1
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Gong F, Lin R, Liu Z, Huang X, Sun MX, Peng X. FGM1/rPPR4-dependent female gamete maturation is essential for seed development initiation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025. [PMID: 40396630 DOI: 10.1111/jipb.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2025] [Accepted: 04/08/2025] [Indexed: 05/22/2025]
Abstract
Gamete maturation is critical for fertility of both animals and plants; however, the molecular mechanisms underlying these processes remain poorly understood in plants. Here, we report the Female Gamete Maturation 1 (FGM1/rPPR4), a component of mitoribosome large subunit in Arabidopsis directly interacts with the mitochondrial protein GAMETE CELL DEFECTIVE 1 (GCD1) and plays an essential role in female gamete maturation and subsequent zygote-embryo transition and endosperm development. We reveal that FGM1/rPPR4, assisted by GCD1, is an essential factor for female gamete maturation. We also confirm that female gamete maturation is necessary for the capacity of post-fertilization zygote-embryo transition and endosperm development, but not for double fertilization, indicating that essential mechanisms are established during female gamete maturation to provide a molecular basis for seed development initiation and plant fertility.
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Affiliation(s)
- Feng Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rongxin Lin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zonglin Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaorong Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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2
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Stępiński D. Decoding Plant Ribosomal Proteins: Multitasking Players in Cellular Games. Cells 2025; 14:473. [PMID: 40214427 PMCID: PMC11987935 DOI: 10.3390/cells14070473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/10/2025] [Accepted: 03/20/2025] [Indexed: 04/14/2025] Open
Abstract
Ribosomal proteins (RPs) were traditionally considered as ribosome building blocks, serving exclusively in ribosome assembly. However, contemporary research highlights their involvement in additional translational roles, as well as diverse non-ribosomal activities. The functional diversity of RPs is further enriched by the presence of 2-7 paralogs per RP family in plants, suggesting that these proteins may perform distinct, specialized functions. The spatiotemporal expression of RP paralogs allows for the assembly of unique ribosomes (ribosome heterogeneity), enabling the selective translation of specific mRNAs, and producing specialized proteins essential for plant functioning. Additionally, RPs that operate independently of ribosomes as free molecules may regulate a wide range of physiological processes. RPs involved in protein biosynthesis within the cytosol, mitochondria, or plastids are encoded by distinct genes, which account for their functional specialization. Notably, RPs associated with plastid or mitochondrial ribosomes, beyond their canonical roles in these organelles, also contribute to overall plant development and functionality, akin to their cytosolic counterparts. This review explores the roles of RPs in different cellular compartments, the presumed molecular mechanisms underlying their functions, and the involvement of other molecular factors that cooperate with RPs in these processes. In addition to the new RP nomenclature introduced in 2022/2023, the old names are also applied.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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3
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Wang Y, Tan BC. Pentatricopeptide repeat proteins in plants: Cellular functions, action mechanisms, and potential applications. PLANT COMMUNICATIONS 2025; 6:101203. [PMID: 39644091 PMCID: PMC11897456 DOI: 10.1016/j.xplc.2024.101203] [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: 10/02/2024] [Revised: 11/28/2024] [Accepted: 12/04/2024] [Indexed: 12/09/2024]
Abstract
Pentatricopeptide repeat (PPR) proteins are involved in nearly all aspects of post-transcriptional processing in plant mitochondria and plastids, playing vital roles in plant growth, development, cytoplasmic male sterility restoration, and responses to biotic and abiotic stresses. Over the last three decades, significant advances have been made in understanding the functions of PPR proteins and the primary mechanisms through which they mediate post-transcriptional processing. This review aims to summarize these advancements, highlighting the mechanisms by which PPR proteins facilitate RNA editing, intron splicing, and RNA maturation in the context of organellar gene expression. We also present the latest progress in PPR engineering and discuss its potential as a biotechnological tool. Additionally, we discuss key challenges and questions that remain in PPR research.
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Affiliation(s)
- Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
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4
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Nie Y, Li Y, Yuan P, Wu C, Wang X, Wang C, Xu X, Shen Z, Hu Z. Arabidopsis Pentatricopeptide Repeat Protein GEND2 Participates in Mitochondrial RNA Editing. PLANT & CELL PHYSIOLOGY 2024; 65:1849-1861. [PMID: 39301683 DOI: 10.1093/pcp/pcae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 09/11/2024] [Accepted: 09/18/2024] [Indexed: 09/22/2024]
Abstract
In Arabidopsis, RNA editing alters more than 500 cytidines (C) to uridines (U) in mitochondrial transcripts, a process involving the family of pentatricopeptide repeat (PPR) proteins. Here, we report a previously uncharacterized mitochondrial PLS-type PPR protein, GEND2, which functions in the mitochondrial RNA editing. The T-DNA insertion in the 5'-untranslated region of GEND2, referred to as gend2-1, results in defective root development compared to wild-type (WT) plants. A comprehensive examination of mitochondrial RNA-editing sites revealed a significant reduction in the gend2-1 mutant compared to WT plants, affecting six specific mitochondrial RNA editing sites, notably within the mitochondrial genes CcmFn-1, RPSL2 and ORFX. These genes encode critical components of cytochrome protein maturation pathway, mitochondrial ribosomal subunit and twin arginine translocation subunits, respectively. Further analysis of the transcriptional profile of the gend2-1 mutant and WT revealed a striking induction of expression in a cluster of genes associated with mitochondrial dysfunction and regulated by ANAC017, a key regulator coordinating organelle functions and stress responses. Intriguingly, the gend2-1 mutation activated an ANAC017-dependent signaling aimed at countering cell wall damage induced by cellulose synthase inhibitors, as well as an ANAC017-independent pathway that retarded root growth under normal condition. Collectively, our findings identify a novel mitochondrial PLS-type PPR protein GEND2, which participates in the editing of six specific mitochondrial RNA editing sites. Furthermore, the gend2-1 mutation triggers two distinct pathways in plants: an ANAC017-dependent pathway and ANAC017-independent pathway.
