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Zhu L, Su Y, Ma S, Guo L, Yang S, Yu H. Comparative Proteomic Analysis Reveals Candidate Pathways Related to the Effect of Different Light Qualities on the Development of Mycelium and Fruiting Body of Pleurotus ostreatus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1361-1375. [PMID: 38166381 DOI: 10.1021/acs.jafc.3c06083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Light affects the morphology and physiology of Pleurotus ostreatus. However, the underlying molecular mechanism of this effect remains unclear. In this study, a label-free comparative proteomic analysis was conducted to investigate the global protein expression profile of the mycelia and fruiting bodies of P. ostreatus PH11 growing under four different light quality treatments. Among all the 2234 P. ostreatus proteins, 1349 were quantifiable under all tested conditions. A total of 1100 differentially expressed proteins were identified by comparing the light group data with those of the darkness group. GO and KEGG enrichment analyses indicated that the oxidative phosphorylation, proteasome, and mRNA surveillance pathways were the most related pathways under the light condition. qRT-PCR verified that the expression of the white collar 1 protein was significantly enhanced under white light. Additionally, glutamine synthetase and aldehyde dehydrogenase played important roles during light exposure. This study provides valuable insight into the P. ostreatus light response mechanism, which will lay the foundation for improved cultivation.
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Affiliation(s)
- Liping Zhu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
| | - Yao Su
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
| | - Shunan Ma
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
| | - Song Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, Shandong Province266109, People's Republic of China
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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: 7] [Impact Index Per Article: 3.5] [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.
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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)
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Kwak Y. An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma. Microorganisms 2021; 9:1564. [PMID: 34442643 PMCID: PMC8401334 DOI: 10.3390/microorganisms9081564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.
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Affiliation(s)
- Yunyoung Kwak
- Écologie, Systématique et Évolution, CNRS, Université Paris Sud (Paris XI), Université Paris Saclay, AgroParisTech, 91400 Orsay, France;
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Institute for Quality and Safety Assessment of Agricultural Products, Kyungpook National University, Daegu 41566, Korea
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4
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Mamouei Z, Singh S, Lemire B, Gu Y, Alqarihi A, Nabeela S, Li D, Ibrahim A, Uppuluri P. An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans. PLoS Biol 2021; 19:e3000957. [PMID: 33720927 PMCID: PMC8007014 DOI: 10.1371/journal.pbio.3000957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/29/2021] [Accepted: 01/29/2021] [Indexed: 11/19/2022] Open
Abstract
A forward genetic screening approach identified orf19.2500 as a gene controlling Candida albicans biofilm dispersal and biofilm detachment. Three-dimensional (3D) protein modeling and bioinformatics revealed that orf19.2500 is a conserved mitochondrial protein, structurally similar to, but functionally diverged from, the squalene/phytoene synthases family. The C. albicans orf19.2500 is distinguished by 3 evolutionarily acquired stretches of amino acid inserts, absent from all other eukaryotes except a small number of ascomycete fungi. Biochemical assays showed that orf19.2500 is required for the assembly and activity of the NADH ubiquinone oxidoreductase Complex I (CI) of the respiratory electron transport chain (ETC) and was thereby named NDU1. NDU1 is essential for respiration and growth on alternative carbon sources, important for immune evasion, required for virulence in a mouse model of hematogenously disseminated candidiasis, and for potentiating resistance to antifungal drugs. Our study is the first report on a protein that sets the Candida-like fungi phylogenetically apart from all other eukaryotes, based solely on evolutionary "gain" of new amino acid inserts that are also the functional hub of the protein.
