and evolution in L. sulphureus and other species in this family.
Collapse
Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, 617061, Sichuan, P.R. China
| | - Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
| |
Collapse
|
37
|
Lambie SC, Kretschmer M, Croll D, Haslam TM, Kunst L, Klose J, Kronstad JW. The putative phospholipase Lip2 counteracts oxidative damage and influences the virulence of Ustilago maydis. MOLECULAR PLANT PATHOLOGY 2017; 18:210-221. [PMID: 26950180 PMCID: PMC6638309 DOI: 10.1111/mpp.12391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Ustilago maydis is an obligate biotrophic fungal pathogen which causes common smut disease of corn. To proliferate in host tissue, U. maydis must gain access to nutrients and overcome plant defence responses, such as the production of reactive oxygen species. The elucidation of the mechanisms by which U. maydis meets these challenges is critical for the development of strategies to combat smut disease. In this study, we focused on the contributions of phospholipases (PLs) to the pathogenesis of corn smut disease. We identified 11 genes encoding putative PLs and characterized the transcript levels for these genes in the fungus grown in culture and during infection of corn tissue. To assess the contributions of specific PLs, we focused on two genes, lip1 and lip2, which encode putative phospholipase A2 (PLA2 ) enzymes with similarity to platelet-activating factor acetylhydrolases. PLA2 enzymes are known to counteract oxidative damage to lipids in other organisms. Consistent with a role in the mitigation of oxidative damage, lip2 mutants were sensitive to oxidative stress provoked by hydrogen peroxide and by increased production of reactive oxygen species caused by inhibitors of mitochondrial functions. Importantly, mutants defective in lip2, but not lip1, were attenuated for virulence in corn seedlings. Finally, a comparative analysis of fatty acid and cardiolipin profiles in the wild-type strain and a lip2 mutant revealed differences consistent with a protective role for Lip2 in maintaining lipid homeostasis and mitochondrial health during proliferation in the hostile host environment.
Collapse
Affiliation(s)
- Scott C. Lambie
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouver V6T 1Z3BCCanada
- The Michael Smith Laboratories, University of British ColumbiaVancouver V6T 1Z4BCCanada
| | - Matthias Kretschmer
- The Michael Smith Laboratories, University of British ColumbiaVancouver V6T 1Z4BCCanada
| | - Daniel Croll
- The Michael Smith Laboratories, University of British ColumbiaVancouver V6T 1Z4BCCanada
- Present address:
Institute of Integrative Biology, ETH Zürich8092 ZürichSwitzerland
| | - Tegan M. Haslam
- Department of BotanyUniversity of British ColumbiaVancouver V6T 1Z4BCCanada
| | - Ljerka Kunst
- Department of BotanyUniversity of British ColumbiaVancouver V6T 1Z4BCCanada
| | - Jana Klose
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouver V6T 1Z3BCCanada
- The Michael Smith Laboratories, University of British ColumbiaVancouver V6T 1Z4BCCanada
| | - James W. Kronstad
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouver V6T 1Z3BCCanada
- The Michael Smith Laboratories, University of British ColumbiaVancouver V6T 1Z4BCCanada
| |
Collapse
|
38
|
Alanio A, Gits-Muselli M, Mercier-Delarue S, Dromer F, Bretagne S. Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing. Front Microbiol 2016; 7:733. [PMID: 27252684 PMCID: PMC4877386 DOI: 10.3389/fmicb.2016.00733] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023] Open
Abstract
Pneumocystis jirovecii is an uncultivable fungal pathogen responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, the physiopathology of which is only partially understood. The diversity of the Pneumocystis strains associated with acute infection has mainly been studied by Sanger sequencing techniques precluding any identification of rare genetic events (< 20% frequency). We used next-generation sequencing to detect minority variants causing infection, and analyzed the complexity of the genomes of infection-causing P. jirovecii. Ultra-deep pyrosequencing (UDPS) of PCR amplicons of two nuclear target region [internal transcribed spacer 2 (ITS2) and dihydrofolate reductase (DHFR)] and one mitochondrial DNA target region [the mitochondrial ribosomal RNA large subunit gene (mtLSU)] was performed on 31 samples from 25 patients. UDPS revealed that almost all patients (n = 23/25, 92%) were infected with mixtures of strains. An analysis of repeated samples from six patients showed that the proportion of each variant change significantly (by up to 30%) over time on treatment in three of these patients. A comparison of mitochondrial and nuclear UDPS data revealed heteroplasmy in P. jirovecii. The recognition site for the homing endonuclease I-SceI was recovered from the mtLSU gene, whereas its two conserved motifs of the enzyme were not. This suggests that heteroplasmy may result from recombination induced by unidentified homing endonucleases. This study sheds new light on the biology of P. jirovecii during infection. PCP results from infection not with a single microorganism, but with a complex mixture of different genotypes, the proportions of which change over time due to intricate selection and reinfection mechanisms that may differ between patients, treatments, and predisposing diseases.