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Affiliation(s)
- Yaqing Nie
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Penglai Yuan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Chengyun Wu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoqing Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
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5
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Ali NA, Song W, Huang J, Wu D, Zhao X. Recent advances and biotechnological applications of RNA metabolism in plant chloroplasts and mitochondria. Crit Rev Biotechnol 2024; 44:1552-1573. [PMID: 38238104 DOI: 10.1080/07388551.2023.2299789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 11/20/2024]
Abstract
The chloroplast and mitochondrion are semi-autonomous organelles that play essential roles in cell function. These two organelles are embellished with prokaryotic remnants and contain many new features emerging from the co-evolution of organelles and the nucleus. A typical plant chloroplast or mitochondrion genome encodes less than 100 genes, and the regulation of these genes' expression is remarkably complex. The regulation of chloroplast and mitochondrion gene expression can be achieved at multiple levels during development and in response to environmental cues, in which, RNA metabolism, including: RNA transcription, processing, translation, and degradation, plays an important role. RNA metabolism in plant chloroplasts and mitochondria combines bacterial-like traits with novel features evolved in the host cell and is regulated by a large number of nucleus-encoded proteins. Among these, pentatricopeptide repeat (PPR) proteins are deeply involved in multiple aspects of the RNA metabolism of organellar genes. Research over the past decades has revealed new insights into different RNA metabolic events in plant organelles, such as the composition of chloroplast and mitochondrion RNA editosomes. We summarize and discuss the most recent knowledge and biotechnological implications of various RNA metabolism processes in plant chloroplasts and mitochondria, with a focus on the nucleus-encoded factors supporting them, to gain a deeper understanding of the function and evolution of these two organelles in plant cells. Furthermore, a better understanding of the role of nucleus-encoded factors in chloroplast and mitochondrion RNA metabolism will motivate future studies on manipulating the plant gene expression machinery with engineered nucleus-encoded factors.
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Affiliation(s)
- Nadia Ahmed Ali
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenjian Song
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianyan Huang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants of Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaobo Zhao
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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6
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Song C, Li Y, Yang M, Li T, Hou Y, Liu Y, Xu C, Liu J, Millar AH, Wang N, Li L. Protein aggregation in plant mitochondria lacking Lon1 inhibits translation and induces unfolded protein responses. PLANT, CELL & ENVIRONMENT 2024; 47:4383-4397. [PMID: 38988259 DOI: 10.1111/pce.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
Loss of Lon1 led to stunted plant growth and accumulation of nuclear-encoded mitochondrial proteins including Lon1 substrates. However, an in-depth label-free proteomics quantification of mitochondrial proteins in lon1 revealed that the majority of mitochondrial-encoded proteins decreased in abundance. Additionally, we found that lon1 mutants contained protein aggregates in the mitochondrial that were enriched in metabolic enzymes, ribosomal subunits and PPR-containing proteins of the translation apparatus. These mutants exhibited reduced general mitochondrial translation as well as deficiencies in RNA splicing and editing. These findings support the role of Lon1 in maintaining a functional translational apparatus for mitochondrial-encoded gene translation. Transcriptome analysis of lon1 revealed a mitochondrial unfolded protein response reminiscent of the mitochondrial retrograde signalling dependent on the transcription factor ANAC017. Notably, lon1 mutants exhibited transiently elevated ethylene production, and the shortened hypocotyl observed in lon1 mutants during skotomorphogenesis was partially alleviated by ethylene inhibitors. Furthermore, the short root phenotype was partially ameliorated by introducing a mutation in the ethylene receptor ETR1. Interestingly, the upregulation of only a select few target genes was linked to ETR1-mediated ethylene signalling. Together this provides multiple steps in the link between loss of Lon1 and signalling responses to restore mitochondrial protein homoeostasis in plants.
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Affiliation(s)
- Ce Song
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuanyuan Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mengmeng Yang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tiantian Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuqi Hou
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yinyin Liu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chang Xu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinjian Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ningning Wang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
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7
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Wang Y, Williams-Carrier R, Meeley R, Fox T, Chamusco K, Nashed M, Hannah LC, Gabay-Laughnan S, Barkan A, Chase C. Mutations in nuclear genes encoding mitochondrial ribosome proteins restore pollen fertility in S male-sterile maize. G3 (BETHESDA, MD.) 2024; 14:jkae201. [PMID: 39163571 DOI: 10.1093/g3journal/jkae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024]
Abstract
The interaction of plant mitochondrial and nuclear genetic systems is exemplified by mitochondria-encoded cytoplasmic male sterility (CMS) under the control of nuclear restorer-of-fertility genes. The S type of CMS in maize is characterized by a pollen collapse phenotype and a unique paradigm for fertility restoration in which numerous nuclear restorer-of-fertility lethal mutations rescue pollen function but condition homozygous-lethal seed phenotypes. Two nonallelic restorer mutations recovered from Mutator transposon-active lines were investigated to determine the mechanisms of pollen fertility restoration and seed lethality. Mu Illumina sequencing of transposon-flanking regions identified insertion alleles of nuclear genes encoding mitochondrial ribosomal proteins RPL6 and RPL14 as candidate restorer-of-fertility lethal mutations. Both candidates were associated with lowered abundance of mitochondria-encoded proteins in developing maize pollen, and the rpl14 mutant candidate was confirmed by independent insertion alleles. While the restored pollen functioned despite reduced accumulation of mitochondrial respiratory proteins, normal-cytoplasm plants heterozygous for the mutant alleles showed a significant pollen transmission bias in favor of the nonmutant Rpl6 and Rpl14 alleles. CMS-S fertility restoration affords a unique forward genetic approach to investigate the mitochondrial requirements for, and contributions to, pollen and seed development.
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Affiliation(s)
- Yan Wang
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Robert Meeley
- Corteva AgriScience (retired), Johnston, IA 50131, USA
| | - Timothy Fox
- Corteva AgriScience (retired), Johnston, IA 50131, USA
| | - Karen Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mina Nashed
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - L Curtis Hannah
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Christine Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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8
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Kwasniak-Owczarek M, Janska H. Experimental approaches to studying translation in plant semi-autonomous organelles. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5175-5187. [PMID: 38592734 PMCID: PMC11389837 DOI: 10.1093/jxb/erae151] [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: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria that have retained reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding organellar translation is critical for a thorough comprehension of key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present experimental approaches used for studying translation in plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps, are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.
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Affiliation(s)
- Malgorzata Kwasniak-Owczarek
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
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9
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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.
