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Varassas SP, Amillis S, Pappas KM, Kouvelis VN. The Identification of the Mitochondrial DNA Polymerase γ (Mip1) of the Entomopathogenic Fungus Metarhizium brunneum. Microorganisms 2024; 12:1052. [PMID: 38930434 PMCID: PMC11205540 DOI: 10.3390/microorganisms12061052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Replication of the mitochondrial (mt) genome in filamentous fungi is under-studied, and knowledge is based mainly on data from yeasts and higher eukaryotes. In this study, the mitochondrial DNA polymerase γ (Mip1) of the entomopathogenic fungus Metarhizium brunneum is characterized and analyzed with disruption experiments and its in silico interactions with key proteins implicated in mt gene transcription, i.e., mt RNA polymerase Rpo41 and mt transcription factor Mtf1. Disruption of mip1 gene and its partial expression influences cell growth, morphology, germination and stress tolerance. A putative in silico model of Mip1-Rpo41-Mtf1, which is known to be needed for the initiation of replication, was proposed and helped to identify potential amino acid residues of Mip1 that interact with the Rpo41-Mtf1 complex. Moreover, the reduced expression of mip1 indicates that Mip1 is not required for efficient transcription but only for replication. Functional differences between the M. brunneum Mip1 and its counterparts from Saccharomyces cerevisiae and higher eukaryotes are discussed.
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Affiliation(s)
- Stylianos P. Varassas
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (S.P.V.); (K.M.P.)
| | - Sotiris Amillis
- Section of Botany, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Katherine M. Pappas
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (S.P.V.); (K.M.P.)
| | - Vassili N. Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (S.P.V.); (K.M.P.)
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2
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Golik P. RNA processing and degradation mechanisms shaping the mitochondrial transcriptome of budding yeasts. IUBMB Life 2024; 76:38-52. [PMID: 37596708 DOI: 10.1002/iub.2779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
Yeast mitochondrial genes are expressed as polycistronic transcription units that contain RNAs from different classes and show great evolutionary variability. The promoters are simple, and transcriptional control is rudimentary. Posttranscriptional mechanisms involving RNA maturation, stability, and degradation are thus the main force shaping the transcriptome and determining the expression levels of individual genes. Primary transcripts are fragmented by tRNA excision by RNase P and tRNase Z, additional processing events occur at the dodecamer site at the 3' end of protein-coding sequences. groups I and II introns are excised in a self-splicing reaction that is supported by protein splicing factors encoded by the nuclear genes, or by the introns themselves. The 3'-to-5' exoribonucleolytic complex called mtEXO is the main RNA degradation activity involved in RNA turnover and processing, supported by an auxiliary 5'-to-3' exoribonuclease Pet127p. tRNAs and, to a lesser extent, rRNAs undergo several different base modifications. This complex gene expression system relies on the coordinated action of mitochondrial and nuclear genes and undergoes rapid evolution, contributing to speciation events. Moving beyond the classical model yeast Saccharomyces cerevisiae to other budding yeasts should provide important insights into the coevolution of both genomes that constitute the eukaryotic genetic system.
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Affiliation(s)
- Pawel Golik
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Case NT, Westman J, Hallett MT, Plumb J, Farheen A, Maxson ME, MacAlpine J, Liston SD, Hube B, Robbins N, Whitesell L, Grinstein S, Cowen LE. Respiration supports intraphagosomal filamentation and escape of Candida albicans from macrophages. mBio 2023; 14:e0274523. [PMID: 38038475 PMCID: PMC10746240 DOI: 10.1128/mbio.02745-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Candida albicans is a leading human fungal pathogen that often causes life-threatening infections in immunocompromised individuals. The ability of C. albicans to transition between yeast and filamentous forms is key to its virulence, and this occurs in response to many host-relevant cues, including engulfment by host macrophages. While previous efforts identified C. albicans genes required for filamentation in other conditions, the genes important for this morphological transition upon internalization by macrophages remained largely enigmatic. Here, we employed a functional genomic approach to identify genes that enable C. albicans filamentation within macrophages and uncovered a role for the mitochondrial ribosome, respiration, and the SNF1 AMP-activated kinase complex. Additionally, we showed that glucose uptake and glycolysis by macrophages support C. albicans filamentation. This work provides insights into the metabolic dueling that occurs during the interaction of C. albicans with macrophages and identifies vulnerabilities in C. albicans that could serve as promising therapeutic targets.