Collapse
Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Séverine Mercier-Delarue
- Laboratoire de Microbiologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-Louis Paris, France
| | - Françoise Dromer
- Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| |
Collapse
|
39
|
Kroll K, Shekhova E, Mattern DJ, Thywissen A, Jacobsen ID, Strassburger M, Heinekamp T, Shelest E, Brakhage AA, Kniemeyer O. The hypoxia-induced dehydrogenase HorA is required for coenzyme Q10 biosynthesis, azole sensitivity and virulence ofAspergillus fumigatus. Mol Microbiol 2016; 101:92-108. [DOI: 10.1111/mmi.13377] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Kristin Kroll
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Jena Germany
| | - Elena Shekhova
- Department of Molecular and Applied Microbiology; 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
| | - Andreas Thywissen
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Jena Germany
| | - Ilse D. Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, and Friedrich Schiller University Jena; Jena Germany
| | - Maria Strassburger
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Jena Germany
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Jena Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University; Jena Germany
| | - Ekaterina Shelest
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, and Friedrich Schiller University Jena; 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
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University; Jena Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Jena Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University; Jena Germany
| |
Collapse
|
40
|
Shlezinger N, Israeli M, Mochly E, Oren-Young L, Zhu W, Sharon A. Translocation from nuclei to cytoplasm is necessary for anti A-PCD activity and turnover of the Type II IAP BcBir1. Mol Microbiol 2015; 99:393-406. [DOI: 10.1111/mmi.13238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Neta Shlezinger
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| | - Maayan Israeli
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| | - Elad Mochly
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| | - Liat Oren-Young
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| | - Wenjun Zhu
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv 69978 Israel
| |
Collapse
|
41
|
Augmenting the antifungal activity of an oxidizing agent with kojic Acid: control of penicillium strains infecting crops. Molecules 2014; 19:18448-64. [PMID: 25397736 PMCID: PMC6271881 DOI: 10.3390/molecules191118448] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 11/24/2022] Open
Abstract
Oxidative treatment is one of the strategies for preventing Penicillium contamination in crops/foods. The antifungal efficacy of hydrogen peroxide (H2O2; oxidant) was investigated in Penicillium strains by using kojic acid (KA) as a chemosensitizing agent, which can enhance the susceptibility of pathogens to antifungal agents. Co-application of KA with H2O2 (chemosensitization) resulted in the enhancement of antifungal activity of either compound, when compared to the independent application of each agent alone. Of note, heat enhanced the activity of H2O2 to a greater extent during chemosensitization, whereby the minimum inhibitory or minimum fungicidal concentrations of H2O2 was decreased up to 4 or 13 fold, respectively, at 35–45 °C (heat), when compared to that at 28 °C (normal growth temperature). However, heat didn’t increase the antifungal activity of KA, indicating specificity exists between heat and types of antifungals applied. The effect of chemosensitization was also strain-specific, where P. expansum (both parental and fludioxonil-resistant mutants) or P. italicum 983 exhibited relatively higher susceptibility to the chemosensitization, comparing to other Penicillium strains tested. Collectively, chemosensitization can serve as a potent antifungal strategy to lower effective dosages of toxic antifungal substances, such as H2O2. This can lead to coincidental lowering of environmental and health risks.
Collapse
|