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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
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10
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J Proteome Res 2024; 23:185-214. [PMID: 38104260 DOI: 10.1021/acs.jproteome.3c00536] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Alyssa Kearly
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Isabell Guzchenko
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Erica Debley
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Georgia Sauermann
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Pratyush Routray
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Sagunya Malhotra
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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11
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Dimnet L, Salinas-Giegé T, Pullara S, Moyet L, Genevey C, Kuntz M, Duchêne AM, Rolland N. Isolation of Cytosolic Ribosomes Associated with Plant Mitochondria and Chloroplasts. Methods Mol Biol 2024; 2776:289-302. [PMID: 38502512 DOI: 10.1007/978-1-0716-3726-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Excluding the few dozen proteins encoded by the chloroplast and mitochondrial genomes, the majority of plant cell proteins are synthesized by cytosolic ribosomes. Most of these nuclear-encoded proteins are then targeted to specific cell compartments thanks to localization signals present in their amino acid sequence. These signals can be specific amino acid sequences known as transit peptides, or post-translational modifications, ability to interact with specific proteins or other more complex regulatory processes. Furthermore, in eukaryotic cells, protein synthesis can be regulated so that certain proteins are synthesized close to their destination site, thus enabling local protein synthesis in specific compartments of the cell. Previous studies have revealed that such locally translating cytosolic ribosomes are present in the vicinity of mitochondria and emerging views suggest that localized translation near chloroplasts could also occur. However, in higher plants, very little information is available on molecular mechanisms controlling these processes and there is a need to characterize cytosolic ribosomes associated with organelles membranes. To this goal, this protocol describes the purification of higher plant chloroplast and mitochondria and the organelle-associated cytosolic ribosomes.
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Affiliation(s)
- Laura Dimnet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg Cedex, France
| | - Sara Pullara
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Chloé Genevey
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg Cedex, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France.
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12
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Nagaraj PH. Determining Macromolecular Structures Using Cryo-Electron Microscopy. Methods Mol Biol 2024; 2787:315-332. [PMID: 38656500 DOI: 10.1007/978-1-0716-3778-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.
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Affiliation(s)
- Pradeep Hiriyur Nagaraj
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
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13
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Arrivé M, Bruggeman M, Skaltsogiannis V, Coudray L, Quan YF, Schelcher C, Cognat V, Hammann P, Chicher J, Wolff P, Gobert A, Giegé P. A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei. NATURE PLANTS 2023; 9:2031-2041. [PMID: 37945696 DOI: 10.1038/s41477-023-01564-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the m22G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a m22G modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the m22G-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.
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Affiliation(s)
- Mathilde Arrivé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Vasileios Skaltsogiannis
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Léna Coudray
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Yi-Fat Quan
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Philippe Wolff
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France.
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14
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Baleva MV, Piunova UE, Chicherin IV, Levitskii SA, Kamenski PA. Diversity and Evolution of Mitochondrial Translation Apparatus. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1832-1843. [PMID: 38105202 DOI: 10.1134/s0006297923110135] [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: 07/18/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 12/19/2023]
Abstract
The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.
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Affiliation(s)
- Mariya V Baleva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ulyana E Piunova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan V Chicherin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey A Levitskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Piotr A Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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15
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Wei YM, Wang BH, Shao DJ, Yan RY, Wu JW, Zheng GM, Zhao YJ, Zhang XS, Zhao XY. Defective kernel 66 encodes a GTPase essential for kernel development in maize. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5694-5708. [PMID: 37490479 PMCID: PMC10540730 DOI: 10.1093/jxb/erad289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
The mitochondrion is a semi-autonomous organelle that provides energy for cell activities through oxidative phosphorylation. In this study, we identified a defective kernel 66 (dek66)-mutant maize with defective kernels. We characterized a candidate gene, DEK66, encoding a ribosomal assembly factor located in mitochondria and possessing GTPase activity (which belongs to the ribosome biogenesis GTPase A family). In the dek66 mutant, impairment of mitochondrial structure and function led to the accumulation of reactive oxygen species and promoted programmed cell death in endosperm cells. Furthermore, the transcript levels of most of the key genes associated with nutrient storage, mitochondrial respiratory chain complex, and mitochondrial ribosomes in the dek66 mutant were significantly altered. Collectively, the results suggest that DEK66 is essential for the development of maize kernels by affecting mitochondrial function. This study provides a reference for understanding the impact of a mitochondrial ribosomal assembly factor in maize kernel development.
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Affiliation(s)
- Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Bo Hui Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Dong Jie Shao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Ru Yu Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
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16
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Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Sultan K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science 2023; 381:eadg0995. [PMID: 37651534 DOI: 10.1126/science.adg0995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that "mitochondrial translation factors" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal "small" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.
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Affiliation(s)
| | | | - Sbatie Lama
- Department of Biology, Lund University, Lund, Sweden
| | - Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Katja Bernfur
- Department of Chemistry, Lund University, Lund, Sweden
| | - Kristin Sultan
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Arnaud Liehrmann
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université Paris-Saclay, CNRS, Université d'Évry, Laboratoire de Mathématiques et Modélisation d'Évry, 91037 Évry-Courcouronnes, France
| | - Benoît Castandet
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | | | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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17
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Hu R, Li X, Hu Y, Zhang R, Lv Q, Zhang M, Sheng X, Zhao F, Chen Z, Ding Y, Yuan H, Wu X, Xing S, Yan X, Bao F, Wan P, Xiao L, Wang X, Xiao W, Decker EL, van Gessel N, Renault H, Wiedemann G, Horst NA, Haas FB, Wilhelmsson PKI, Ullrich KK, Neumann E, Lv B, Liang C, Du H, Lu H, Gao Q, Cheng Z, You H, Xin P, Chu J, Huang CH, Liu Y, Dong S, Zhang L, Chen F, Deng L, Duan F, Zhao W, Li K, Li Z, Li X, Cui H, Zhang YE, Ma C, Zhu R, Jia Y, Wang M, Hasebe M, Fu J, Goffinet B, Ma H, Rensing SA, Reski R, He Y. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 2023; 186:3558-3576.e17. [PMID: 37562403 DOI: 10.1016/j.cell.2023.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/23/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.
