1
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Gomes RMODS, Silva KJGD, Theodoro RC. Group I introns: Structure, splicing and their applications in medical mycology. Genet Mol Biol 2024; 47Suppl 1:e20230228. [PMID: 38525907 DOI: 10.1590/1678-4685-gmb-2023-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
Group I introns are small RNAs (250-500 nt) capable of catalyzing their own splicing from the precursor RNA. They are widely distributed across the tree of life and have intricate relationships with their host genomes. In this work, we review its basic structure, self-splicing and its mechanisms of gene mobility. As they are widely found in unicellular eukaryotes, especially fungi, we gathered information regarding their possible impact on the physiology of fungal cells and the possible application of these introns in medical mycology.
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Affiliation(s)
| | | | - Raquel Cordeiro Theodoro
- Universidade Federal do Rio Grande do Norte, Instituto de Medicina Tropical do Rio Grande do Norte, Natal, RN, Brazil
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular de Genética, Natal, RN, Brazil
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2
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Wang J, Quan R, He X, Fu Q, Tian S, Zhao L, Li S, Shi L, Li R, Chen B. Hypovirus infection induces proliferation and perturbs functions of mitochondria in the chestnut blight fungus. Front Microbiol 2023; 14:1206603. [PMID: 37448575 PMCID: PMC10336323 DOI: 10.3389/fmicb.2023.1206603] [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: 04/16/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction The chestnut blight fungus, Cryphonectria parasitica, and hypovirus have been used as a model to probe the mechanism of virulence and regulation of traits important to the host fungus. Previous studies have indicated that mitochondria could be the primary target of the hypovirus. Methods In this study, we report a comprehensive and comparative study comprising mitochondrion quantification, reactive oxygen species (ROS) and respiratory efficiency, and quantitative mitochondrial proteomics of the wild-type and virus-infected strains of the chestnut blight fungus. Results and discussion Our data show that hypovirus infection increases the total number of mitochondria, lowers the general ROS level, and increases mitochondrial respiratory efficiency. Quantification of mitochondrial proteomes revealed that a set of proteins functioning in energy metabolism and mitochondrial morphogenesis, as well as virulence, were regulated by the virus. In addition, two viral proteins, p29 and p48, were found to co-fractionate with the mitochondrial membrane and matrix. These results suggest that hypovirus perturbs the host mitochondrial functions to result in hypovirulence.
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Affiliation(s)
- Jinzi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Key Laboratory of Protection and Utilization of Marine Resources, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Rui Quan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xipu He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qiang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Shigen Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Lijiu Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Shuangcai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Liming Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Life Science and Technology, Guangxi University, Nanning, China
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3
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González-Blanco G, García-Rivera G, Talmás-Rohana P, Orozco E, Galindo-Rosales JM, Vélez C, Salucedo-Cárdenas O, Azuara-Liceaga E, Rodríguez-Rodríguez MA, Nozaki T, Valdés J. An Unusual U2AF2 Inhibits Splicing and Attenuates the Virulence of the Human Protozoan Parasite Entamoeba histolytica. Front Cell Infect Microbiol 2022; 12:888428. [PMID: 35782149 PMCID: PMC9247205 DOI: 10.3389/fcimb.2022.888428] [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: 03/02/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
E. histolytica is the etiological agent of intestinal amebiasis and liver abscesses, which still poses public health threat globally. Metronidazole is the drug of choice against amebiasis. However, metronidazole-resistant amoebic clinical isolates and strains have been reported recently, challenging the efforts for amebiasis eradication. In search of alternative treatments, E. histolytica transcriptomes have shown the association of genes involved in RNA metabolism with the virulence of the parasite. Among the upregulated genes in amoebic liver abscesses are the splicing factors EhU2AF2 and a paralog of EhSF3B1. For this reason and because EhU2AF2 contains unusual KH-QUA2 (84KQ) motifs in its lengthened C-terminus domain, here we investigated how the role of EhU2AF2 in pre-mRNA processing impacts the virulence of the parasite. We found that 84KQ is involved in splicing inhibition/intron retention of several virulence and non-virulence-related genes. The 84KQ domain interacts with the same domain of the constitutive splicing factor SF1 (SF1KQ), both in solution and when SF1KQ is bound to branchpoint signal RNA probes. The 84KQ–SF1KQ interaction prevents splicing complex E to A transition, thus inhibiting splicing. Surprisingly, the deletion of the 84KQ domain in EhU2AF2 amoeba transformants increased splicing and enhanced the in vitro and in vivo virulence phenotypes. We conclude that the interaction of the 84KQ and SF1KQ domains, probably involving additional factors, tunes down Entamoeba virulence by favoring intron retention.
