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Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
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Affiliation(s)
- Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
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Chen Y, Miao Y, Bai W, Lin K, Pang E. Characteristics and potential functional effects of long insertions in Asian butternuts. BMC Genomics 2022; 23:732. [PMID: 36307757 PMCID: PMC9617325 DOI: 10.1186/s12864-022-08961-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species.
Results
We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS (https://github.com/CMB-BNU/PLAINS.git), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing.
Conclusions
Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.
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Schröder L, Hegermann J, Pille P, Braun HP. The photosynthesis apparatus of European mistletoe (Viscum album). PLANT PHYSIOLOGY 2022; 190:1896-1914. [PMID: 35976139 PMCID: PMC9614478 DOI: 10.1093/plphys/kiac377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
European mistletoe (Viscum album) is known for its special mode of cellular respiration. It lacks the mitochondrial NADH dehydrogenase complex (Complex I of the respiratory chain) and has restricted capacities to generate mitochondrial adenosine triphosphate (ATP). Here, we present an investigation of the V. album energy metabolism taking place in chloroplasts. Thylakoids were purified from young V. album leaves, and membrane-bound protein complexes were characterized by Blue native polyacrylamide gel electrophoresis as well as by the complexome profiling approach. Proteins were systematically identified by label-free quantitative shotgun proteomics. We identified >1,800 distinct proteins (accessible at https://complexomemap.de/va_leaves), including nearly 100 proteins forming part of the protein complexes involved in the light-dependent part of photosynthesis. The photosynthesis apparatus of V. album has distinct features: (1) comparatively low amounts of Photosystem I; (2) absence of the NDH complex (the chloroplast pendant of mitochondrial Complex I involved in cyclic electron transport (CET) around Photosystem I); (3) reduced levels of the proton gradient regulation 5 (PGR5) and proton gradient regulation 5-like 1 (PGRL1) proteins, which offer an alternative route for CET around Photosystem I; (4) comparable amounts of Photosystem II and the chloroplast ATP synthase complex to other seed plants. Our data suggest a restricted capacity for chloroplast ATP biosynthesis by the photophosphorylation process. This is in addition to the limited ATP supply by the mitochondria. We propose a view on mistletoe's mode of life, according to which its metabolism relies to a greater extent on energy-rich compounds provided by the host trees.
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Affiliation(s)
- Lucie Schröder
- Institut für Pflanzgenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jan Hegermann
- Institut für Funktionelle und Angewandte Anatomie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Patrick Pille
- Institut für Pflanzgenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Schröder L, Hohnjec N, Senkler M, Senkler J, Küster H, Braun HP. The gene space of European mistletoe (Viscum album). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:278-294. [PMID: 34713513 DOI: 10.1111/tpj.15558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
European mistletoe (Viscum album) is a hemiparasitic flowering plant that is known for its very special life cycle and extraordinary biochemical properties. Particularly, V. album has an unusual mode of cellular respiration that takes place in the absence of mitochondrial complex I. However, insights into the molecular biology of V. album so far are very limited. Since the genome of V. album is extremely large (estimated 600 times larger than the genome of the model plant Arabidopsis thaliana) it has not been sequenced up to now. We here report sequencing of the V. album gene space (defined as the space including and surrounding genic regions, encompassing coding as well as 5' and 3' non-coding regions). mRNA fractions were isolated from different V. album organs harvested in summer or winter and were analyzed via single-molecule real-time sequencing. We determined sequences of 39 092 distinct open reading frames encoding 32 064 V. album proteins (designated V. album protein space). Our data give new insights into the metabolism and molecular biology of V. album, including the biosynthesis of lectins and viscotoxins. The benefits of the V. album gene space information are demonstrated by re-evaluating mass spectrometry-based data of the V. album mitochondrial proteome, which previously had been evaluated using the A. thaliana genome sequence. Our re-examination allowed the additional identification of nearly 200 mitochondrial proteins, including four proteins related to complex I, which all have a secondary function not related to respiratory electron transport. The V. album gene space sequences are available at the NCBI.
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Affiliation(s)
- Lucie Schröder
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Natalija Hohnjec
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Michael Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Helge Küster
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Petersen G, Anderson B, Braun HP, Meyer EH, Møller IM. Mitochondria in parasitic plants. Mitochondrion 2020; 52:173-182. [DOI: 10.1016/j.mito.2020.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
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Bernal-Conde LD, Ramos-Acevedo R, Reyes-Hernández MA, Balbuena-Olvera AJ, Morales-Moreno ID, Argüero-Sánchez R, Schüle B, Guerra-Crespo M. Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles. Front Neurosci 2020; 13:1399. [PMID: 32038126 PMCID: PMC6989544 DOI: 10.3389/fnins.2019.01399] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022] Open
Abstract
Alpha-synuclein (α-syn) is localized in cellular organelles of most neurons, but many of its physiological functions are only partially understood. α-syn accumulation is associated with Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy as well as other synucleinopathies; however, the exact pathomechanisms that underlie these neurodegenerative diseases remain elusive. In this review, we describe what is known about α-syn function and pathophysiological changes in different cellular structures and organelles, including what is known about its behavior as a prion-like protein. We summarize current knowledge of α-syn and its pathological forms, covering its effect on each organelle, including aggregation and toxicity in different model systems, with special interest on the mitochondria due to its relevance during the apoptotic process of dopaminergic neurons. Moreover, we explore the effect that α-syn exerts by interacting with chromatin remodeling proteins that add or remove histone marks, up-regulate its own expression, and resume the impairment that α-syn induces in vesicular traffic by interacting with the endoplasmic reticulum. We then recapitulate the events that lead to Golgi apparatus fragmentation, caused by the presence of α-syn. Finally, we report the recent findings about the accumulation of α-syn, indirectly produced by the endolysosomal system. In conclusion, many important steps into the understanding of α-syn have been made using in vivo and in vitro models; however, the time is right to start integrating observational studies with mechanistic models of α-syn interactions, in order to look at a more complete picture of the pathophysiological processes underlying α-synucleinopathies.
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Affiliation(s)
- Luis D. Bernal-Conde
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Ramos-Acevedo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mario A. Reyes-Hernández
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrea J. Balbuena-Olvera
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ishbelt D. Morales-Moreno
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rubén Argüero-Sánchez
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Birgitt Schüle
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, CA, United States
| | - Magdalena Guerra-Crespo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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da Fonseca-Pereira P, Silva WB, Araújo WL, Nunes-Nesi A. How Does European Mistletoe Survive Without Complex I? TRENDS IN PLANT SCIENCE 2018; 23:847-850. [PMID: 30097375 DOI: 10.1016/j.tplants.2018.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Two independent but complementary studies recently provided the first biochemical proof of the complete absence of mitochondrial Complex I in a multicellular eukaryote. The mitochondrial electron transport chain (mETC) of the hemiparasitic European mistletoe (Viscum album) displays dramatic rearrangements of its components, most likely reflecting its parasitic lifestyle.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Willian Batista Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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