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Affiliation(s)
- Zeinab Mamouei
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
| | - Shakti Singh
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Bernard Lemire
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Yiyou Gu
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Abdullah Alqarihi
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Sunna Nabeela
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Ashraf Ibrahim
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Priya Uppuluri
- David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America
- Division of Infectious Disease, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
- * E-mail:
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Liang L, Cheng X, Dai T, Wang Z, Li J, Li X, Lei B, Liu P, Hao J, Liu X. Metabolic Fingerprinting for Identifying the Mode of Action of the Fungicide SYP-14288 on Rhizoctonia solani. Front Microbiol 2020; 11:574039. [PMID: 33362733 PMCID: PMC7755717 DOI: 10.3389/fmicb.2020.574039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/11/2020] [Indexed: 01/11/2023] Open
Abstract
The fungicide SYP-14288 has a high efficiency, low toxicity, and broad spectrum in inhibiting both fungi and oomycetes, but its mode of action (MoA) remains unclear on inhibiting fungi. In this study, the MoA was determined by analyzing the metabolism and respiratory activities of Rhizoctonia solani treated by SYP-14288. Wild-type strains and SYP-14288-resistant mutants of R. solani were incubated on potato dextrose agar amended with either SYP-14288 or one of select fungicides acting on fungal respiration, including complex I, II, and III inhibitors; uncouplers; and ATP synthase inhibitors. Mycelial growth was measured under fungicides treatments. ATP content was determined using an ATP assay kit, membrane potential of mitochondria was detected with the JC-1 kit, and respiratory rate was calculated based on the measurement of oxygen consumption of R. solani. A model of metabolic fingerprinting cluster was established to separate oxidation inhibitors and phosphorylation inhibitors. All the results together displayed a clear discrimination between oxidation inhibitors and phosphorylation inhibitors, and the latter inhibited ATP synthase production having or uncoupling activities. Based on the model, SYP-14288 was placed in phosphorylation inhibitor group, because it significantly reduced ATP content and membrane potential of mitochondria while increasing respiratory rate in R. solani. Therefore, the MoA of SYP-14288 on R. solani was confirmed to involve phosphorylation inhibition and possibly uncoupling activity.
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Affiliation(s)
- Li Liang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xingkai Cheng
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Tan Dai
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhiwen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jin Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xueming Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Bin Lei
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Pengfei Liu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME, United States
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, China
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6
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Zhang Y, Yang G, Fang M, Deng C, Zhang KQ, Yu Z, Xu J. Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi. Front Microbiol 2020; 11:617. [PMID: 32351475 PMCID: PMC7174627 DOI: 10.3389/fmicb.2020.00617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Guangzhu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Meiling Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Chu Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
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7
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Abstract
Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolism. Mitochondria, which have a central metabolic role, have undergone many lineage-specific adaptations in association with their eukaryotic host. A screen for lineage-specific genes identified seven such genes specific to the CTG clade of fungi, of which C. albicans is a member. Each is required for respiratory growth and is integral to expression of complex I, III, or IV of the electron transport chain. Two genes, NUO3 and NUO4, encode supernumerary subunits of complex I, whereas NUE1 and NUE2 have nonstructural roles in expression of complex I. Similarly, the other three genes have nonstructural roles in expression of complex III (QCE1) or complex IV (COE1 and COE2). In addition to these novel additions, an alternative functional assignment was found for the mitochondrial protein encoded by MNE1 MNE1 was required for complex I expression in C. albicans, whereas the distantly related Saccharomyces cerevisiae ortholog participates in expression of complex III. Phenotypic analysis of deletion mutants showed that fermentative metabolism is unable to support optimal growth rates or yields of C. albicans However, yeast-hypha morphogenesis, an important virulence attribute, did not require respiratory metabolism under hypoxic conditions. The inability to respire also resulted in hypersensitivity to the antifungal fluconazole and in attenuated virulence in a Galleria mellonella infection model. The results show that lineage-specific adaptations have occurred in C. albicans mitochondria and highlight the significance of respiratory metabolism in the pathobiology of C. albicans IMPORTANCE Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolic behavior, and mitochondria have a central role in that metabolism. Mitochondria have undergone many evolutionary changes, which include lineage-specific adaptations in association with their eukaryotic host. Seven lineage-specific genes required for electron transport chain function were identified in the CTG clade of fungi, of which C. albicans is a member. Additionally, examination of several highly diverged orthologs encoding mitochondrial proteins demonstrated functional reassignment for one of these. Deficits imparted by deletion of these genes revealed the critical role of respiration in virulence attributes of the fungus and highlight important evolutionary adaptations in C. albicans metabolism.
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Pogoda CS, Keepers KG, Lendemer JC, Kane NC, Tripp EA. Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses. Mol Ecol 2018; 27:1155-1169. [DOI: 10.1111/mec.14519] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 12/21/2017] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
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9
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Robicheau BM, Young AP, LaButti K, Grigoriev IV, Walker AK. The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex. Fungal Biol 2016; 121:212-221. [PMID: 28215349 DOI: 10.1016/j.funbio.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/10/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada
| | - Alexander P Young
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Allison K Walker
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada.
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10
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Complete Mitochondrial Genome Sequence of the Pezizomycete Pyronema confluens. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00355-16. [PMID: 27174271 PMCID: PMC4866847 DOI: 10.1128/genomea.00355-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The complete mitochondrial genome of the ascomycete Pyronema confluens has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes.