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Affiliation(s)
- Ruoyang Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xuedong Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yong Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Runjie Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Qiang Lv
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Min Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xianyong Sheng
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Feng Zhao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Zhijia Chen
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yuhan Ding
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Huan Yuan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaofeng Wu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Shuang Xing
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaoyu Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Fang Bao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Ping Wan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Lihong Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Xiaoqin Wang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hugues Renault
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Inselspital, University of Bern, 3010 Bern, Switzerland
| | - Nelly A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; MetaSystems Hard & Software GmbH, 68804 Altlussheim, Germany
| | - Fabian B Haas
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | | | - Kristian K Ullrich
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Eva Neumann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Bin Lv
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
| | - Chengzhi Liang
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Hongwei Lu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Qiang Gao
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhukuan Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hanli You
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010031, China
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA; Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518085, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fei Chen
- Sanya Nanfan Research Institute from Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Lei Deng
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Fuzhou Duan
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Wenji Zhao
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Kai Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Zhongfeng Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Xingru Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Hengjian Cui
- School of Mathematical Sciences, CNU, Beijing 100048, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Ma
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruiliang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meizhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan A Rensing
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
| | - Yikun He
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China.
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18
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543322. [PMID: 37333403 PMCID: PMC10274743 DOI: 10.1101/2023.06.01.543322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.
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19
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Xie E, Chen J, Wang B, Shen Y, Tang D, Du G, Li Y, Cheng Z. The transcribed centromeric gene OsMRPL15 is essential for pollen development in rice. PLANT PHYSIOLOGY 2023; 192:1063-1079. [PMID: 36905369 PMCID: PMC10231452 DOI: 10.1093/plphys/kiad153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 06/01/2023]
Abstract
Centromeres consist of highly repetitive sequences that are challenging to map, clone, and sequence. Active genes exist in centromeric regions, but their biological functions are difficult to explore owing to extreme suppression of recombination in these regions. In this study, we used the CRISPR/Cas9 system to knock out the transcribed gene Mitochondrial Ribosomal Protein L15 (OsMRPL15), located in the centromeric region of rice (Oryza sativa) chromosome 8, resulting in gametophyte sterility. Osmrpl15 pollen was completely sterile, with abnormalities appearing at the tricellular stage including the absence of starch granules and disrupted mitochondrial structure. Loss of OsMRPL15 caused abnormal accumulation of mitoribosomal proteins and large subunit rRNA in pollen mitochondria. Moreover, the biosynthesis of several proteins in mitochondria was defective, and expression of mitochondrial genes was upregulated at the mRNA level. Osmrpl15 pollen contained smaller amounts of intermediates related to starch metabolism than wild-type pollen, while biosynthesis of several amino acids was upregulated, possibly to compensate for defective mitochondrial protein biosynthesis and initiate consumption of carbohydrates necessary for starch biosynthesis. These results provide further insight into how defects in mitoribosome development cause gametophyte male sterility.
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Affiliation(s)
- En Xie
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiawei Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingxin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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20
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Small I, Melonek J, Bohne AV, Nickelsen J, Schmitz-Linneweber C. Plant organellar RNA maturation. THE PLANT CELL 2023; 35:1727-1751. [PMID: 36807982 PMCID: PMC10226603 DOI: 10.1093/plcell/koad049] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 05/30/2023]
Abstract
Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.
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Affiliation(s)
- Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | | | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
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21
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Scarpin MR, Busche M, Martinez RE, Harper LC, Reiser L, Szakonyi D, Merchante C, Lan T, Xiong W, Mo B, Tang G, Chen X, Bailey-Serres J, Browning KS, Brunkard JO. An updated nomenclature for plant ribosomal protein genes. THE PLANT CELL 2023; 35:640-643. [PMID: 36423343 PMCID: PMC9940865 DOI: 10.1093/plcell/koac333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Affiliation(s)
- M Regina Scarpin
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin 53706, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California 94720, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, California 94710, USA
| | - Michael Busche
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin 53706, USA
| | - Ryan E Martinez
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin 53706, USA
| | - Lisa C Harper
- Corn Insects and Crop Genetics Research Unit, USDA Agricultural Research Service, Ames, Iowa 50011, USA
| | - Leonore Reiser
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, California 94538, USA
| | - Dóra Szakonyi
- Plant Molecular Biology, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Catharina Merchante
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Facultad de Ciencias, Campus, de Teatinos, Universidad de Málaga, 29071 Málaga, Spain
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Xiong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, Michigan 49931, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California – Riverside, Riverside, California 92521, USA
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California – Riverside, Riverside, California 92521, USA
| | - Karen S Browning
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, USA
| | - Jacob O Brunkard
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin 53706, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California 94720, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, California 94710, USA
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22
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Hariharan N, Ghosh S, Palakodeti D. The story of rRNA expansion segments: Finding functionality amidst diversity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1732. [PMID: 35429135 DOI: 10.1002/wrna.1732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/24/2022] [Accepted: 03/19/2022] [Indexed: 01/31/2023]
Abstract
Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs. Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine-tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species-specific regulatory hub of protein synthesis. In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Ribosome Structure/Function Translation > Regulation.
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Affiliation(s)
- Nivedita Hariharan
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India.,The University of Trans-disciplinary Health Sciences and Technology, Bangalore, India
| | - Sumana Ghosh
- Manipal Academy of Higher Education, Manipal, India
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
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23
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Agrawal RK, Majumdar S. Evolution: Mitochondrial Ribosomes Across Species. Methods Mol Biol 2023; 2661:7-21. [PMID: 37166629 DOI: 10.1007/978-1-0716-3171-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ribosome is among the most complex and ancient cellular macromolecular assemblies that plays a central role in protein biosynthesis in all living cells. Its function of translation of genetic information encoded in messenger RNA into protein molecules also extends to subcellular compartments in eukaryotic cells such as apicoplasts, chloroplasts, and mitochondria. The origin of mitochondria is primarily attributed to an early endosymbiotic event between an alpha-proteobacterium and a primitive (archaeal) eukaryotic cell. The timeline of mitochondrial acquisition, the nature of the host, and their diversification have been studied in great detail and are continually being revised as more genomic and structural data emerge. Recent advancements in high-resolution cryo-EM structure determination have provided architectural details of mitochondrial ribosomes (mitoribosomes) from various species, revealing unprecedented diversifications among them. These structures provide novel insights into the evolution of mitoribosomal structure and function. Here, we present a brief overview of the existing mitoribosomal structures in the context of the eukaryotic evolution tree showing their diversification from their last common ancestor.
