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Pines O, Horwitz M, Herrmann JM. Privileged proteins with a second residence: dual targeting and conditional re-routing of mitochondrial proteins. FEBS J 2024. [PMID: 38857249 DOI: 10.1111/febs.17191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Almost all mitochondrial proteins are encoded by nuclear genes and synthesized in the cytosol as precursor proteins. Signals in the amino acid sequence of these precursors ensure their targeting and translocation into mitochondria. However, in many cases, only a certain fraction of a specific protein is transported into mitochondria, while the rest either remains in the cytosol or undergoes reverse translocation to the cytosol, and can populate other cellular compartments. This phenomenon is called dual localization which can be instigated by different mechanisms. These include alternative start or stop codons, differential transcripts, and ambiguous or competing targeting sequences. In many cases, dual localization might serve as an economic strategy to reduce the number of required genes; for example, when the same groups of enzymes are required both in mitochondria and chloroplasts or both in mitochondria and the nucleus/cytoplasm. Such cases frequently employ ambiguous targeting sequences to distribute proteins between both organelles. However, alternative localizations can also be used for signaling, for example when non-imported precursors serve as mitophagy signals or when they represent transcription factors in the nucleus to induce the mitochondrial unfolded stress response. This review provides an overview regarding the mechanisms and the physiological consequences of dual targeting.
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Affiliation(s)
- Ophry Pines
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Margalit Horwitz
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
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2
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Bhattacharya O, Ortiz I, Hendricks N, Walling LL. The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas. FRONTIERS IN PLANT SCIENCE 2023; 14:1020275. [PMID: 37701797 PMCID: PMC10493611 DOI: 10.3389/fpls.2023.1020275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/22/2023] [Indexed: 09/14/2023]
Abstract
Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
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Affiliation(s)
- Oindrila Bhattacharya
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Irma Ortiz
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Nathan Hendricks
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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3
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Wang Y, Yang Z, Zhang M, Ai P. A chloroplast-localized pentatricopeptide repeat protein involved in RNA editing and splicing and its effects on chloroplast development in rice. BMC PLANT BIOLOGY 2022; 22:437. [PMID: 36096762 PMCID: PMC9469629 DOI: 10.1186/s12870-022-03819-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The chloroplast is the organelle responsible for photosynthesis in higher plants. The generation of functional chloroplasts depends on the precise coordination of gene expression in the nucleus and chloroplasts and is essential for the development of plants. However, little is known about nuclear-plastid regulatory mechanisms at the early stage of chloroplast generation in rice. RESULTS In this study, we identified a rice (Oryza sativa) mutant that exhibited albino and seedling-lethal phenotypes and named it ssa1(seedling stage albino1). Transmission electron microscopy (TEM) analysis indicated that the chloroplasts of ssa1 did not have organized thylakoid lamellae and that the chloroplast structure was destroyed. Genetic analysis revealed that the albino phenotypes of ssa1 were controlled by a pair of recessive nuclear genes. Map-based cloning experiments found that SSA1 encoded a pentapeptide repeat (PPR) protein that was allelic to OSOTP51,which was previously reported to participate in Photosystem I (PSI) assembly. The albino phenotype was reversed to the wild type (WT) phenotype when the normal SSA1 sequence was expressed in ssa1 under the drive of the actin promoter. Knockout experiments further created mutants ssa1-2/1-9, which had a phenotype similar to that of ssa1. SSA1 consisted of 7 pentatricopeptide repeat domains and two C-terminal LAGLIDADG tandem sequence motifs and was located in the chloroplast. GUS staining and qRT-PCR analysis showed that SSA1 was mainly expressed in young leaves and stems. In the ssa1 mutants, plastid genes transcribed by plastid-encoded RNA polymerase decreased, while those transcribed by nuclear-encoded RNA polymerase increased at the mRNA level. Loss-of-function SSA1 destroys RNA editing of ndhB-737 and intron splicing of atpF and ycf3-2 in the plastid genome. Yeast two-hybrid and BiFC assays revealed that SSA1 physically interacted with two new RNA editing partners, OsMORF8 and OsTRXz, which have potential functions in RNA editing and chloroplast biogenesis. CONCLUSIONS Rice SSA1 encodes a pentatricopeptide repeat protein, which is targeted to the chloroplast. SSA1 regulates early chloroplast development and plays a critical role in RNA editing and intron splicing in rice. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.
