1
|
Vera-Vives AM, Novel P, Zheng K, Tan SL, Schwarzländer M, Alboresi A, Morosinotto T. Mitochondrial respiration is essential for photosynthesis-dependent ATP supply of the plant cytosol. THE NEW PHYTOLOGIST 2024. [PMID: 39073122 DOI: 10.1111/nph.19989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/29/2024] [Indexed: 07/30/2024]
Abstract
Plants rely on solar energy to synthesize ATP and NADPH for photosynthetic carbon fixation and all cellular need. Mitochondrial respiration is essential in plants, but this may be due to heterotrophic bottlenecks during plant development or because it is also necessary in photosynthetically active cells. In this study, we examined in vivo changes of cytosolic ATP concentration in response to light, employing a biosensing strategy in the moss Physcomitrium patens and revealing increased cytosolic ATP concentration caused by photosynthetic activity. Plants depleted of respiratory Complex I showed decreased cytosolic ATP accumulation, highlighting a critical role of mitochondrial respiration in light-dependent ATP supply of the cytosol. Consistently, targeting mitochondrial ATP production directly, through the construction of mutants deficient in mitochondrial ATPase (complex V), led to drastic growth reduction, despite only minor alterations in photosynthetic electron transport activity. Since P. patens is photoautotrophic throughout its development, we conclude that heterotrophic bottlenecks cannot account for the indispensable role of mitochondrial respiration in plants. Instead, our results support that mitochondrial respiration is essential for ATP provision to the cytosol in photosynthesizing cells. Mitochondrial respiration provides metabolic integration, ensuring supply of cytosolic ATP essential for supporting plant growth and development.
Collapse
Affiliation(s)
- Antoni M Vera-Vives
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Piero Novel
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Ke Zheng
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, Münster, D-48143, Germany
| | - Shun-Ling Tan
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, Münster, D-48143, Germany
| | - Alessandro Alboresi
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| |
Collapse
|
2
|
Su T, Zhang XF, Wu GZ. Functional conservation of GENOMES UNCOUPLED1 in plastid-to-nucleus retrograde signaling in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112053. [PMID: 38417718 DOI: 10.1016/j.plantsci.2024.112053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/20/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Retrograde signaling between plastids and the nucleus is vital for chloroplast biogenesis and environmental responses. GENOMES UNCOUPLED1 (GUN1) was proposed to be a central integrator of multiple retrograde signaling pathways in the model plant Arabidopsis thaliana (Arabidopsis). However, the function of GUN1 orthologs in other plant species has not been well studied. Here, we found that many GUN1 orthologs from the Solanaceae family have a short N-terminus before the first pentatricopeptide repeat (PPR) motif which is predicted as intrinsically disordered regions (IDRs). Functional analyses of tomato (Solanum lycopersicum L.) GUN1 (SlGUN1), which does not contain N-terminal IDRs, show that it can complement the GUN phenotype of the Arabidopsis gun1 mutant (Atgun1). However, in contrast to the AtGUN1 protein, which does contain the N-terminal IDRs, the SlGUN1 protein is highly accumulated even after chloroplast biogenesis is completed, suggesting that the N-terminal IDRs may determine the stability of the GUN1 protein. Furthermore, we generated tomato Slgun1 genome-edited mutants via the CRISPR-Cas9 system. The Slgun1 mutants exhibited a typical GUN phenotype under lincomycin (Lin) or norflurazon (NF) treatment. Moreover, Slgun1 mutants are hypersensitive to low concentrations of Lin or NF. Taken together, our results suggest that, although lacking the N-terminal IDRs, SlGUN1 plays conserved roles in plastid retrograde signaling in tomato plants.
Collapse
Affiliation(s)
- Tong Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Xiao-Fan Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
| |
Collapse
|
3
|
Rugen N, Senkler M, Braun HP. Deep proteomics reveals incorporation of unedited proteins into mitochondrial protein complexes in Arabidopsis. PLANT PHYSIOLOGY 2024; 195:1180-1199. [PMID: 38060994 PMCID: PMC11142381 DOI: 10.1093/plphys/kiad655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/12/2023] [Indexed: 06/02/2024]
Abstract
The mitochondrial proteome consists of numerous types of proteins which either are encoded and synthesized in the mitochondria, or encoded in the cell nucleus, synthesized in the cytoplasm and imported into the mitochondria. Their synthesis in the mitochondria, but not in the nucleus, relies on the editing of the primary transcripts of their genes at defined sites. Here, we present an in-depth investigation of the mitochondrial proteome of Arabidopsis (Arabidopsis thaliana) and a public online platform for the exploration of the data. For the analysis of our shotgun proteomic data, an Arabidopsis sequence database was created comprising all available protein sequences from the TAIR10 and Araport11 databases, supplemented with sequences of proteins translated from edited and nonedited transcripts of mitochondria. Amino acid sequences derived from partially edited transcripts were also added to analyze proteins encoded by the mitochondrial genome. Proteins were digested in parallel with six different endoproteases to obtain maximum proteome coverage. The resulting peptide fractions were finally analyzed using liquid chromatography coupled to ion mobility spectrometry and tandem mass spectrometry. We generated a "deep mitochondrial proteome" of 4,692 proteins. 1,339 proteins assigned to mitochondria by the SUBA5 database (https://suba.live) accounted for >80% of the total protein mass of our fractions. The coverage of proteins by identified peptides was particularly high compared to single-protease digests, allowing the exploration of differential splicing and RNA editing events at the protein level. We show that proteins translated from nonedited transcripts can be incorporated into native mitoribosomes and the ATP synthase complex. We present a portal for the use of our data, based on "proteomaps" with directly linked protein data. The portal is available at www.proteomeexplorer.de.
Collapse
Affiliation(s)
- Nils Rugen
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Michael Senkler
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| |
Collapse
|
4
|
Sanchez-Puerta MV, Ceriotti LF, Gatica-Soria LM, Roulet ME, Garcia LE, Sato HA. Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. ANNALS OF BOTANY 2023; 132:909-928. [PMID: 37503831 PMCID: PMC10808021 DOI: 10.1093/aob/mcad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. SCOPE This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. CONCLUSIONS Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.