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Affiliation(s)
- Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health Empire State Plaza, Albany, NY, USA.
- Department of Biomedical Sciences, University at Albany, SUNY, Rensselaer, NY, USA.
| | - Soneya Majumdar
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health Empire State Plaza, Albany, NY, USA
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24
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Jung L, Schleicher S, Alsaied Taha F, Takenaka M, Binder S. The MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4) is essential for the accumulation of dicistronic rpl5-cob mRNAs in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:375-386. [PMID: 36468791 DOI: 10.1111/tpj.16053] [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: 04/20/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis thaliana genome harbors more than 450 nuclear genes encoding pentatricopeptide repeat (PPR) proteins that operate in the RNA metabolism of mitochondria and/or plastids. To date, the molecular function of many PPR proteins is still unknown. Here we analyzed the nucleus-encoded gene At4g19440 coding for a P-type PPR protein. Knockout of this gene interferes with normal embryo development and seed maturation. Two experimental approaches were applied to overcome lethality and to investigate the outcome of At4g19440 knockout in adult plants. These studies revealed changes in the abundance of several mitochondria-encoded transcripts. In particular, steady-state levels of dicistronic rpl5-cob RNAs were markedly reduced, whereas levels of mature ccmC and rpl2-mttB transcripts were clearly increased. Predictions according to the one repeat to one nucleotide code for PPR proteins indicate binding of the At4g19440 protein to a previously detected small RNA at the 3' termini of the dicistronic rpl5-cob transcripts. This potential interaction indicates a function of this protein in 3' end formation and stabilization of these RNA species, whereas the increase in the levels of the ccmC mRNA along with other mitochondria-encoded RNAs seems to be a secondary effect of At4g19440 knockout. Since the inactivation of At4g19440 influences the stability of several mitochondrial RNAs we call this gene MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4). This factor will be an interesting subject to study opposing effects of a single nucleus-encoded protein on mitochondrial transcript levels.
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Affiliation(s)
- Lisa Jung
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Fatema Alsaied Taha
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Mizuki Takenaka
- Plant Molecular Genetics, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
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25
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Hemono M, Salinas‐Giegé T, Roignant J, Vingadassalon A, Hammann P, Ubrig E, Ngondo P, Duchêne A. FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:309-321. [PMID: 36050837 PMCID: PMC9826127 DOI: 10.1111/tpj.15962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.
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Affiliation(s)
- Mickaele Hemono
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Thalia Salinas‐Giegé
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Jeanne Roignant
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Audrey Vingadassalon
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Université des Antilles, COVACHIM M2E (EA 3592), UFR SEN, Campus de FouilloleF‐97 110Pointe‐à‐PitreFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg‐EsplanadeInstitut de Biologie Moléculaire et CellulaireFR1589 du CNRS, 2 Allée Konrad Roentgen67084Strasbourg CedexFrance
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Patryk Ngondo
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 du CNRS, Université de Strasbourg2 Allée Konrad Roentgen67 084Strasbourg CedexFrance
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
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26
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Chen S, Zeng X, Li Y, Qiu S, Peng X, Xie X, Liu Y, Liao C, Tang X, Wu J. The nuclear-encoded plastid ribosomal protein L18s are essential for plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:949897. [PMID: 36212366 PMCID: PMC9538462 DOI: 10.3389/fpls.2022.949897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Plastid ribosomal proteins (PRPs) are necessary components for plastid ribosome biogenesis, playing essential roles in plastid development. The ribosomal protein L18 involved in the assemble of 5S rRNA and 23S rRNA, is vital for E. coli viability, but the functions of its homologs in plant plastid remain elusive. Here, we characterized the functions of the plant plastid ribosomal protein L18s (PRPL18s) in Arabidopsis and rice. AtPRPL18 was ubiquitously expressed in most of the plant tissues, but with higher expression levels in seedling shoots, leaves, and flowers. AtPRPL18 was localized in chloroplast. Genetic and cytological analyses revealed that a loss of function of AtPRPL18 resulted in embryo development arrest at globular stage. However, overexpression of AtPRPL18 did not show any visible phenotypical changes in Arabidopsis. The rice OsPRPL18 was localized in chloroplast. In contrast to AtPRPL18, knockout of OsPRPL18 did not affect embryo development, but led to an albino lethal phenotype at the seedling stage. Cytological analyses showed that chloroplast development was impaired in the osprpl18-1 mutant. Moreover, a loss-function of OsPRPL18 led to defects in plastid ribosome biogenesis and a serious reduction in the efficiency of plastid intron splicing. In all, these results suggested that PRPL18s play critical roles in plastid ribosome biogenesis, plastid intron splicing, and chloroplast development, and are essential for plant survival.
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Affiliation(s)
- Shujing Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinhuang Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yiqi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shijun Qiu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoqun Peng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinjue Xie
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yujie Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chancan Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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27
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Sugita M. An Overview of Pentatricopeptide Repeat (PPR) Proteins in the Moss Physcomitrium patens and Their Role in Organellar Gene Expression. PLANTS 2022; 11:plants11172279. [PMID: 36079663 PMCID: PMC9459714 DOI: 10.3390/plants11172279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
Abstract
Pentatricopeptide repeat (PPR) proteins are one type of helical repeat protein that are widespread in eukaryotes. In particular, there are several hundred PPR members in flowering plants. The majority of PPR proteins are localized in the plastids and mitochondria, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional and translational steps during gene expression. Among the early land plants, the moss Physcomitrium (formerly Physcomitrella) patens has at least 107 PPR protein-encoding genes, but most of their functions remain unclear. To elucidate the functions of PPR proteins, a reverse-genetics approach has been applied to P. patens. To date, the molecular functions of 22 PPR proteins were identified as essential factors required for either mRNA processing and stabilization, RNA splicing, or RNA editing. This review examines the P. patens PPR gene family and their current functional characterization. Similarities and a diversity of functions of PPR proteins between P. patens and flowering plants and their roles in the post-transcriptional regulation of organellar gene expression are discussed.