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Affiliation(s)
- Nicola T. Case
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Johannes Westman
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Jonathan Plumb
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aiman Farheen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michelle E. Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sean D. Liston
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sergio Grinstein
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Center of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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4
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Zhang YJ, Fan XP, Li JN, Zhang S. Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps. IMA Fungus 2023; 14:13. [PMID: 37415259 DOI: 10.1186/s43008-023-00118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
Cordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
| | - Xiang-Ping Fan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia-Ni Li
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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5
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Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA. Curr Genet 2023; 69:55-65. [PMID: 36447017 PMCID: PMC9925561 DOI: 10.1007/s00294-022-01259-7] [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: 08/30/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 12/05/2022]
Abstract
Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.
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Łabędzka-Dmoch K, Rażew M, Gapińska M, Piątkowski J, Kolondra A, Salmonowicz H, Wenda JM, Nowotny M, Golik P. The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts. RNA (NEW YORK, N.Y.) 2022; 28:711-728. [PMID: 35197365 PMCID: PMC9014873 DOI: 10.1261/rna.079083.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/31/2022] [Indexed: 06/01/2023]
Abstract
Pet127 is a mitochondrial protein found in multiple eukaryotic lineages, but absent from several taxa, including plants and animals. Distant homology suggests that it belongs to the divergent PD-(D/E)XK superfamily which includes various nucleases and related proteins. Earlier yeast genetics experiments suggest that it plays a nonessential role in RNA degradation and 5' end processing. Our phylogenetic analysis suggests that it is a primordial eukaryotic invention that was retained in diverse groups, and independently lost several times in the evolution of other organisms. We demonstrate for the first time that the fungal Pet127 protein in vitro is a processive 5'-to-3' exoribonuclease capable of digesting various substrates in a sequence nonspecific manner. Mutations in conserved residues essential in the PD-(D/E)XK superfamily active site abolish the activity of Pet127. Deletion of the PET127 gene in the pathogenic yeast Candida albicans results in a moderate increase in the steady-state levels of several transcripts and in accumulation of unspliced precursors and intronic sequences of three introns. Mutations in the active site residues result in a phenotype identical to that of the deletant, confirming that the exoribonuclease activity is related to the physiological role of the Pet127 protein. Pet127 activity is, however, not essential for maintaining the mitochondrial respiratory activity in C. albicans.