Collapse
Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Hector A Sato
- Facultad de Ciencias Agrarias, Cátedra de Botánica General–Herbario JUA, Alberdi 47, Universidad Nacional de Jujuy, 4600 Jujuy, Argentina
| |
Collapse
|
5
|
Forner J, Kleinschmidt D, Meyer EH, Gremmels J, Morbitzer R, Lahaye T, Schöttler MA, Bock R. Targeted knockout of a conserved plant mitochondrial gene by genome editing. NATURE PLANTS 2023; 9:1818-1831. [PMID: 37814021 PMCID: PMC10654050 DOI: 10.1038/s41477-023-01538-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/07/2023] [Indexed: 10/11/2023]
Abstract
Fusion proteins derived from transcription activator-like effectors (TALEs) have emerged as genome editing tools for mitochondria. TALE nucleases (TALENs) have been applied to delete chimaeric reading frames and duplicated (redundant) genes but produced complex genomic rearrangements due to the absence of non-homologous end-joining. Here we report the targeted deletion of a conserved mitochondrial gene, nad9, encoding a subunit of respiratory complex I. By generating a large number of TALEN-mediated mitochondrial deletion lines, we isolated, in addition to mutants with rearranged genomes, homochondriomic mutants harbouring clean nad9 deletions. Characterization of the knockout plants revealed impaired complex I biogenesis, male sterility and defects in leaf and flower development. We show that these defects can be restored by expressing a functional Nad9 protein from the nuclear genome, thus creating a synthetic cytoplasmic male sterility system. Our data (1) demonstrate the feasibility of using genome editing to study mitochondrial gene functions by reverse genetics, (2) highlight the role of complex I in plant development and (3) provide proof-of-concept for the construction of synthetic cytoplasmic male sterility systems for hybrid breeding by genome editing.
Collapse
Affiliation(s)
- Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Dennis Kleinschmidt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jürgen Gremmels
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Robert Morbitzer
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Thomas Lahaye
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
| |
Collapse
|
6
|
Cochella L, Chaker Z. Development, regeneration and aging: a bizarre love triangle. Development 2023; 150:dev202086. [PMID: 37791585 DOI: 10.1242/dev.202086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Jacques Monod Conference on 'Growth and regeneration during development and aging' was organized by Claude Desplan and Allison Bardin in May 2023. The conference took place in Roscoff, France, where participants shared recent conceptual advances under the general motto that developmental processes do not end with embryogenesis. The meeting covered various aspects of how development relates to fitness, regeneration and aging across a refreshing diversity of evolutionarily distant organisms.
Collapse
Affiliation(s)
- Luisa Cochella
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zayna Chaker
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
7
|
Nicoletti M. The Antioxidant Activity of Mistletoes ( Viscum album and Other Species). PLANTS (BASEL, SWITZERLAND) 2023; 12:2707. [PMID: 37514321 PMCID: PMC10384781 DOI: 10.3390/plants12142707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
In addition to the European mistletoe, Viscum album, which is the most known and utilized one, there are several species commonly known as mistletoe. They are spread in various regions of the planet and are all characterized by hemiparasitism and epiphytic behaviour. The published studies evidence other similarities, including the sharing of important biological properties, with the common presence of antioxidant effects. However, whereas the European mistletoe is largely utilized in medical treatments, although with controversial aspects, the scientific knowledge and medical uses of other mistletoes are still insufficient. This review focuses on the controversial medical story of European mistletoe regarding its antioxidant activity and the potentiality of the other species named mistletoe pertaining to botanical families and genera different from Viscum.
Collapse
Affiliation(s)
- Marcello Nicoletti
- Department of Environmental Biology, Foundation in Unam Sapientiam, Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
8
|
Schröder L, Rupp O, Senkler M, Rugen N, Hohnjec N, Goesmann A, Küster H, Braun HP. The Viscum album Gene Space database. FRONTIERS IN PLANT SCIENCE 2023; 14:1193122. [PMID: 37484460 PMCID: PMC10359728 DOI: 10.3389/fpls.2023.1193122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 07/25/2023]
Abstract
The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on 'Benchmarking Universal Single-Copy Orthologs' (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).
Collapse
Affiliation(s)
- Lucie Schröder
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Michael Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Nils Rugen
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Natalija Hohnjec
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Helge Küster
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| |
Collapse
|
9
|
Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [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: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
Collapse
Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| |
Collapse
|
10
|
Darshetkar AM, Pable AA, Nadaf AB, Barvkar VT. Understanding parasitism in Loranthaceae: Insights from plastome and mitogenome of Helicanthes elastica. Gene 2023; 861:147238. [PMID: 36736502 DOI: 10.1016/j.gene.2023.147238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
Loranthaceae is the largest family of the order Santalales and includes root and stem hemiparasites. The parasites are known to exhibit reductions in the genomic features as well as relaxed or intensified selection shifts. In this study, we report plastome and mitogenome sequence of Helicanthes elastica (subtribe Amyeminae, tribe Lorantheae), an endemic, monotypic genus of Western Ghats, India growing on remarkably diverse host range. The length of plastome sequence was 1,28,805 bp while that of mitogenome was 1,65,273 bp. This is the smallest mitogenome from Loranthaceae reported till date. The plastome of Helicanthes exhibited loss of ndh genes (ψndhB), ψinfA, rps15, rps16, rpl32, trnK-UUU, trnG-UCC, trnV-UAC and trnA-UGC while mitogenome exhibited pseudogenized cox2, nad1 and nad4 genes. The comparative study of Loranthaceae plastomes revealed that the pseudogenization or loss of genes was not specific to any genus or tribe and variation was noted in the number of introns of clpP gene in the family. Several photosynthetic genes have undergone relaxed selection supporting lower photosynthetic rates in parasitic plants while some respiratory genes exhibited intensified selection supporting the idea of host-parasite arm race in Loranthaceae. The plastome gene content was found conserved in root hemiparasites compared to stem hemiparasites. The atp1 gene of mitogenome was chimeric and part of it exhibited similarities with Lamiales members. The phylogenetic analysis based on plastid genes placed Helicanthes sister to the members of subtribe Dendrophthoinae.