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Affiliation(s)
- Gretter González-Blanco
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Patricia Talmás-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Ester Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - José Manuel Galindo-Rosales
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Cristina Vélez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Odila Salucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX, Mexico
| | - Mario Alberto Rodríguez-Rodríguez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Tomoyoshi Nozaki
- Laboratory of Biomedical Chemistry, Department of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
- *Correspondence: Jesús Valdés,
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4
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Liu T, Pyle AM. Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi. Nucleic Acids Res 2021; 49:12422-12432. [PMID: 34850132 PMCID: PMC8643640 DOI: 10.1093/nar/gkab1077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/27/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
Fungal pathogens represent an expanding global health threat for which treatment options are limited. Self-splicing group II introns have emerged as promising drug targets, but their development has been limited by a lack of information on their distribution and architecture in pathogenic fungi. To meet this challenge, we developed a bioinformatic workflow for scanning sequence data to identify unique RNA structural signatures within group II introns. Using this approach, we discovered a set of ubiquitous introns within thermally dimorphic fungi (genera of Blastomyces, Coccidioides and Histoplasma). These introns are the most biochemically reactive group II introns ever reported, and they self-splice rapidly under near-physiological conditions without protein cofactors. Moreover, we demonstrated the small molecule targetability of these introns by showing that they can be inhibited by the FDA-approved drug mitoxantrone in vitro. Taken together, our results highlight the utility of structure-based informatic searches for identifying riboregulatory elements in pathogens, revealing a striking diversity of reactive self-splicing introns with great promise as antifungal drug targets.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA
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5
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Mukhopadhyay J, Hausner G. Organellar Introns in Fungi, Algae, and Plants. Cells 2021; 10:cells10082001. [PMID: 34440770 PMCID: PMC8393795 DOI: 10.3390/cells10082001] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022] Open
Abstract
Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.
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MESH Headings
- Evolution, Molecular
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Plant
- Genome, Fungal
- Genome, Plant
- Introns
- Organelles/genetics
- Organelles/metabolism
- RNA Splicing
- RNA Stability
- RNA, Algal/genetics
- RNA, Algal/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Transcription, Genetic
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6
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Mayers CG, Harrington TC, Wai A, Hausner G. Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens. Front Microbiol 2021; 12:656609. [PMID: 34149643 PMCID: PMC8208691 DOI: 10.3389/fmicb.2021.656609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022] Open
Abstract
Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid ‘ōhi‘a Death (ROD) in Hawai‘i. Despite being sexually incompatible, the two pathogens often co-occur in diseased ‘ōhi‘a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of ‘ōhi‘a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.
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Affiliation(s)
- Chase G Mayers
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Thomas C Harrington
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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7
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Wai A, Hausner G. The mitochondrial genome of Ophiostoma himal-ulmi and comparison with other fungi causing Dutch elm disease. Can J Microbiol 2021; 67:584-598. [PMID: 33566742 DOI: 10.1139/cjm-2020-0589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mitochondrial genome of Ophiostoma himal-ulmi, a species endemic to the Western Himalayas and one of the fungi that cause Dutch elm disease, has been sequenced and characterized. The mitochondrial genome was compared with other available genomes for members of the Ophiostomatales, including other agents of Dutch elm disease (Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi, and Ophiostoma novo-ulmi subspecies americana), and it was observed that gene synteny is highly conserved, and variability among members of the fungi that cause Dutch-elm disease is primarily due to the number of intron insertions. Among the fungi that cause Dutch elm disease that we examined, O. himal-ulmi has the largest mitochondrial genomes (ranging from 94 934 to 111 712 bp), owing to the expansion of the number of introns.