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11
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Freel KC, Friedrich A, Schacherer J. Mitochondrial genome evolution in yeasts: an all-encompassing view. FEMS Yeast Res 2015; 15:fov023. [PMID: 25969454 DOI: 10.1093/femsyr/fov023] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2015] [Indexed: 12/26/2022] Open
Abstract
Mitochondria are important organelles that harbor their own genomes encoding a key set of proteins that ensure respiration and provide the eukaryotic cell with energy. Recent advances in high-throughput sequencing technologies present a unique opportunity to explore mitochondrial (mt) genome evolution. The Saccharomycotina yeasts have proven to be the leading organisms for mt comparative and population genomics. In fact, the explosion of complete yeast mt genome sequences has allowed for a broader view of the mt diversity across this incredibly diverse subphylum, both within and between closely related species. Here, we summarize the present state of yeast mitogenomics, including the currently available data and what it reveals concerning the diversity of content, organization, structure and evolution of mt genomes.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
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12
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Mardanov AV, Beletsky AV, Kadnikov VV, Ignatov AN, Ravin NV. The 203 kbp mitochondrial genome of the phytopathogenic fungus Sclerotinia borealis reveals multiple invasions of introns and genomic duplications. PLoS One 2014; 9:e107536. [PMID: 25216190 PMCID: PMC4162613 DOI: 10.1371/journal.pone.0107536] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/19/2014] [Indexed: 01/13/2023] Open
Abstract
Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.
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Affiliation(s)
| | | | | | | | - Nikolai V. Ravin
- Centre “Bioengineering”, Russian Academy of Sciences, Moscow, Russia
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13
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FUNGALOXPHOS: An integrated database for oxidative phosphorylation in fungi. Mitochondrion 2013; 13:357-9. [DOI: 10.1016/j.mito.2013.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/29/2013] [Accepted: 04/19/2013] [Indexed: 11/15/2022]
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14
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Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA. NDUFA4 is a subunit of complex IV of the mammalian electron transport chain. Cell Metab 2012; 16:378-86. [PMID: 22902835 DOI: 10.1016/j.cmet.2012.07.015] [Citation(s) in RCA: 274] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/18/2012] [Accepted: 07/26/2012] [Indexed: 12/19/2022]
Abstract
The oxidative phosphorylation system is one of the best-characterized metabolic pathways. In mammals, the protein components and X-ray structures are defined for all complexes except complex I. Here, we show that NDUFA4, formerly considered a constituent of NADH Dehydrogenase (CI), is instead a component of the cytochrome c oxidase (CIV). Deletion of NDUFA4 does not perturb CI. Rather, proteomic, genetic, evolutionary, and biochemical analyses reveal that NDUFA4 plays a role in CIV function and biogenesis. The change in the attribution of the NDUFA4 protein requires renaming of the gene and reconsideration of the structure of CIV. Furthermore, NDUFA4 should be considered a candidate gene for CIV rather than CI deficiencies in humans.
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Affiliation(s)
- Eduardo Balsa
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, 28029, Spain
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Duò A, Bruggmann R, Zoller S, Bernt M, Grünig CR. Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex. BMC Genomics 2012; 13:166. [PMID: 22559219 PMCID: PMC3434094 DOI: 10.1186/1471-2164-13-166] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 05/04/2012] [Indexed: 01/01/2023] Open
Abstract
Background Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC). PAC belongs to the Helotiales, which is one of the most diverse groups of ascomycetes including more than 2,000 species. The gene order was compared to deduce the mt genome evolution in the Pezizomycotina. Genetic variation in coding and intergenic regions of the mtDNA was studied for PAC to assess the usefulness of mt DNA for species diagnosis. Results The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) and a putative N-acetyl-transferase were recognized. A complete set of tRNA genes as well as the large and small rRNA genes but no introns were found. All protein-coding genes were confirmed by EST sequences. The gene order in P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, the only other helotialean species with a fully sequenced and annotated mt genome. Gene order analysis within Pezizomycotina suggests that the evolution of gene orders is mostly driven by transpositions. Furthermore, sequence diversity in coding and non-coding mtDNA regions in seven additional PAC species was pronounced and allowed for unequivocal species diagnosis in PAC. Conclusions The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, which can be used as a reference for the annotation of other mt genomes in the Helotiales. In addition, our analyses show that mtDNA loci will be the marker of choice for future analysis of PAC communities.