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Affiliation(s)
- Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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28
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Grüttner S, Nguyen TT, Bruhs A, Mireau H, Kempken F. The P-type pentatricopeptide repeat protein DWEORG1 is a non-previously reported rPPR protein of Arabidopsis mitochondria. Sci Rep 2022; 12:12492. [PMID: 35864185 PMCID: PMC9304396 DOI: 10.1038/s41598-022-16812-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Gene expression in plant mitochondria is mainly regulated by nuclear-encoded proteins on a post-transcriptional level. Pentatricopeptide repeat (PPR) proteins play a major role by participating in mRNA stability, splicing, RNA editing, and translation initiation. PPR proteins were also shown to be part of the mitochondrial ribosome (rPPR proteins), which may act as regulators of gene expression in plants. In this study, we focus on a mitochondrial-located P-type PPR protein—DWEORG1—from Arabidopsis thaliana. Its abundance in mitochondria is high, and it has a similar expression pattern as rPPR proteins. Mutant dweorg1 plants exhibit a slow-growth phenotype. Using ribosome profiling, a decrease in translation efficiency for cox2, rps4, rpl5, and ccmFN2 was observed in dweorg1 mutants, correlating with a reduced accumulation of the Cox2 protein in these plants. In addition, the mitochondrial rRNA levels are significantly reduced in dweorg1 compared with the wild type. DWEORG1 co-migrates with the ribosomal proteins Rps4 and Rpl16 in sucrose gradients, suggesting an association of DWEORG1 with the mitoribosome. Collectively, this data suggests that DWEORG1 encodes a novel rPPR protein that is needed for the translation of cox2, rps4, rpl5, and ccmFN2 and provides a stabilizing function for mitochondrial ribosomes.
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Affiliation(s)
- Stefanie Grüttner
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany
| | - Tan-Trung Nguyen
- Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Anika Bruhs
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
| | - Frank Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany.
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29
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Sahoo S, Singh D, Singh A, Pandit M, Vasu K, Som S, Pullagurla NJ, Laha D, Eswarappa SM. Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. J Biol Chem 2022; 298:102173. [PMID: 35752360 PMCID: PMC9293766 DOI: 10.1016/j.jbc.2022.102173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India; Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Divyoj Singh
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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30
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Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants. Biochem Soc Trans 2022; 50:1119-1132. [PMID: 35587610 PMCID: PMC9246333 DOI: 10.1042/bst20220195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Abstract
Mitochondrial function relies on the homeostasis and quality control of their proteome, including components of the oxidative phosphorylation (OXPHOS) pathway that generates energy in form of ATP. OXPHOS subunits are under constant exposure to reactive oxygen species due to their oxidation-reduction activities, which consequently make them prone to oxidative damage, misfolding, and aggregation. As a result, quality control mechanisms through turnover and degradation are required for maintaining mitochondrial activity. Degradation of OXPHOS subunits can be achieved through proteomic turnover or modular degradation. In this review, we present multiple protein degradation pathways in plant mitochondria. Specifically, we focus on the intricate turnover of OXPHOS subunits, prior to protein import via cytosolic proteasomal degradation and post import and assembly via intra-mitochondrial proteolysis involving multiple AAA+ proteases. Together, these proteolytic pathways maintain the activity and homeostasis of OXPHOS components.
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31
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Identification and Validation of Toxoplasma gondii Mitoribosomal Large Subunit Components. Microorganisms 2022; 10:microorganisms10050863. [PMID: 35630308 PMCID: PMC9145746 DOI: 10.3390/microorganisms10050863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 12/10/2022] Open
Abstract
Mitochondrial ribosomes are fundamental to mitochondrial function, and thus survival, of nearly all eukaryotes. Despite their common ancestry, mitoribosomes have evolved divergent features in different eukaryotic lineages. In apicomplexans, the mitochondrial rRNA is extremely fragmented raising questions about its evolution, protein composition and structure. Apicomplexan mitochondrial translation and the mitoribosomes are essential in all parasites and life stages studied, highlighting mitoribosomes as a promising target for drugs. Still, the apicomplexan mitoribosome is understudied, with one of the obstacles being that its composition is unknown. Here, to facilitate the study of apicomplexan mitoribosomes, we identified and validated components of the mitoribosomal large subunit in the model apicomplexan Toxoplasma gondii.
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32
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Scaltsoyiannes V, Corre N, Waltz F, Giegé P. Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes. Int J Mol Sci 2022; 23:ijms23073474. [PMID: 35408834 PMCID: PMC8998825 DOI: 10.3390/ijms23073474] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.
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Affiliation(s)
- Vassilis Scaltsoyiannes
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Nicolas Corre
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Florent Waltz
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
| | - Philippe Giegé
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
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33
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MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23052670. [PMID: 35269810 PMCID: PMC8910670 DOI: 10.3390/ijms23052670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players in plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1, and thus respiratory complex I biogenesis, are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.
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34
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Lenarčič T, Niemann M, Ramrath DJF, Calderaro S, Flügel T, Saurer M, Leibundgut M, Boehringer D, Prange C, Horn EK, Schneider A, Ban N. Mitoribosomal small subunit maturation involves formation of initiation-like complexes. Proc Natl Acad Sci U S A 2022; 119:e2114710118. [PMID: 35042777 PMCID: PMC8784144 DOI: 10.1073/pnas.2114710118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/29/2021] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps involved in the assembly of the mitoribosomal small subunit (mt-SSU) we determined the cryoelectron microscopy structures of middle and late assembly intermediates of the Trypanosoma brucei mitochondrial small subunit (mt-SSU) at 3.6- and 3.7-Å resolution, respectively. We identified five additional assembly factors that together with the mitochondrial initiation factor 2 (mt-IF-2) specifically interact with functionally important regions of the rRNA, including the decoding center, thereby preventing premature mRNA or large subunit binding. Structural comparison of assembly intermediates with mature mt-SSU combined with RNAi experiments suggests a noncanonical role of mt-IF-2 and a stepwise assembly process, where modular exchange of ribosomal proteins and assembly factors together with mt-IF-2 ensure proper 9S rRNA folding and protein maturation during the final steps of assembly.
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Affiliation(s)
- Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Timo Flügel
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland;
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35
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Tirumalai MR, Rivas M, Tran Q, Fox GE. The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev 2021; 85:e0010421. [PMID: 34756086 PMCID: PMC8579967 DOI: 10.1128/mmbr.00104-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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36
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Waltz F, Salinas-Giegé T, Englmeier R, Meichel H, Soufari H, Kuhn L, Pfeffer S, Förster F, Engel BD, Giegé P, Drouard L, Hashem Y. How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Nat Commun 2021; 12:7176. [PMID: 34887394 PMCID: PMC8660880 DOI: 10.1038/s41467-021-27200-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.