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Affiliation(s)
- Karolina Łabędzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Michal Rażew
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Marta Gapińska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Hanna Salmonowicz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Laboratory of Metabolic Quality Control, IMOL, Polish Academy of Sciences, Warsaw 00-783, Poland
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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7
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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
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8
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Varassas SP, Kouvelis VN. Mitochondrial Transcription of Entomopathogenic Fungi Reveals Evolutionary Aspects of Mitogenomes. Front Microbiol 2022; 13:821638. [PMID: 35387072 PMCID: PMC8979003 DOI: 10.3389/fmicb.2022.821638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Entomopathogenic fungi and more specifically genera Beauveria and Metarhizium have been exploited for the biological control of pests. Genome analyses are important to understand better their mode of action and thus, improve their efficacy against their hosts. Until now, the sequences of their mitochondrial genomes were studied, but not at the level of transcription. Except of yeasts and Neurospora crassa, whose mt gene transcription is well described, in all other Ascomycota, i.e., Pezizomycotina, related information is extremely scarce. In this work, mt transcription and key enzymes of this function were studied. RT-PCR experiments and Northern hybridizations reveal the transcriptional map of the mt genomes of B. bassiana and M. brunneum species. The mt genes are transcribed in six main transcripts and undergo post-transcriptional modifications to create single gene transcripts. Promoters were determined in both mt genomes with a comparative in silico analysis, including all known information from other fungal mt genomes. The promoter consensus sequence is 5'-ATAGTTATTAT-3' which is in accordance with the definition of the polycistronic transcripts determined with the experiments described above. Moreover, 5'-RACE experiments in the case of premature polycistronic transcript nad1-nad4-atp8-atp6 revealed the 5' end of the RNA transcript immediately after the in silico determined promoter, as also found in other fungal species. Since several conserved elements were retrieved from these analyses compared to the already known data from yeasts and N. crassa, the phylogenetic analyses of mt RNA polymerase (Rpo41) and its transcriptional factor (Mtf1) were performed in order to define their evolution. As expected, it was found that fungal Rpo41 originate from the respective polymerase of T7/T3 phages, while the ancestor of Mtf1 is of alpha-proteobacterial origin. Therefore, this study presents insights about the fidelity of the mt single-subunit phage-like RNA polymerase during transcription, since the correct identification of mt promoters from Rpo41 requires an ortholog to bacterial sigma factor, i.e., Mtf1. Thus, a previously proposed hypothesis of a phage infected alpha-proteobacterium as the endosymbiotic progenitor of mitochondrion is confirmed in this study and further upgraded by the co-evolution of the bacterial (Mtf1) and viral (Rpo41) originated components in one functional unit.
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Affiliation(s)
| | - Vassili N. Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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9
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Global view of dynamic expression and precise mapping of mitochondrial tRNAs-derived fragments during stressed conditions in S. pombe. Mitochondrion 2021; 60:219-227. [PMID: 34428580 DOI: 10.1016/j.mito.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/14/2021] [Accepted: 08/19/2021] [Indexed: 01/30/2023]
Abstract
In this study, we provide a global view of population and processing of mitochondrial tRNAs-derived fragments (mt-tRFs) in fission yeast Schizosaccharomyces pombe. Here, mt-tRFs of 15-30 nucleotides were retrieved from S. pombe small RNA libraries obtained from unstressed, stress, and during stationary phase conditions. We demonstrate that production of these fragments increase during heat stress and stationary phase conditions in S. pombe, especially (most notably) in stationary phase. Analysis of data also reveals depending on the tRNA, either 5'-mt-tRF or 3'-mt-tRF was found and major mt-tRNA processing sites have been precisely identified. Furthermore, RNA-seq reveals that inactivation of trz2 encoding S. pombe mitochondrial tRNase ZL globally impairs mt-tRF processing. Finally, our result showed mt-tRFs were predicted to target mitochondrial genome mapping mtDNA-encoded protein gene. These observations suggest that mitochondrial tRFs may play an important regulatory role in response to stress and development.