Collapse
Affiliation(s)
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India.
| | | | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
| |
Collapse
|
11
|
Nicoletti M. The Anti-Inflammatory Activity of Viscum album. PLANTS (BASEL, SWITZERLAND) 2023; 12:1460. [PMID: 37050086 PMCID: PMC10096603 DOI: 10.3390/plants12071460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The therapeutic story of European mistletoe (Viscum album L.) presents a seesawing profile. In ancient times, this hemiparasitic plant was considered a panacea and even to be endowed with exceptional beneficial properties. In more recent times, despite its multiple uses in traditional medicines, some parts of the plant, in particular the berries, were considered poisonous and dangerous, including concerns of cytotoxicity, which spread serious suspicion on its medicinal utility. However, since the last century, medical interest in mistletoe has come back in force due to its utilization in clinical cancer treatments, based on its selective action on tumor cells. In Central Europe, the hydro-alcoholic extracts of European mistletoe register a relevant and continuous utilization in anthroposophic medicine, which is a holistic system that includes the utilization of phytomedicinal substances. In Switzerland and Germany, most physicians and patients use these products as complementary therapy in oncological treatments. However, despite its increasing use in this field, the results of mistletoe's use are not always convincing, and other aspects have appeared. Nowadays, products that contain mistletoe are utilized in several fields, including diet, phytotherapy, veterinary medicine and homeopathy, but in particular in cancer therapies as coadjuvant factors, in consideration of several positive effects including effects in the improvement of quality-of-life conditions and reinforcement of the immune system. In this review, based on the understanding of the association between cancer and inflammation, we propose a relationship between these recent uses of mistletoe, based on its antioxidant properties, which are supported by phytochemical and pharmacological data. The unicity of mistletoe metabolism, which is a direct consequence of its hemiparasitism, is utilized as a key interpretation element to explain its biological properties and steer its consequent therapeutic uses.
Collapse
Affiliation(s)
- Marcello Nicoletti
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
12
|
Borysiuk K, Ostaszewska-Bugajska M, Kryzheuskaya K, Gardeström P, Szal B. Glyoxalase I activity affects Arabidopsis sensitivity to ammonium nutrition. PLANT CELL REPORTS 2022; 41:2393-2413. [PMID: 36242617 PMCID: PMC9700585 DOI: 10.1007/s00299-022-02931-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Elevated methylglyoxal levels contribute to ammonium-induced growth disorders in Arabidopsis thaliana. Methylglyoxal detoxification pathway limitation, mainly the glyoxalase I activity, leads to enhanced sensitivity of plants to ammonium nutrition. Ammonium applied to plants as the exclusive source of nitrogen often triggers multiple phenotypic effects, with severe growth inhibition being the most prominent symptom. Glycolytic flux increase, leading to overproduction of its toxic by-product methylglyoxal (MG), is one of the major metabolic consequences of long-term ammonium nutrition. This study aimed to evaluate the influence of MG metabolism on ammonium-dependent growth restriction in Arabidopsis thaliana plants. As the level of MG in plant cells is maintained by the glyoxalase (GLX) system, we analyzed MG-related metabolism in plants with a dysfunctional glyoxalase pathway. We report that MG detoxification, based on glutathione-dependent glyoxalases, is crucial for plants exposed to ammonium nutrition, and its essential role in ammonium sensitivity relays on glyoxalase I (GLXI) activity. Our results indicated that the accumulation of MG-derived advanced glycation end products significantly contributes to the incidence of ammonium toxicity symptoms. Using A. thaliana frostbite1 as a model plant that overcomes growth repression on ammonium, we have shown that its resistance to enhanced MG levels is based on increased GLXI activity and tolerance to elevated MG-derived advanced glycation end-product (MAGE) levels. Furthermore, our results show that glyoxalase pathway activity strongly affects cellular antioxidative systems. Under stress conditions, the disruption of the MG detoxification pathway limits the functioning of antioxidant defense. However, under optimal growth conditions, a defect in the MG detoxification route results in the activation of antioxidative systems.
Collapse
Affiliation(s)
- Klaudia Borysiuk
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Ostaszewska-Bugajska
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katsiaryna Kryzheuskaya
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Per Gardeström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Bożena Szal
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
| |
Collapse
|
13
|
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.
Collapse
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
| | | |
Collapse
|
14
|
Wang G, Wang Y, Ni J, Li R, Zhu F, Wang R, Tian Q, Shen Q, Yang Q, Tang J, Murcha MW, Wang G. An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize. MOLECULAR PLANT 2022; 15:1470-1487. [PMID: 35957532 DOI: 10.1016/j.molp.2022.08.001] [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: 09/01/2021] [Revised: 05/13/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
During adaptive radiation, mitochondria have co-evolved with their hosts, leading to gain or loss of subunits and assembly factors of respiratory complexes. Plant mitochondrial complex I harbors ∼40 nuclear- and 9 mitochondrial-encoded subunits, and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors. In mammals, the mitochondrial complex I intermediate assembly (MCIA) complex is required for building the membrane arm module. However, plants have lost almost all of the MCIA complex components, giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits. Here, we characterize a maize crumpled seed mutant, crk1, and reveal by map-based cloning that CRK1 encodes an ortholog of human complex I assembly factor 1, zNDUFAF1, the only evolutionarily conserved MCIA subunit in plants. zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex I membrane arm subunits. Disruption of zNDUFAF1 results in severe defects in complex I assembly and activity, a cellular bioenergetic shift to aerobic glycolysis, and mitochondrial vacuolation. Moreover, we found that zNDUFAF1, the putative mitochondrial import inner membrane translocase ZmTIM17-1, and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other, and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates. Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex I stability and activity as well as defective seeds. These results suggest that zNDUFAF1, ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex I and seed development in maize. Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex I assembly, highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.
Collapse
Affiliation(s)
- Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongyan Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiacheng Ni
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Rongrong Li
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Fengling Zhu
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruyin Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiuzhen Tian
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qingwen Shen
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qinghua Yang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Monika W Murcha
- School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.
| |
Collapse
|
15
|
Yin Y, Shen H. Common methods in mitochondrial research (Review). Int J Mol Med 2022; 50:126. [PMID: 36004457 PMCID: PMC9448300 DOI: 10.3892/ijmm.2022.5182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yiyuan Yin
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Haitao Shen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| |
Collapse
|
16
|
Meyer EH, Letts JA, Maldonado M. Structural insights into the assembly and the function of the plant oxidative phosphorylation system. THE NEW PHYTOLOGIST 2022; 235:1315-1329. [PMID: 35588181 DOI: 10.1111/nph.18259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 05/23/2023]
Abstract
One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. We also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.