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Affiliation(s)
- Florent Waltz
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
| | - Robert Englmeier
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Herrade Meichel
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France.
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France.
| | - Yaser Hashem
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France.
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37
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van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. THE PLANT CELL 2021; 33:3421-3453. [PMID: 34411258 PMCID: PMC8566204 DOI: 10.1093/plcell/koab211] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 05/02/2023]
Abstract
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, USA
| | - Sascha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
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38
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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: 121] [Impact Index Per Article: 30.3] [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.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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39
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Takahashi A, Sugita C, Ichinose M, Sugita M. Moss PPR-SMR protein PpPPR_64 influences the expression of a psaA-psaB-rps14 gene cluster and processing of the 23S-4.5S rRNA precursor in chloroplasts. PLANT MOLECULAR BIOLOGY 2021; 107:417-429. [PMID: 33128724 DOI: 10.1007/s11103-020-01090-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Moss PPR-SMR protein PpPPR_64 is a pTAC2 homolog but is functionally distinct from pTAC2. PpPPR_64 is required for psaA gene expression and its function may have evolved in mosses. The pentatricopeptide repeat (PPR) proteins are key regulatory factors responsible for the control of plant organellar gene expression. A small subset of PPR proteins possess a C-terminal small MutS-related (SMR) domain and have diverse roles in plant organellar biogenesis. However, the function of PPR-SMR proteins is not fully understood. Here, we report the function of PPR-SMR protein PpPPR_64 in the moss Physcomitrium patens. Phylogenetic analysis indicated that PpPPR_64 belongs to the same clade as the Arabidopsis PPR-SMR protein pTAC2. PpPPR_64 knockout (KO) mutants grew autotrophically but with reduced protonemata growth and the poor formation of photosystems' antenna complexes. Quantitative reverse transcription-polymerase chain reaction and RNA gel blot hybridization analyses revealed a significant reduction in transcript levels of the psaA-psaB-rps14 gene cluster but no alteration to transcript levels of most photosynthesis- and non-photosynthesis-related genes. In addition, RNA processing of 23S-4.5S rRNA precursor was impaired in the PpPPR_64 KO mutants. This suggests that PpPPR_64 is specifically involved in the expression level of the psaA-psaB-rps14 gene and in processing of the 23S-4.5S rRNA precursor. Our results indicate that PpPPR_64 is functionally distinct from pTAC2 and is a novel PPR-SMR protein required for proper chloroplast biogenesis in P. patens.
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Affiliation(s)
- Ayumu Takahashi
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Chieko Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.
- Graduate School of Informatics, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan.
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40
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Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
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Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Hirayama T. PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation. Int J Mol Sci 2021; 22:ijms221910776. [PMID: 34639116 PMCID: PMC8509313 DOI: 10.3390/ijms221910776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 10/02/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.
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Affiliation(s)
- Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurahiki 710-0046, Okayama, Japan
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42
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Waltz F, Giegé P, Hashem Y. Purification and Cryo-electron Microscopy Analysis of Plant Mitochondrial Ribosomes. Bio Protoc 2021; 11:e4111. [PMID: 34458405 DOI: 10.21769/bioprotoc.4111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/12/2021] [Accepted: 03/29/2021] [Indexed: 11/02/2022] Open
Abstract
Plants make up by far the largest part of biomass on Earth. They are the primary source of food and the basis of most drugs used for medicinal purposes. Similarly to all eukaryotes, plant cells also use mitochondria for energy production. Among mitochondrial gene expression processes, translation is the least understood; although, recent advances have revealed the specificities of its main component, the mitochondrial ribosome (mitoribosome). Here, we present a detailed protocol to extract highly pure cauliflower mitochondria by differential centrifugation for the purification of mitochondrial ribosomes using a sucrose gradient and the preparation of cryo-electron microscopy (cryo-EM) grids. Finally, the specific bioinformatics pipeline used for image acquisition, the processing steps, and the data analysis used for cryo-EM of the plant mitoribosome are described. This protocol will be used for further analysis of the critical steps of mitochondrial translation, such as its initiation and regulation.
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Affiliation(s)
- Florent Waltz
- Institut Europeen de Chimie et Biologie, U1212 Inserm, Universite de Bordeaux, Pessac, France
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Yaser Hashem
- Institut Europeen de Chimie et Biologie, U1212 Inserm, Universite de Bordeaux, Pessac, France
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43
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Nguyen TT, Planchard N, Dahan J, Arnal N, Balzergue S, Benamar A, Bertin P, Brunaud V, Dargel-Graffin C, Macherel D, Martin-Magniette ML, Quadrado M, Namy O, Mireau H. A Case of Gene Fragmentation in Plant Mitochondria Fixed by the Selection of a Compensatory Restorer of Fertility-Like PPR Gene. Mol Biol Evol 2021; 38:3445-3458. [PMID: 33878189 PMCID: PMC8321540 DOI: 10.1093/molbev/msab115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The high mutational load of mitochondrial genomes combined with their uniparental inheritance and high polyploidy favors the maintenance of deleterious mutations within populations. How cells compose and adapt to the accumulation of disadvantageous mitochondrial alleles remains unclear. Most harmful changes are likely corrected by purifying selection, however, the intimate collaboration between mitochondria- and nuclear-encoded gene products offers theoretical potential for compensatory adaptive changes. In plants, cytoplasmic male sterilities are known examples of nucleo-mitochondrial coadaptation situations in which nuclear-encoded restorer of fertility (Rf) genes evolve to counteract the effect of mitochondria-encoded cytoplasmic male sterility (CMS) genes and restore fertility. Most cloned Rfs belong to a small monophyletic group, comprising 26 pentatricopeptide repeat genes in Arabidopsis, called Rf-like (RFL). In this analysis, we explored the functional diversity of RFL genes in Arabidopsis and found that the RFL8 gene is not related to CMS suppression but essential for plant embryo development. In vitro-rescued rfl8 plantlets are deficient in the production of the mitochondrial heme-lyase complex. A complete ensemble of molecular and genetic analyses allowed us to demonstrate that the RFL8 gene has been selected to permit the translation of the mitochondrial ccmFN2 gene encoding a heme-lyase complex subunit which derives from the split of the ccmFN gene, specifically in Brassicaceae plants. This study represents thus a clear case of nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants and demonstrates that RFL genes can be selected in response to other mitochondrial deviancies than CMS suppression.