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10
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Łabędzka-Dmoch K, Kolondra A, Karpińska MA, Dębek S, Grochowska J, Grochowski M, Piątkowski J, Hoang Diu Bui T, Golik P. Pervasive transcription of the mitochondrial genome in Candida albicans is revealed in mutants lacking the mtEXO RNase complex. RNA Biol 2021; 18:303-317. [PMID: 34229573 PMCID: PMC8677008 DOI: 10.1080/15476286.2021.1943929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The mitochondrial genome of the pathogenic yeast Candida albicans displays a typical organization of several (eight) primary transcription units separated by noncoding regions. Presence of genes encoding Complex I subunits and the stability of its mtDNA sequence make it an attractive model to study organellar genome expression using transcriptomic approaches. The main activity responsible for RNA degradation in mitochondria is a two-component complex (mtEXO) consisting of a 3ʹ-5ʹ exoribonuclease, in yeasts encoded by the DSS1 gene, and a conserved Suv3p helicase. In C. albicans, deletion of either DSS1 or SUV3 gene results in multiple defects in mitochondrial genome expression leading to the loss of respiratory competence. Transcriptomic analysis reveals pervasive transcription in mutants lacking the mtEXO activity, with evidence of the entire genome being transcribed, whereas in wild-type strains no RNAs corresponding to a significant fraction of the noncoding genome can be detected. Antisense (‘mirror’) transcripts, absent from normal mitochondria are also prominent in the mutants. The expression of multiple mature transcripts, particularly those translated from bicistronic mRNAs, as well as those that contain introns is affected in the mutants, resulting in a decreased level of proteins and reduced respiratory complex activity. The phenotype is most severe in the case of Complex IV, where a decrease of mature COX1 mRNA level to ~5% results in a complete loss of activity. These results show that RNA degradation by mtEXO is essential for shaping the mitochondrial transcriptome and is required to maintain the functional demarcation between transcription units and non-coding genome segments.
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Affiliation(s)
- Karolina Łabędzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena A Karpińska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Sonia Dębek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Joanna Grochowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej Grochowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Thi Hoang Diu Bui
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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11
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The mitochondrial genome of the grape powdery mildew pathogen Erysiphe necator is intron rich and exhibits a distinct gene organization. Sci Rep 2021; 11:13924. [PMID: 34230575 PMCID: PMC8260586 DOI: 10.1038/s41598-021-93481-5] [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: 04/05/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Powdery mildews are notorious fungal plant pathogens but only limited information exists on their genomes. Here we present the mitochondrial genome of the grape powdery mildew fungus Erysiphe necator and a high-quality mitochondrial gene annotation generated through cloning and Sanger sequencing of full-length cDNA clones. The E. necator mitochondrial genome consists of a circular DNA sequence of 188,577 bp that harbors a core set of 14 protein-coding genes that are typically present in fungal mitochondrial genomes, along with genes encoding the small and large ribosomal subunits, a ribosomal protein S3, and 25 mitochondrial-encoded transfer RNAs (mt-tRNAs). Interestingly, it also exhibits a distinct gene organization with atypical bicistronic-like expression of the nad4L/nad5 and atp6/nad3 gene pairs, and contains a large number of 70 introns, making it one of the richest in introns mitochondrial genomes among fungi. Sixty-four intronic ORFs were also found, most of which encoded homing endonucleases of the LAGLIDADG or GIY-YIG families. Further comparative analysis of five E. necator isolates revealed 203 polymorphic sites, but only five were located within exons of the core mitochondrial genes. These results provide insights into the organization of mitochondrial genomes of powdery mildews and represent valuable resources for population genetic and evolutionary studies.