Collapse
Affiliation(s)
- Etienne H Meyer
- Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Maria Maldonado
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| |
Collapse
|
17
|
Oocytes maintain ROS-free mitochondrial metabolism by suppressing complex I. Nature 2022; 607:756-761. [PMID: 35859172 PMCID: PMC9329100 DOI: 10.1038/s41586-022-04979-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/15/2022] [Indexed: 12/23/2022]
Abstract
Oocytes form before birth and remain viable for several decades before fertilization1. Although poor oocyte quality accounts for most female fertility problems, little is known about how oocytes maintain cellular fitness, or why their quality eventually declines with age2. Reactive oxygen species (ROS) produced as by-products of mitochondrial activity are associated with lower rates of fertilization and embryo survival3-5. Yet, how healthy oocytes balance essential mitochondrial activity with the production of ROS is unknown. Here we show that oocytes evade ROS by remodelling the mitochondrial electron transport chain through elimination of complex I. Combining live-cell imaging and proteomics in human and Xenopus oocytes, we find that early oocytes exhibit greatly reduced levels of complex I. This is accompanied by a highly active mitochondrial unfolded protein response, which is indicative of an imbalanced electron transport chain. Biochemical and functional assays confirm that complex I is neither assembled nor active in early oocytes. Thus, we report a physiological cell type without complex I in animals. Our findings also clarify why patients with complex-I-related hereditary mitochondrial diseases do not experience subfertility. Complex I suppression represents an evolutionarily conserved strategy that allows longevity while maintaining biological activity in long-lived oocytes.
Collapse
|
18
|
Ibarra-Laclette E, Venancio-Rodríguez CA, Vásquez-Aguilar AA, Alonso-Sánchez AG, Pérez-Torres CA, Villafán E, Ramírez-Barahona S, Galicia S, Sosa V, Rebollar EA, Lara C, González-Rodríguez A, Díaz-Fleisher F, Ornelas JF. Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. Front Genet 2022; 13:929490. [PMID: 35769994 PMCID: PMC9235361 DOI: 10.3389/fgene.2022.929490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.
Collapse
Affiliation(s)
- Enrique Ibarra-Laclette
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
| | | | | | | | - Claudia-Anahí Pérez-Torres
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigador por Mexico-CONACyT en el Instituto de Ecología A.C. (INECOL), Xalapa, Mexico
| | - Emanuel Villafán
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico, Mexico
| | - Sonia Galicia
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Victoria Sosa
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Morelia, Mexico
| | | | - Juan Francisco Ornelas
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
| |
Collapse
|
19
|
Wang S, Li Y, He L, Yang J, Fernie AR, Luo J. Natural variance at the interface of plant primary and specialized metabolism. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102201. [PMID: 35349968 DOI: 10.1016/j.pbi.2022.102201] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Plants produce a large number of diverse metabolites when they grow and develop as well as when they respond to the changing external environment. These are an important source of human nutrition and medicine. In this review we emphasized the major issues of the primary-specialized metabolic interface in plant metabolism, described the metabolic flow from primary to specialized metabolism, and the conservation and diversity of primary and specialized metabolites. At the same time, we summarized the regulatory mechanisms underpinning the dynamic balance primary and specialized metabolism based on multi-omics integration analysis, as well as the natural variation of primary and specialized metabolic pathways and genes during the plant evolution. Moreover, the discovery and optimization of the synthesis and regulation elements of various primary to specialized metabolic flows provide the possibility for precise modification and personalized customization of metabolic pathways, which will greatly promote the development of synthetic biology.
Collapse
Affiliation(s)
| | - Yan Li
- College of Tropical Crops, Hainan University, Haikou, China
| | - Liqiang He
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jun Yang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China.
| |
Collapse
|
20
|
Gatica-Soria LM, Ceriotti LF, Garcia LE, Virginia Sanchez-Puerta M. Native and foreign mitochondrial and nuclear encoded proteins conform the OXPHOS complexes of a holoparasitic plant. Gene 2022; 817:146176. [PMID: 35031426 DOI: 10.1016/j.gene.2021.146176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 12/31/2022]
Abstract
The intimate contact between the holoparasitic plant Lophophytum mirabile (Balanophoraceae) and its host plant (Fabaceae) facilitates the exchange of genetic information, increasing the frequency of horizontal gene transfer (HGT). Lophophytum stands out because it acquired a large number of mitochondrial genes (greater than 20) from its legume host that replaced the majority of the native homologs. These foreign genes code for proteins that form multisubunit enzyme complexes, such as those in the oxidative phosphorylation system (OXPHOS) and cytochrome c maturation (ccm) system, together with dozens of nuclear-encoded subunits. However, the existence and the origin of the nuclear subunits that form the major part of the OXPHOS and ccm system in Lophophytum remain unknown. It was proposed that nuclear-encoding genes whose products interact with foreign mitochondrial proteins are also foreign, minimizing the incompatibilities that could arise in the assembly and functioning of these multiprotein complexes. We identified a nearly complete set of OXPHOS and ccm system subunits evolving under selective constraints in the transcriptome of Lophophytum, indicating that OXPHOS is functional and resembles that of free-living angiosperms. Maximum Likelihood phylogenetic analyses revealed a single case of HGT in the nuclear genes, which results in mosaic OXPHOS and ccm system in Lophophytum. These observations raise new questions about the evolution and physiology of this parasitic plant. A putative case of cooperation between two foreign (one mitochondrial and one nuclear) genes is presented.
Collapse
Affiliation(s)
- Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
López-López A, Keech O, Rouhier N. Maturation and Assembly of Iron-Sulfur Cluster-Containing Subunits in the Mitochondrial Complex I From Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:916948. [PMID: 35677241 PMCID: PMC9168917 DOI: 10.3389/fpls.2022.916948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 05/13/2023]
Abstract
In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.
Collapse
Affiliation(s)
- Alicia López-López
- INRAE, IAM, Université de Lorraine, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nicolas Rouhier
- INRAE, IAM, Université de Lorraine, Nancy, France
- *Correspondence: Nicolas Rouhier,
| |
Collapse
|
23
|
Petersen G, Shyama Prasad Rao R, Anderson B, Zervas A, Seberg O, Rasmusson AG, Max Møller I. Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I. Mitochondrion 2021; 62:1-12. [PMID: 34740863 DOI: 10.1016/j.mito.2021.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/09/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arabidopsis with approximately 40 nuclear complex I genes, we recover only transcripts of two dual-function genes: gamma carbonic anhydrase and L-galactono-1,4-lactone dehydrogenase. The complement of genes belonging to complexes II-V of the oxidative phosphorylation pathway appears to be in accordance with other vascular plants. Additionally, transcripts encoding alternative NAD(P)H dehydrogenases and alternative oxidase were found. Despite sequence divergence, structural modeling suggests that the encoded proteins are structurally conserved. Complex I loss is a special feature in Viscum species and relatives, as all other parasitic flowering plants investigated to date seem to have a complete OXPHOS system. Hence, Viscum offers a unique system for specifically investigating molecular consequences of complex I absence, such as the role of complex I subunits involved in secondary functions.