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Affiliation(s)
- Tan-Trung Nguyen
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Noelya Planchard
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Paris-Sud University, Université Paris-Saclay, Orsay, France
| | - Jennifer Dahan
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Nadège Arnal
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sandrine Balzergue
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Abdelilah Benamar
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
| | - Céline Dargel-Graffin
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - David Macherel
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
| | - Martine Quadrado
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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Valach M, Gonzalez Alcazar JA, Sarrasin M, Lang BF, Gray MW, Burger G. An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. Mol Biol Evol 2021; 38:788-804. [PMID: 32886790 PMCID: PMC7947838 DOI: 10.1093/molbev/msaa223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - José Angel Gonzalez Alcazar
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Matt Sarrasin
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - B Franz Lang
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gertraud Burger
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
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45
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Kaur G, Iyer LM, Burroughs AM, Aravind L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 2021; 10:70394. [PMID: 34061031 PMCID: PMC8195603 DOI: 10.7554/elife.70394] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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46
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Forsythe ES, Williams AM, Sloan DB. Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms. THE PLANT CELL 2021; 33:980-997. [PMID: 33764472 PMCID: PMC8226287 DOI: 10.1093/plcell/koab021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/16/2021] [Indexed: 05/05/2023]
Abstract
Nuclear and plastid (chloroplast) genomes experience different mutation rates, levels of selection, and transmission modes, yet key cellular functions depend on their coordinated interactions. Functionally related proteins often show correlated changes in rates of sequence evolution across a phylogeny [evolutionary rate covariation (ERC)], offering a means to detect previously unidentified suites of coevolving and cofunctional genes. We performed phylogenomic analyses across angiosperm diversity, scanning the nuclear genome for genes that exhibit ERC with plastid genes. As expected, the strongest hits were highly enriched for genes encoding plastid-targeted proteins, providing evidence that cytonuclear interactions affect rates of molecular evolution at genome-wide scales. Many identified nuclear genes functioned in post-transcriptional regulation and the maintenance of protein homeostasis (proteostasis), including protein translation (in both the plastid and cytosol), import, quality control, and turnover. We also identified nuclear genes that exhibit strong signatures of coevolution with the plastid genome, but their encoded proteins lack organellar-targeting annotations, making them candidates for having previously undescribed roles in plastids. In sum, our genome-wide analyses reveal that plastid-nuclear coevolution extends beyond the intimate molecular interactions within chloroplast enzyme complexes and may be driven by frequent rewiring of the machinery responsible for maintenance of plastid proteostasis in angiosperms.
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Affiliation(s)
- Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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47
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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: 48] [Impact Index Per Article: 12.0] [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.
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Affiliation(s)
- Olivier Van Aken
- Department of Biology, Lund University, Lund, Sweden
- Author for communication:
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48
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Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation. Sci Rep 2021; 11:2410. [PMID: 33510206 PMCID: PMC7844247 DOI: 10.1038/s41598-021-81610-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Arabidopsis REIL proteins are cytosolic ribosomal 60S-biogenesis factors. After shift to 10 °C, reil mutants deplete and slowly replenish non-translating eukaryotic ribosome complexes of root tissue, while controlling the balance of non-translating 40S- and 60S-subunits. Reil mutations respond by hyper-accumulation of non-translating subunits at steady-state temperature; after cold-shift, a KCl-sensitive 80S sub-fraction remains depleted. We infer that Arabidopsis may buffer fluctuating translation by pre-existing non-translating ribosomes before de novo synthesis meets temperature-induced demands. Reil1 reil2 double mutants accumulate 43S-preinitiation and pre-60S-maturation complexes and alter paralog composition of ribosomal proteins in non-translating complexes. With few exceptions, e.g. RPL3B and RPL24C, these changes are not under transcriptional control. Our study suggests requirement of de novo synthesis of eukaryotic ribosomes for long-term cold acclimation, feedback control of NUC2 and eIF3C2 transcription and links new proteins, AT1G03250, AT5G60530, to plant ribosome biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for cold acclimation.
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49
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Levitskii SA, Baleva MV, Chicherin IV, Krasheninnikov IA, Kamenski PA. Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite. BIOCHEMISTRY (MOSCOW) 2021; 85:257-263. [PMID: 32564730 DOI: 10.1134/s0006297920030013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.
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Affiliation(s)
- S A Levitskii
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M V Baleva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I V Chicherin
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I A Krasheninnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - P A Kamenski
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.
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50
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Di Silvestre D, Vigani G, Mauri P, Hammadi S, Morandini P, Murgia I. Network Topological Analysis for the Identification of Novel Hubs in Plant Nutrition. FRONTIERS IN PLANT SCIENCE 2021; 12:629013. [PMID: 33679842 PMCID: PMC7928335 DOI: 10.3389/fpls.2021.629013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 05/08/2023]
Abstract
Network analysis is a systems biology-oriented approach based on graph theory that has been recently adopted in various fields of life sciences. Starting from mitochondrial proteomes purified from roots of Cucumis sativus plants grown under single or combined iron (Fe) and molybdenum (Mo) starvation, we reconstructed and analyzed at the topological level the protein-protein interaction (PPI) and co-expression networks. Besides formate dehydrogenase (FDH), already known to be involved in Fe and Mo nutrition, other potential mitochondrial hubs of Fe and Mo homeostasis could be identified, such as the voltage-dependent anion channel VDAC4, the beta-cyanoalanine synthase/cysteine synthase CYSC1, the aldehyde dehydrogenase ALDH2B7, and the fumaryl acetoacetate hydrolase. Network topological analysis, applied to plant proteomes profiled in different single or combined nutritional conditions, can therefore assist in identifying novel players involved in multiple homeostatic interactions.
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Affiliation(s)
| | - Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Pierluigi Mauri
- Proteomic and Metabolomic Laboratory, ITB-CNR, Segrate, Italy
| | - Sereen Hammadi
- Proteomic and Metabolomic Laboratory, ITB-CNR, Segrate, Italy
| | - Piero Morandini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Irene Murgia
- Department of Biosciences, University of Milan, Milan, Italy
- *Correspondence: Irene Murgia,
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