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12
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Sekizuka T, Iguchi S, Umeyama T, Inamine Y, Makimura K, Kuroda M, Miyazaki Y, Kikuchi K. Clade II Candida auris possess genomic structural variations related to an ancestral strain. PLoS One 2019; 14:e0223433. [PMID: 31596885 PMCID: PMC6785063 DOI: 10.1371/journal.pone.0223433] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/20/2019] [Indexed: 01/09/2023] Open
Abstract
Candida auris is an invasive and multidrug-resistant ascomycetous yeast that is under global surveillance. All clinical cases of C. auris infection diagnosed from 1997 to 2019 in Japan were non-invasive and sporadic otitis media cases. In the present study, we performed whole-genome sequencing of seven C. auris strains isolated from patients with otitis media in Japan, all of which belonged to clade II. Comparative genome analysis using the high-quality draft genome sequences JCM 15448T revealed that single nucleotide variations (SNVs), clade-specific accessory genes, and copy number variations (CNVs) were identified in each C. auris clade. A total of 61 genes involved in cell wall and stress response-related functions was absent in clade II, and the pattern of conserved CNVs in each clade was more stable in clade II than in other clades. Our data suggest that the genomic structural diversity is stable in C. auris isolated from each biogeographic location, and Japanese strains isolated from patients with otitis media might belong to an ancestral type of C. auris. One Japanese strain, TWCC 58362, with reduced susceptibility to fluconazole, exhibited no mutation in ergosterol biosynthesis-related genes (ERG). However, TWCC 58362-specific variations, including SNVs, indels, and CNVs were detected, suggesting that gene duplication events in C. auris might contribute to antifungal drug resistance. Taken together, we demonstrated that genomic structural variations in C. auris could correlate to geographical dissemination, epidemiology, lesions in the host, and antifungal resistance.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (TS); (KK)
| | - Shigekazu Iguchi
- Department of Infectious Diseases, Tokyo Women’s Medical University, Tokyo, Japan
| | - Takashi Umeyama
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuba Inamine
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Makimura
- Department of Medical Mycology, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshitsugu Miyazaki
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Kikuchi
- Department of Infectious Diseases, Tokyo Women’s Medical University, Tokyo, Japan
- * E-mail: (TS); (KK)
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13
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Phan HE, Northorp M, Lalonde RL, Ngo D, Akimenko MA. Differential actinodin1 regulation in embryonic development and adult fin regeneration in Danio rerio. PLoS One 2019; 14:e0216370. [PMID: 31048899 PMCID: PMC6497306 DOI: 10.1371/journal.pone.0216370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Actinotrichia are the first exoskeletal elements formed during zebrafish fin development. These rigid fibrils serve as skeletal support for the fin fold and as substrates for mesenchymal cell migration. In the adult intact fins, actinotrichia are restricted to the distal domain of the fin. Following fin amputation, actinotrichia also reform during regeneration. The actinodin gene family codes for structural proteins of actinotrichia. We have previously identified cis-acting regulatory elements in a 2kb genomic region upstream of the first exon of actinodin1, termed 2P, required for tissue-specific expression in the fin fold ectoderm and mesenchyme during embryonic development. Indeed, 2P contains an ectodermal enhancer in a 150bp region named epi. Deletion of epi from 2P results in loss of ectodermal-specific activity. In the present study, we sought to further characterize the activity of these regulatory sequences throughout fin development and during adult fin regeneration. Using a reporter transgenic approach, we show that a site within the epi region, termed epi3, contains an early mesenchymal-specific repressor. We also show that the larval fin fold ectodermal enhancer within epi3 remains functional in the basal epithelial layer during fin regeneration. We show that the first non-coding exon and first intron of actinodin1 contains a transcriptional enhancer and an alternative promoter that are necessary for the persistence of reporter expression reminiscent of actinodin1 expression during adulthood. Altogether, we have identified cis-acting regulatory elements that are required for tissue-specific expression as well as full recapitulation of actinodin1 expression during adulthood. Furthermore, the characterization of these elements provides us with useful molecular tools for the enhancement of transgene expression in adulthood.