Collapse
Affiliation(s)
- Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru 575018, Karnataka, India
| | - Benjamin Anderson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, DK-4000 Roskilde, Denmark
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | | | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, DK-4200 Slagelse, Denmark
| |
Collapse
|
24
|
Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
Collapse
Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | | | | |
Collapse
|
25
|
Mellon M, Storti M, Vera-Vives AM, Kramer DM, Alboresi A, Morosinotto T. Inactivation of mitochondrial complex I stimulates chloroplast ATPase in Physcomitrium patens. PLANT PHYSIOLOGY 2021; 187:931-946. [PMID: 34608952 PMCID: PMC8491079 DOI: 10.1093/plphys/kiab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/18/2021] [Indexed: 06/11/2023]
Abstract
Light is the ultimate source of energy for photosynthetic organisms, but respiration is fundamental for supporting metabolism during the night or in heterotrophic tissues. In this work, we isolated Physcomitrella (Physcomitrium patens) plants with altered respiration by inactivating Complex I (CI) of the mitochondrial electron transport chain by independently targeting on two essential subunits. Inactivation of CI caused a strong growth impairment even in fully autotrophic conditions in tissues where all cells are photosynthetically active, demonstrating that respiration is essential for photosynthesis. CI mutants showed alterations in the stoichiometry of respiratory complexes while the composition of photosynthetic apparatus was substantially unaffected. CI mutants showed altered photosynthesis with high activity of both Photosystems I and II, likely the result of high chloroplast ATPase activity that led to smaller ΔpH formation across thylakoid membranes, decreasing photosynthetic control on cytochrome b6f in CI mutants. These results demonstrate that alteration of respiratory activity directly impacts photosynthesis in P. patens and that metabolic interaction between organelles is essential in their ability to use light energy for growth.
Collapse
Affiliation(s)
- Marco Mellon
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Mattia Storti
- Department of Biology, University of Padova, 35121 Padova, Italy
| | | | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | |
Collapse
|
26
|
Zhang Y, Fernie AR. Stable and Temporary Enzyme Complexes and Metabolons Involved in Energy and Redox Metabolism. Antioxid Redox Signal 2021; 35:788-807. [PMID: 32368925 DOI: 10.1089/ars.2019.7981] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Significance: Alongside well-characterized permanent multimeric enzymes and multienzyme complexes, relatively unstable transient enzyme-enzyme assemblies, including metabolons, provide an important mechanism for the regulation of energy and redox metabolism. Critical Issues: Despite the fact that enzyme-enzyme assemblies have been proposed for many decades and experimentally analyzed for at least 40 years, there are very few pathways for which unequivocal evidence for the presence of metabolite channeling, the most frequently evoked reason for their formation, has been provided. Further, in contrast to the stronger, permanent interactions for which a deep understanding of the subunit interface exists, the mechanism(s) underlying transient enzyme-enzyme interactions remain poorly studied. Recent Advances: The widespread adoption of proteomic and cell biological approaches to characterize protein-protein interaction is defining an ever-increasing number of enzyme-enzyme assemblies as well as enzyme-protein interactions that likely identify factors which stabilize such complexes. Moreover, the use of microfluidic technologies provided compelling support of a role for substrate-specific chemotaxis in complex assemblies. Future Directions: Embracing current and developing technologies should render the delineation of metabolons from other enzyme-enzyme complexes more facile. In parallel, attempts to confirm that the findings reported in microfluidic systems are, indeed, representative of the cellular situation will be critical to understanding the physiological circumstances requiring and evoking dynamic changes in the levels of the various transient enzyme-enzyme assemblies of the cell. Antioxid. Redox Signal. 35, 788-807.
Collapse
Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| |
Collapse
|
27
|
Abstract
Most molecular functions depend on defined associations of proteins. Protein-protein interactions may be transient or long-lasting; they may lead to labile assemblies or more stable particles termed protein complexes. Studying protein-protein interactions is of prime importance for understanding molecular functions in cells. The complexome profiling approach allows to systematically analyze protein assemblies of cells or subcellular compartments. It combines separation of intact protein fractions by blue native (BN) polyacrylamide gel electrophoresis (PAGE) and protein identification as well as quantification by mass spectrometry. Complexome profiling has been successfully applied to characterize mitochondrial fractions of plants. In a typical experiment, more than 1000 mitochondrial proteins are identified and assigned to defined protein assemblies. It allows discovering so far unknown protein complexes, studying assembly pathways of protein complexes and even characterizing labile super- and megacomplexes in the >10 mega-Dalton range. We here present a complexome profiling protocol for the straightforward definition of the protein complex inventory of mitochondria or other subcellular compartments from plants.
Collapse
Affiliation(s)
- Lucie Schröder
- Institute of Plant Genetics, Plant Proteomics Group, Leibniz University Hannover, Hannover, Germany
| | - Holger Eubel
- Institute of Plant Genetics, Plant Proteomics Group, Leibniz University Hannover, Hannover, Germany.