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Affiliation(s)
- Angelo Duò
- Forest Pathology and Dendrology, Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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16
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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Dequard-Chablat M, Sellem CH, Golik P, Bidard F, Martos A, Bietenhader M, di Rago JP, Sainsard-Chanet A, Hermann-Le Denmat S, Contamine V. Two Nuclear Life Cycle-Regulated Genes Encode Interchangeable Subunits c of Mitochondrial ATP Synthase in Podospora anserina. Mol Biol Evol 2011; 28:2063-75. [DOI: 10.1093/molbev/msr025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Hayashi M, Schilke B, Marszalek J, Williams B, Craig EA. Ancient gene duplication provided a key molecular step for anaerobic growth of Baker's yeast. Mol Biol Evol 2011; 28:2005-17. [PMID: 21245414 DOI: 10.1093/molbev/msr019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mitochondria are essential organelles required for a number of key cellular processes. As most mitochondrial proteins are nuclear encoded, their efficient translocation into the organelle is critical. Transport of proteins across the inner membrane is driven by a multicomponent, matrix-localized "import motor," which is based on the activity of the molecular chaperone Hsp70 and a J-protein cochaperone. In Saccharomyces cerevisiae, two paralogous J-proteins, Pam18 and Mdj2, can form the import motor. Both contain transmembrane and matrix domains, with Pam18 having an additional intermembrane space (IMS) domain. Evolutionary analyses revealed that the origin of the IMS domain of S. cerevisiae Pam18 coincides with a gene duplication event that generated the PAM18/MDJ2 gene pair. The duplication event and origin of the Pam18 IMS domain occurred at the relatively ancient divergence of the fungal subphylum Saccharomycotina. The timing of the duplication event also corresponds with a number of additional functional changes related to mitochondrial function and respiration. Physiological and genetic studies revealed that the IMS domain of Pam18 is required for efficient growth under anaerobic conditions, even though it is dispensable when oxygen is present. Thus, the gene duplication was beneficial for growth capacity under particular environmental conditions as well as diversification of the import motor components.
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Affiliation(s)
- Masaya Hayashi
- Department of Biochemistry, University of Wisconsin-Madison, USA
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Marcet-Houben M, Marceddu G, Gabaldón T. Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. BMC Evol Biol 2009; 9:295. [PMID: 20025735 PMCID: PMC2803194 DOI: 10.1186/1471-2148-9-295] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 12/21/2009] [Indexed: 11/10/2022] Open
Abstract
Background Oxidative phosphorylation is central to the energy metabolism of the cell. Due to adaptation to different life-styles and environments, fungal species have shaped their respiratory pathways in the course of evolution. To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species. Results Besides clarifying orthology and paralogy relationships among respiratory proteins, our results reveal three parallel losses of the entire complex I, two of which are coupled to duplications in alternative dehydrogenases. Duplications in respiratory proteins have been common, affecting 76% of the protein families surveyed. We detect several instances of paralogs of genes coding for subunits of respiratory complexes that have been recruited to other multi-protein complexes inside and outside the mitochondrion, emphasizing the role of evolutionary tinkering. Conclusions Processes of gene loss and gene duplication followed by functional divergence have been rampant in the evolution of fungal respiration. Overall, the core proteins of the respiratory pathways are conserved in most lineages, with major changes affecting the lineages of microsporidia, Schizosaccaromyces and Saccharomyces/Kluyveromyces due to adaptation to anaerobic life-styles. We did not observe specific adaptations of the respiratory metabolism common to all pathogenic species.
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Abstract
NADH:ubiquinone oxidoreductase (complex I) is an entry point for electrons into the respiratory chain in many eukaryotes. It couples NADH oxidation and ubiquinone reduction to proton translocation across the mitochondrial inner membrane. Because complex I deficiencies occur in a wide range of neuromuscular diseases, including Parkinson's disease, there is a clear need for model eukaryotic systems to facilitate structural, functional and mutational studies. In the present study, we describe the purification and characterization of the complexes I from two yeast species, Pichia pastoris and Pichia angusta. They are obligate aerobes which grow to very high cell densities on simple medium, as yeast-like, spheroidal cells. Both Pichia enzymes catalyse inhibitor-sensitive NADH:ubiquinone oxidoreduction, display EPR spectra which match closely to those from other eukaryotic complexes I, and show patterns characteristic of complex I in SDS/PAGE analysis. Mass spectrometry was used to identify several canonical complex I subunits. Purified P. pastoris complex I has a particularly high specific activity, and incorporating it into liposomes demonstrates that NADH oxidation is coupled to the generation of a protonmotive force. Interestingly, the rate of NADH-induced superoxide production by the Pichia enzymes is more than twice as high as that of the Bos taurus enzyme. Our results both resolve previous disagreement about whether Pichia species encode complex I, furthering understanding of the evolution of complex I within dikarya, and they provide two new, robust and highly active model systems for study of the structure and catalytic mechanism of eukaryotic complexes I.
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