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Affiliation(s)
- Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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8
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Zubaer A, Wai A, Patel N, Perillo J, Hausner G. The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales. Front Microbiol 2021; 12:618649. [PMID: 33643245 PMCID: PMC7902536 DOI: 10.3389/fmicb.2021.618649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
Fungi assigned to the Ophiostomatales are of economic concern as many are blue-stain fungi and some are plant pathogens. The mitogenomes of two blue-stain fungi, Ophiostoma minus and Ophiostoma piliferum, were sequenced and compared with currently available mitogenomes for other members of the Ophiostomatales. Species representing various genera within the Ophiostomatales have been examined for gene content, gene order, phylogenetic relationships, and the distribution of mobile elements. Gene synteny is conserved among the Ophiostomatales but some members were missing the atp9 gene. A genome wide intron landscape has been prepared to demonstrate the distribution of the mobile genetic elements (group I and II introns and homing endonucleases) and to provide insight into the evolutionary dynamics of introns among members of this group of fungi. Examples of complex introns or nested introns composed of two or three intron modules have been observed in some species. The size variation among the mitogenomes (from 23.7 kb to about 150 kb) is mostly due to the presence and absence of introns. Members of the genus Sporothrix sensu stricto appear to have the smallest mitogenomes due to loss of introns. The taxonomy of the Ophiostomatales has recently undergone considerable revisions; however, some lineages remain unresolved. The data showed that genera such as Raffaelea appear to be polyphyletic and the separation of Sporothrix sensu stricto from Ophiostoma is justified.
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Affiliation(s)
- Abdullah Zubaer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Nikita Patel
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Jordan Perillo
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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9
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Kulik T, Van Diepeningen AD, Hausner G. Editorial: The Significance of Mitogenomics in Mycology. Front Microbiol 2021; 11:628579. [PMID: 33488569 PMCID: PMC7817700 DOI: 10.3389/fmicb.2020.628579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/10/2020] [Indexed: 01/30/2023] 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 & Research, Wageningen, Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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10
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
- Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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11
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Zubaer A, Wai A, Hausner G. The fungal mitochondrial Nad5 pan-genic intron landscape. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:835-842. [PMID: 31698975 DOI: 10.1080/24701394.2019.1687691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
An intron landscape was prepared for the fungal mitochondrial nad5 gene. A hundred and eighty-eight fungal species were examined and a total of 265 introns were noted to be located in 29 intron insertion sites within the examined nad5 genes. Two hundred and sixty-three introns could be classified as group I types and two group II introns were noted. One additional group II intron module was identified nested within a composite group I intron. Based on features related to RNA secondary structures, introns can be classified into different subtypes and it was observed that intron insertion-sites are biased towards phase 0 and they appear to be specific to an intron type. Intron landscapes could be used as a guide map to predict the location of fungal mtDNA mobile introns, which are composite elements that include a ribozyme component and in some instances open reading frames encoding homing endonucleases or reverse transcriptases and all of these have applications in biotechnology.
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Affiliation(s)
- Abdullah Zubaer
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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12
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Abboud TG, Zubaer A, Wai A, Hausner G. The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. Can J Microbiol 2018; 64:339-348. [DOI: 10.1139/cjm-2017-0605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.
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Affiliation(s)
- Talal George Abboud
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Abdullah Zubaer
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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13
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Abstract
Plant-associated fungi are infected by viruses at the incidence rates from a few % to over 90%. Multiple viruses often coinfect fungal hosts, and occasionally alter their phenotypes, but most of the infections are asymptomatic. Phenotypic alterations are grouped into two types: harmful or beneficial to the host fungi. Harmful interactions between viruses and hosts include hypovirulence and/or debilitation that are documented in a number of phytopathogenic fungi, exemplified by the chestnut blight, white root rot, and rapeseed rot fungi. Beneficial interactions are observed in a limited number of plant endophytic and pathogenic fungi where heat tolerance and virulence are enhanced, respectively. Coinfections of fungi provided a platform for discoveries of interesting virus/virus interactions that include synergistic, as in the case for those in plants, and unique antagonistic and mutualistic interactions between unrelated RNA viruses. Also discussed here are coinfection-induced genome rearrangements and frequently observed coinfections by the simplest positive-strand RNA virus, the mitoviruses.
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Affiliation(s)
- Bradley I Hillman
- Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, United States.
| | - Aulia Annisa
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan.