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Proteomics Group, Leibniz University Hannover, Hannover, Germany.
| |
Collapse
|
28
|
Clark NF, Taylor-Robinson AW. An Ecologically Framed Comparison of The Potential for Zoonotic Transmission of Non-Human and Human-Infecting Species of Malaria Parasite. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:361-373. [PMID: 34211355 PMCID: PMC8223545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The threats, both real and perceived, surrounding the development of new and emerging infectious diseases of humans are of critical concern to public health and well-being. Among these risks is the potential for zoonotic transmission to humans of species of the malaria parasite, Plasmodium, that have been considered historically to infect exclusively non-human hosts. Recently observed shifts in the mode, transmission, and presentation of malaria among several species studied are evidenced by shared vectors, atypical symptoms, and novel host-seeking behavior. Collectively, these changes indicate the presence of environmental and ecological pressures that are likely to influence the dynamics of these parasite life cycles and physiological make-up. These may be further affected and amplified by such factors as increased urban development and accelerated rate of climate change. In particular, the extended host-seeking behavior of what were once considered non-human malaria species indicates the specialist niche of human malaria parasites is not a limiting factor that drives the success of blood-borne parasites. While zoonotic transmission of non-human malaria parasites is generally considered to not be possible for the vast majority of Plasmodium species, failure to consider the feasibility of its occurrence may lead to the emergence of a potentially life-threatening blood-borne disease of humans. Here, we argue that recent trends in behavior among what were hitherto considered to be non-human malaria parasites to infect humans call for a cross-disciplinary, ecologically-focused approach to understanding the complexities of the vertebrate host/mosquito vector/malaria parasite triangular relationship. This highlights a pressing need to conduct a multi-species investigation for which we recommend the construction of a database to determine ecological differences among all known Plasmodium species, vectors, and hosts. Closing this knowledge gap may help to inform alternative means of malaria prevention and control.
Collapse
Affiliation(s)
- Nicole F. Clark
- Institute for Applied Ecology, University of Canberra,
Bruce, Australia,College of Medicine and Public Health, Flinders
University, Australia
| | - Andrew W. Taylor-Robinson
- Infectious Diseases Research Group, School of Health,
Medical & Applied Sciences, Central Queensland University, Brisbane,
Australia,College of Health & Human Sciences, Charles Darwin
University, Casuarina, Australia,To whom all correspondence should be addressed:
Prof Andrew W. Taylor-Robinson, Infectious Diseases Research Group, School of
Health, Medical & Applied Sciences, Central Queensland University, 160 Ann
Street, Brisbane, QLD 4000, Australia; Tel: +61 7 3295 1185;
; ORCID iD: https://orcid.org/0000-0001-7342-8348
| |
Collapse
|
29
|
Van Aken O. Mitochondrial redox systems as central hubs in plant metabolism and signaling. PLANT PHYSIOLOGY 2021; 186:36-52. [PMID: 33624829 PMCID: PMC8154082 DOI: 10.1093/plphys/kiab101] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/11/2021] [Indexed: 05/06/2023]
Abstract
Plant mitochondria are indispensable for plant metabolism and are tightly integrated into cellular homeostasis. This review provides an update on the latest research concerning the organization and operation of plant mitochondrial redox systems, and how they affect cellular metabolism and signaling, plant development, and stress responses. New insights into the organization and operation of mitochondrial energy systems such as the tricarboxylic acid cycle and mitochondrial electron transport chain (mtETC) are discussed. The mtETC produces reactive oxygen and nitrogen species, which can act as signals or lead to cellular damage, and are thus efficiently removed by mitochondrial antioxidant systems, including Mn-superoxide dismutase, ascorbate-glutathione cycle, and thioredoxin-dependent peroxidases. Plant mitochondria are tightly connected with photosynthesis, photorespiration, and cytosolic metabolism, thereby providing redox-balancing. Mitochondrial proteins are targets of extensive post-translational modifications, but their functional significance and how they are added or removed remains unclear. To operate in sync with the whole cell, mitochondria can communicate their functional status via mitochondrial retrograde signaling to change nuclear gene expression, and several recent breakthroughs here are discussed. At a whole organism level, plant mitochondria thus play crucial roles from the first minutes after seed imbibition, supporting meristem activity, growth, and fertility, until senescence of darkened and aged tissue. Finally, plant mitochondria are tightly integrated with cellular and organismal responses to environmental challenges such as drought, salinity, heat, and submergence, but also threats posed by pathogens. Both the major recent advances and outstanding questions are reviewed, which may help future research efforts on plant mitochondria.
Collapse
Affiliation(s)
- Olivier Van Aken
- Department of Biology, Lund University, Lund, Sweden
- Author for communication:
| |
Collapse
|
30
|
Schikora-Tamarit MÀ, Marcet-Houben M, Nosek J, Gabaldón T. Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. Open Biol 2021; 11:200362. [PMID: 33906412 PMCID: PMC8080010 DOI: 10.1098/rsob.200362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.
Collapse
Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| |
Collapse
|
31
|
Przybyla-Toscano J, Christ L, Keech O, Rouhier N. Iron-sulfur proteins in plant mitochondria: roles and maturation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2014-2044. [PMID: 33301571 DOI: 10.1093/jxb/eraa578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe-S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe-S proteins. Several other proteins or complexes present in the matrix require Fe-S clusters as well, or depend either on Fe-S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe-S proteins. In this review, we have listed and discussed the Fe-S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe-S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe-S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.
Collapse
Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | | |
Collapse
|
32
|
Cainzos M, Marchetti F, Popovich C, Leonardi P, Pagnussat G, Zabaleta E. Gamma carbonic anhydrases are subunits of the mitochondrial complex I of diatoms. Mol Microbiol 2021; 116:109-125. [PMID: 33550595 DOI: 10.1111/mmi.14694] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/12/2021] [Accepted: 02/04/2021] [Indexed: 12/21/2022]
Abstract
Diatoms are unicellular organisms containing red algal-derived plastids that probably originated as result of serial endosymbioses between an ancestral heterotrophic organism and a red alga or cryptophyta algae from which has only the chloroplast left. Diatom mitochondria are thus believed to derive from the exosymbiont. Unlike animals and fungi, diatoms seem to contain ancestral respiratory chains. In support of this, genes encoding gamma type carbonic anhydrases (CAs) whose products were shown to be intrinsic complex I subunits in plants, Euglena and Acanthamoeba were found in diatoms, a representative of Stramenopiles. In this work, we experimentally show that mitochondrial complex I in diatoms is a large complex containing gamma type CA subunits, supporting an ancestral origin. By using a bioinformatic approach, a complex I integrated CA domain with heterotrimeric subunit composition is proposed.