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Affiliation(s)
- Hue-Eileen Phan
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marissa Northorp
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert L. Lalonde
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Dung Ngo
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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14
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Shang J, Yang Y, Wu L, Zou M, Huang Y. The S. pombe mitochondrial transcriptome. RNA (NEW YORK, N.Y.) 2018; 24:1241-1254. [PMID: 29954949 PMCID: PMC6097661 DOI: 10.1261/rna.064477.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/26/2018] [Indexed: 05/22/2023]
Abstract
Mitochondrial gene expression is largely controlled through post-transcriptional processes including mitochondrial RNA (mt-RNA) processing, modification, decay, and quality control. Defective mitochondrial gene expression results in mitochondrial oxidative phosphorylation (OXPHOS) deficiency and has been implicated in human disease. To fully understand mitochondrial transcription and RNA processing, we performed RNA-seq analyses of mt-RNAs from the fission yeast Schizosaccharomyces pombe RNA-seq analyses show that the abundance of mt-RNAs vary greatly. Analysis of data also reveals mt-RNA processing sites including an unusual RNA cleavage event by mitochondrial tRNA (mt-tRNA) 5'-end processing enzyme RNase P. Additionally, this analysis reveals previously unknown mitochondrial transcripts including the rnpB-derived fragment, mitochondrial small RNAs (mitosRNAs) such as mt-tRNA-derived fragments (mt-tRFs) and mt-tRNA halves, and mt-tRNAs marked with 3'-CCACCA/CCACC in S. pombe Finally, RNA-seq reveals that inactivation of trz2 encoding S. pombe mitochondrial tRNA 3'-end processing enzyme globally impairs mt-tRNA 3'-end processing, inhibits mt-mRNA 5'-end processing, and causes accumulation of unprocessed transcripts, demonstrating the feasibility of using RNA-seq to examine the protein known or predicted to be involved in mt-RNA processing in S. pombe Our work uncovers the complexity of a fungal mitochondrial transcriptome and provides a framework for future studies of mitochondrial gene expression using S. pombe as a model system.
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Affiliation(s)
- Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yanmei Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Lin Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengting Zou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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15
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Bartelli TF, Bruno DCF, Briones MRS. Evidence for Mitochondrial Genome Methylation in the Yeast Candida albicans: A Potential Novel Epigenetic Mechanism Affecting Adaptation and Pathogenicity? Front Genet 2018; 9:166. [PMID: 29896215 PMCID: PMC5986885 DOI: 10.3389/fgene.2018.00166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/26/2018] [Indexed: 12/23/2022] Open
Abstract
The commensal yeast Candida albicans is an opportunistic pathogen. In order to successfully colonize or infect the human body, the fungus must adapt to the host’s environmental conditions, such as low oxygen tension (hypoxia), temperature (37°C), and the different carbon sources available. Previous studies demonstrated the adaptive importance of C. albicans genetic variability for its pathogenicity, although the contributions of epigenetic and the influence of environmental factors are not fully understood. Mitochondria play important roles in fungal energetic metabolism, regulation of nuclear epigenetic mechanisms and pathogenicity. However, the specific impact of inter-strain mitochondrial genome variability and mitochondrial epigenetics in pathogenicity is unclear. Here, we draw attention to this relevant organelle and its potential role in C. albicans pathogenicity and provide preliminary evidence, for the first time, for methylation of the yeast mitochondrial genome. Our results indicate that environmental conditions, such as continuous exposure for 12 weeks to hypoxia and 37°C, decrease the mitochondrial genome methylation in strains SC5314 and L757. However, the methylation decrease is quantitatively different in specific genome positions when strains SC5314 and L757 are compared. We hypothesize that this phenomenon can be promising for future research to understand how physical factors of the host affect the C. albicans mitochondrial genome and its possible impact on adaptation and pathogenicity.
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Affiliation(s)
- Thais F Bartelli
- Laboratory of Evolutionary Genomics and Biocomplexity, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil.,Laboratory of Medical Genomics, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Danielle C F Bruno
- Laboratory of Evolutionary Genomics and Biocomplexity, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
| | - Marcelo R S Briones
- Laboratory of Evolutionary Genomics and Biocomplexity, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil.,Department of Health Informatics, Federal University of São Paulo, São Paulo, Brazil
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16
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Abstract
The human mitochondrial glutamate dehydrogenase isoenzymes (hGDH1 and hGDH2) are abundant matrix-localized proteins encoded by nuclear genes. The proteins are synthesized in the cytoplasm, with an atypically long N-terminal mitochondrial targeting sequence (MTS). The results of secondary structure predictions suggest the presence of two α-helices within the N-terminal region of the MTS. Results from deletion analyses indicate that individual helices have limited ability to direct protein import and matrix localization, but that there is a synergistic interaction when both helices are present [Biochem. J. (2016) 473: , 2813-2829]. Mutagenesis of the MTS cleavage sites blocked post-import removal of the presequences, but did not impede import. The authors propose that the high matrix levels of hGDH can be attributed to the unusual length and secondary structure of the MTS.