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Guha TK, Wai A, Mullineux ST, Hausner G. The intron landscape of the mtDNA cytb gene among the Ascomycota: introns and intron-encoded open reading frames. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1015-1024. [DOI: 10.1080/24701394.2017.1404042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tuhin K. Guha
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | | | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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15
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Bilto IM, Hausner G. The diversity of mtDNA rns introns among strains of Ophiostoma piliferum, Ophiostoma pluriannulatum and related species. SPRINGERPLUS 2016; 5:1408. [PMID: 27610327 PMCID: PMC4995192 DOI: 10.1186/s40064-016-3076-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/15/2016] [Indexed: 02/08/2023]
Abstract
Background Based on previous studies, it was suspected that the mitochondrial rns gene within the Ophiostomatales is rich in introns. This study focused on a collection of strains representing Ophiostoma piliferum, Ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. This reduces the value of the lumber. The goal was to examine the mtDNA rns intron landscape for these important blue stain fungi in order to facilitate future annotation of mitochondrial genomes (mtDNA) and to potentially identify mtDNA introns that can encode homing endonucleases which may have applications in biotechnology. Results Comparative sequence analysis identified five intron insertion sites among the ophiostomatoid fungi examined. Positions mS379 and mS952 harbor group II introns, the mS379 intron encodes a reverse transcriptase, and the mS952 intron encodes a potential homing endonuclease. Positions mS569, mS1224, and mS1247 have group I introns inserted and these encode intact or eroded homing endonuclease open reading frames (ORF). Phylogenetic analysis of the intron ORFs showed that they can be found in the same insertion site in closely and distantly related species. Conclusions Based on the molecular markers examined (rDNA internal transcribed spacers and rns introns), strains representing O. pilifera, O. pluriannulatum and Ophiostoma novae-zelandiae could not be resolved. Phylogenetic studies suggest that introns are gained and lost and that horizontal transfer could explain the presence of related intron in distantly related fungi. With regard to the mS379 group II intron, this study shows that mitochondrial group II introns and their reverse transcriptases may also follow the life cycle previously proposed for group I introns and their homing endonucleases. This consists of intron invasion, decay of intron ORF, loss of intron, and possible reinvasion. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-3076-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iman M Bilto
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
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16
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Hafez M, Guha TK, Hausner G. I-OmiI and I-OmiII: two intron-encoded homing endonucleases within the Ophiostoma minus rns gene. Fungal Biol 2014; 118:721-31. [PMID: 25110134 DOI: 10.1016/j.funbio.2014.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022]
Abstract
The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively). Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand) of the intron insertion site generating 4 nucleotide 3' overhangs. The endonuclease activity of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was difficult, thus the endonuclease activity of this protein was tested via in vivo assays. Overall this study showed that there are many native forms of functional homing endonucleases yet to be discovered among fungal mtDNA genomes.
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Affiliation(s)
- Mohamed Hafez
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Botany, Faculty of Science, Suez University, Suez, Egypt
| | - Tuhin Kumar Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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17
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Guha TK, Hausner G. A homing endonuclease with a switch: Characterization of a twintron encoded homing endonuclease. Fungal Genet Biol 2014; 65:57-68. [DOI: 10.1016/j.fgb.2014.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
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18
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Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis. Fungal Biol 2013; 117:791-806. [DOI: 10.1016/j.funbio.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/12/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022]
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19
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The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: Twintrons, introns, and intron-encoded proteins. Fungal Genet Biol 2013; 53:71-83. [DOI: 10.1016/j.fgb.2013.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/06/2013] [Accepted: 01/15/2013] [Indexed: 12/17/2022]
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20
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The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus. Fungal Biol 2011; 115:1122-37. [DOI: 10.1016/j.funbio.2011.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 05/28/2011] [Accepted: 07/15/2011] [Indexed: 12/18/2022]
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21
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Baidyaroy D, Hausner G, Fulbright DW, Bertrand H. Mitochondrial plasmid-like elements in some hypovirulent strains of Cryphonectria parasitica. Fungal Genet Biol 2011; 48:764-74. [DOI: 10.1016/j.fgb.2011.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 03/17/2011] [Accepted: 05/08/2011] [Indexed: 10/18/2022]
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