Collapse
Affiliation(s)
- Maximiliano Cainzos
- IIB-CONICET-Universidad Nacional de Mar del Plata, Instituto de Investigaciones Biológicas, Mar del Plata, Argentina
| | - Fernanda Marchetti
- IIB-CONICET-Universidad Nacional de Mar del Plata, Instituto de Investigaciones Biológicas, Mar del Plata, Argentina
| | - Cecilia Popovich
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CONICET-UNS, Bahía Blanca, Argentina.,Centro de Emprendedorismo y Desarrollo Territorial Sostenible (CEDETS) CIC-UPSO, Bahía Blanca, Argentina
| | - Patricia Leonardi
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CONICET-UNS, Bahía Blanca, Argentina
| | - Gabriela Pagnussat
- IIB-CONICET-Universidad Nacional de Mar del Plata, Instituto de Investigaciones Biológicas, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- IIB-CONICET-Universidad Nacional de Mar del Plata, Instituto de Investigaciones Biológicas, Mar del Plata, Argentina
| |
Collapse
|
33
|
Garcia LE, Edera AA, Palmer JD, Sato H, Sanchez-Puerta MV. Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant. THE NEW PHYTOLOGIST 2021; 229:1701-1714. [PMID: 32929737 DOI: 10.1111/nph.16926] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.
Collapse
Affiliation(s)
- Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
| | - Alejandro A Edera
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Hector Sato
- Facultad de Ciencias Agrarias (UNJu), Cátedra de Botánica General-Herbario JUA, Alberdi 47, Jujuy, CP 4600, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
| |
Collapse
|
34
|
Cao SK, Liu R, Sayyed A, Sun F, Song R, Wang X, Xiu Z, Li X, Tan BC. Regulator of Chromosome Condensation 1-Domain Protein DEK47 Functions on the Intron Splicing of Mitochondrial Nad2 and Seed Development in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:695249. [PMID: 34408760 PMCID: PMC8365749 DOI: 10.3389/fpls.2021.695249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 05/10/2023]
Abstract
In flowering plants, mitochondrial genes contain approximately 20-26 introns. Splicing of these introns is essential for mitochondrial gene expression and function. Recent studies have revealed that both nucleus- and mitochondrion-encoded factors are required for intron splicing, but the mechanism of splicing remains largely unknown. Elucidation of the mechanism necessitates a complete understanding of the splicing factors. Here, we report the identification of a regulator of chromosome condensation 1 (RCC1)-domain protein DEK47 that is required for mitochondrial intron splicing and seed development in maize. Loss of function in Dek47 severely arrests embryo and endosperm development, resulting in a defective kernel (dek) phenotype. DEK47 harbors seven RCC1 domains and is targeted to mitochondria. Null mutation of DEK47 causes a deficiency in the splicing of all four nad2 introns, abolishing the production of mature nad2 transcript and resulting in the disassembly and severely reduced activity of mitochondrial complex I. In response, the expression of the alternative oxidase AOX2 is sharply increased in dek47. These results indicate that Dek47 is required for the splicing of all the nad2 introns in mitochondria, and essential for complex I assembly, and kernel development in maize.
Collapse
Affiliation(s)
- Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Ruolin Song
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihui Xiu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaojie Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Bao-Cai Tan,
| |
Collapse
|
35
|
Zancani M, Møller IM. Preface. Mitochondrion 2020; 54:133-135. [PMID: 32569844 DOI: 10.1016/j.mito.2020.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Marco Zancani
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 91, 33100 Udine, Italy.
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark.
| |
Collapse
|
36
|
Marchetti F, Cainzos M, Shevtsov S, Córdoba JP, Sultan LD, Brennicke A, Takenaka M, Pagnussat G, Ostersetzer-Biran O, Zabaleta E. Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2020; 61:1080-1094. [PMID: 32163154 PMCID: PMC7295397 DOI: 10.1093/pcp/pcaa028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/08/2020] [Indexed: 05/14/2023]
Abstract
The Arabidopsis genome encodes >450 proteins containing the pentatricopeptide repeat (PPR) motif. The PPR proteins are classified into two groups, termed as P and P Long-Short (PLS) classes. Typically, the PLS subclass proteins are mainly involved in the RNA editing of mitochondrial and chloroplast transcripts, whereas most of the analyzed P subclass proteins have been mainly implicated in RNA metabolism, such as 5' or 3' transcript stabilization and processing, splicing and translation. Mutations of PPR genes often result in embryogenesis and altered seedling developmental defect phenotypes, but only a limited number of ppr mutants have been characterized in detail. In this report, we show that null mutations in the EMB2794 gene result in embryo arrest, due to altered splicing of nad2 transcripts in the Arabidopsis mitochondria. In angiosperms, nad2 has five exons that are transcribed individually from two mitochondrial DNA regions. Biochemical and in vivo analyses further indicate that recombinant or transgenic EMB2794 proteins bind to the nad2 pre-mRNAs in vitro as well as in vivo, suggesting a role for this protein in trans-splicing of nad2 intron 2 and possibly in the stability of the second pre-mRNA of nad2. Homozygous emb2794 lines, showing embryo-defective phenotypes, can be partially rescued by the addition of sucrose to the growth medium. Mitochondria of rescued homozygous mutant plants contain only traces of respiratory complex I, which lack the NADH-dehydrogenase activity.
Collapse
Affiliation(s)
- Fernanda Marchetti
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Maximiliano Cainzos
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Sofía Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Juan Pablo Córdoba
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Laure Dora Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Axel Brennicke
- Institut für, Molekulare Botanik, Universität Ulm, Ulm 89069, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Gabriela Pagnussat
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
- Corresponding author: E-mail, ; Fax, +54 223 475 30 30
| |
Collapse
|
37
|
Best C, Mizrahi R, Ostersetzer-Biran O. Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life. PLANTS (BASEL, SWITZERLAND) 2020; 9:E598. [PMID: 32397140 PMCID: PMC7284508 DOI: 10.3390/plants9050598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.
Collapse
Affiliation(s)
| | | | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel; (C.B.); (R.M.)
| |
Collapse
|
38
|
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]
|
39
|
Braun HP. The Oxidative Phosphorylation system of the mitochondria in plants. Mitochondrion 2020; 53:66-75. [PMID: 32334143 DOI: 10.1016/j.mito.2020.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/26/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial Oxidative Phosphorylation (OXPHOS) provides ATP for driving cellular functions. In plants, OXPHOS takes place in the context of photosynthesis. Indeed, metabolism of mitochondria and chloroplasts is tightly linked. OXPHOS has several extra functions in plants. This review takes a view on the OXPHOS system of plants, the electron transfer chain (ETC), the ATP synthase complex and the numerous supplementary enzymes involved. Electron transport pathways are especially branched in plants. Furthermore, the "classical" OXPHOS complexes include extra subunits, some of which introduce side activities into these complexes. Consequently, and to a remarkable degree, OXPHOS is a multi-functional system in plants that needs to be efficiently regulated with respect to all its physiological tasks in the mitochondria, the chloroplasts, and beyond. Regulatory mechanisms based on posttranslational protein modifications and formation of supramolecular protein assemblies are summarized and discussed.