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17
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Zhang Y, Avalos JL. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28067471 DOI: 10.1002/wsbm.1373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023]
Abstract
Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans-omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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18
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Kruszewski J, Golik P. Pentatricopeptide Motifs in the N-Terminal Extension Domain of Yeast Mitochondrial RNA Polymerase Rpo41p Are Not Essential for Its Function. BIOCHEMISTRY. BIOKHIMIIA 2016; 81:1101-1110. [PMID: 27908235 DOI: 10.1134/s0006297916100084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The core mitochondrial RNA polymerase is a single-subunit enzyme that in yeast Saccharomyces cerevisiae is encoded by the nuclear RPO41 gene. It is an evolutionary descendant of the bacteriophage RNA polymerases, but it includes an additional unconserved N-terminal extension (NTE) domain that is unique to the organellar enzymes. This domain mediates interactions between the polymerase and accessory regulatory factors, such as yeast Sls1p and Nam1p. Previous studies demonstrated that deletion of the entire NTE domain results only in a temperature-dependent respiratory deficiency. Several sequences related to the pentatricopeptide (PPR) motifs were identified in silico in Rpo41p, three of which are located in the NTE domain. PPR repeat proteins are a large family of organellar RNA-binding factors, mostly involved in posttranscriptional gene expression mechanisms. To study their function, we analyzed the phenotype of strains bearing Rpo41p variants where each of these motifs was deleted. We found that deletion of any of the three PPR motifs in the NTE domain does not affect respiratory growth at normal temperature, and it results in a moderate decrease in mtDNA stability. Steady-state levels of COX1 and COX2 mRNAs are also moderately affected. Only the deletion of the second motif results in a partial respiratory deficiency, manifested only at elevated temperature. Our results thus indicate that the PPR motifs do not play an essential role in the function of the NTE domain of the mitochondrial RNA polymerase.
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Affiliation(s)
- J Kruszewski
- University of Warsaw, Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw, 02-106, Poland.
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19
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Sanitá Lima M, Woods LC, Cartwright MW, Smith DR. The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes. Mol Ecol Resour 2016; 16:1279-1286. [PMID: 27482846 DOI: 10.1111/1755-0998.12585] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 02/04/2023]
Abstract
Not long ago, scientists paid dearly in time, money and skill for every nucleotide that they sequenced. Today, DNA sequencing technologies epitomize the slogan 'faster, easier, cheaper and more', and in many ways, sequencing an entire genome has become routine, even for the smallest laboratory groups. This is especially true for mitochondrial and plastid genomes. Given their relatively small sizes and high copy numbers per cell, organelle DNAs are currently among the most highly sequenced kind of chromosome. But accurately characterizing an organelle genome and the information it encodes can require much more than DNA sequencing and bioinformatics analyses. Organelle genomes can be surprisingly complex and can exhibit convoluted and unconventional modes of gene expression. Unravelling this complexity can demand a wide assortment of experiments, from pulsed-field gel electrophoresis to Southern and Northern blots to RNA analyses. Here, we show that it is exactly these types of 'complementary' analyses that are often lacking from contemporary organelle genome papers, particularly short 'genome announcement' articles. Consequently, crucial and interesting features of organelle chromosomes are going undescribed, which could ultimately lead to a poor understanding and even a misrepresentation of these genomes and the genes they express. High-throughput sequencing and bioinformatics have made it easy to sequence and assemble entire chromosomes, but they should not be used as a substitute for or at the expense of other types of genomic characterization methods.
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Affiliation(s)
- Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Laura C Woods
- Department of Biology, University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Matthew W Cartwright
- Department of Biology, University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada, N6A 5B7.
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