Collapse
Affiliation(s)
- Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| |
Collapse
|
40
|
Murik O, Chandran SA, Nevo-Dinur K, Sultan LD, Best C, Stein Y, Hazan C, Ostersetzer-Biran O. Topologies of N 6 -adenosine methylation (m 6 A) in land plant mitochondria and their putative effects on organellar gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1269-1286. [PMID: 31657869 DOI: 10.1111/tpj.14589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post-transcriptional level. Following transcription, the polycistronic pre-RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6 -methylation of adenosine ribonucleotides (m6 A-RNA) in plant mitochondria. m6 A is a prevalent modification in nuclear-encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6 A mediates structural switches that affect RNA stability and/or activity. Using m6 A-pulldown/RNA-seq (m6 A-RIP-seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6 A-RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6 A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non-coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6 A modifications, N6 -methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.
Collapse
Affiliation(s)
- Omer Murik
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sam Aldrin Chandran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Keren Nevo-Dinur
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Laure D Sultan
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Corinne Best
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Yuval Stein
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Analytical Chemistry Laboratory, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Oren Ostersetzer-Biran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| |
Collapse
|
41
|
Small ID, Schallenberg-Rüdinger M, Takenaka M, Mireau H, Ostersetzer-Biran O. Plant organellar RNA editing: what 30 years of research has revealed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1040-1056. [PMID: 31630458 DOI: 10.1111/tpj.14578] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
Abstract
The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
Collapse
Affiliation(s)
- Ian D Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| |
Collapse
|
42
|
Havird JC, Noe GR, Link L, Torres A, Logan DC, Sloan DB, Chicco AJ. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Mitochondrion 2019; 49:1-11. [PMID: 31229574 PMCID: PMC6885534 DOI: 10.1016/j.mito.2019.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023]
Abstract
Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Some studies have suggested altered respiration in individual taxa, although there are several reasons why mt variation might be neutral in others. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (~11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was also used to characterize inter- and intraspecific variation in mt function. Contributions of the individual "classic" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter- and intraspecific variation. This study suggests that Silene species with peculiar mt genomes still show relatively normal mt respiration. This may be due to strong purifying selection on mt variants, coevolutionary responses in the nucleus, or a combination of both. Future experiments should explore such questions using a comparative framework and investigating other lineages with unusual mitogenomes.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA; Department of Integrative Biology, The University of Texas, Austin, TX, USA.
| | - Gregory R Noe
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Luke Link
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amber Torres
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - David C Logan
- IRHS, INRA, Université d'Angers, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
43
|
Abstract
Eukaryotic life has developed a fascinating and highly optimized system for energy transduction: the mitochondrial respiratory chain. Typically composed of five core protein complexes, we now learn from two studies that plant hemi-parasites of the type Viscum cope without Complex I, the entry point of the classical respiratory system.
Collapse
Affiliation(s)
- Karin B Busch
- Institute of Molecular Cell Biology, Department of Biology, Westfälische Universität Münster, D-48149 Münster, Germany.
| |
Collapse
|
44
|
Gleason FH, Larkum AW, Raven JA, Manohar CS, Lilje O. Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
45
|
C�rdoba JP, Fassolari M, Marchetti F, Soto D, Pagnussat GC, Zabaleta E. Different Types Domains are Present in Complex I from Immature Seeds and of CA Adult Plants in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:986-998. [PMID: 30668784 PMCID: PMC6498749 DOI: 10.1093/pcp/pcz011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/10/2019] [Indexed: 05/10/2023]
Abstract
Mitochondrial Nicotinamide adenine dinucleotide (NADH) dehydrogenase complex is the first complex of the mitochondrial electron transfer chain. In plants and in a variety of eukaryotes except Opisthokonta, complex I (CI) contains an extra spherical domain called carbonic anhydrase (CA) domain. This domain is thought to be composed of trimers of gamma type CA and CA-like subunits. In Arabidopsis, the CA gene family contains five members (CA1, CA2, CA3, CAL1 and CAL2). The CA domain appears to be crucial for CI assembly and is essential for normal embryogenesis. As CA and CA-like proteins are arranged in trimers to form the CA domain, it is possible for the complex to adopt different arrangements that might be tissue-specific or have specialized functions. In this work, we show that the proportion of specific CI changes in a tissue-specific manner. In immature seeds, CI assembly may be indistinctly dependent on CA1, CA2 or CA3. However, in adult plant tissues (or tissues derived from stem cells, as cell cultures), CA2-dependent CI is clearly the most abundant. This difference might account for specific physiological functions. We present evidence suggesting that CA3 does not interact with any other CA family member. As CA3 was found to interact with CI FRO1 (NDUFS4) subunit, which is located in the matrix arm, this suggests a role for CA3 in assembly and stability of CI.
Collapse
Affiliation(s)
- Juan Pablo C�rdoba
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Marisol Fassolari
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Fernanda Marchetti
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - D�bora Soto
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biol�gicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, Mar del Plata, Argentina
- Corresponding author: E-mail, ; Fax, +54 223 475 30 30
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Fernie AR, Zhang Y, Sweetlove LJ. Passing the Baton: Substrate Channelling in Respiratory Metabolism. RESEARCH (WASHINGTON, D.C.) 2018; 2018:1539325. [PMID: 31549022 PMCID: PMC6750097 DOI: 10.1155/2018/1539325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Despite species-specific differences in the pathways of respiratory metabolism are remarkably conserved across the kingdoms of life with glycolysis, the tricarboxylic acid cycle, and mitochondrial electron transport chain representing the major components of the process in the vast majority of organisms. In addition to being of critical importance in fueling life itself these pathways serve as interesting case studies for substrate channelling with research on this theme having been carried out for over 40 years. Here we provide a cross-kingdom review of the ample evidence for protein-protein interaction and enzyme assemblies within the three component pathways as well as describing the scarcer available evidence for substrate channelling itself.
Collapse
Affiliation(s)
- Alisdair R. Fernie
- 1Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- 2Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- 1Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- 2Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Lee J. Sweetlove
- 3Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| |
Collapse
|