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Affiliation(s)
- Yanwei Wang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Zhimin Yang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Meng Zhang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Pengfei Ai
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China.
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Ma L, Yang Y, Wang Y, Cheng K, Zhou X, Li J, Zhang J, Li R, Zhang L, Wang K, Zeng N, Gong Y, Zhu D, Deng Z, Qu G, Zhu B, Fu D, Luo Y, Zhu H. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato. THE PLANT CELL 2022; 34:2747-2764. [PMID: 35385118 PMCID: PMC9252502 DOI: 10.1093/plcell/koac104] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/05/2022] [Indexed: 06/01/2023]
Abstract
Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Yuqiu Wang
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiwen Zhou
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingyu Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Lingling Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ni Zeng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanyan Gong
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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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: 21] [Impact Index Per Article: 7.0] [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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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana. Sci Rep 2021; 11:9948. [PMID: 33976263 PMCID: PMC8113564 DOI: 10.1038/s41598-021-89211-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 01/19/2023] Open
Abstract
The LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.
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Bhattacharya O, Ortiz I, Walling LL. Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins. PLANT METHODS 2020; 16:131. [PMID: 32983250 PMCID: PMC7513546 DOI: 10.1186/s13007-020-00667-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/04/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUND Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the model plant Arabidopsis, however fewer studies have characterized the proteomes of plastids in crops. Tomato (Solanum lycopersicum) is an important world-wide crop and a model system for the study of wounding, herbivory and fruit ripening. While significant advances have been made in understanding proteome and metabolome changes in fruit ripening, far less is known about the tomato chloroplast proteome or its subcompartments. RESULTS With the long-term goal of understanding chloroplast proteome dynamics in response to stress, we describe a high-yielding method to isolate intact tomato chloroplasts and stromal proteins for proteomic studies. The parameters that limit tomato chloroplast yields were identified and revised to increase yields. Compared to published data, our optimized method increased chloroplast yields by 6.7- and 4.3-fold relative to published spinach and Arabidopsis leaf protocols, respectively; furthermore, tomato stromal protein yields were up to 79-fold higher than Arabidopsis stromal proteins yields. We provide immunoblot evidence for the purity of the stromal proteome isolated using our enhanced methods. In addition, we leverage our nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS) data to assess the quality of our stromal proteome. Using strict criteria, proteins detected by 1 peptide spectral match, by one peptide, or were sporadically detected were designated as low-level contaminating proteins. A set of 254 proteins that reproducibly co-isolated with the tomato chloroplast stroma were identified. The subcellular localization, frequency of detection, normalized spectral abundance, and functions of the co-isolating proteins are discussed. CONCLUSIONS Our optimized method for chloroplast isolation increased the yields of tomato chloroplasts eightfold enabling the proteomics analysis of the chloroplast stromal proteome. The set of 254 proteins that co-isolate with the chloroplast stroma provides opportunities for developing a better understanding of the extensive and dynamic interactions of chloroplasts with other organelles. These co-isolating proteins also have the potential for expanding our knowledge of proteins that are co-localized in multiple subcellular organelles.
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Affiliation(s)
- Oindrila Bhattacharya
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
| | - Irma Ortiz
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
| | - Linda L. Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
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8
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Lee K, Kang H. Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses. Int J Mol Sci 2020; 21:ijms21124548. [PMID: 32604726 PMCID: PMC7352785 DOI: 10.3390/ijms21124548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have characterized the functions of nCMRBP families, such as chloroplast ribosome maturation and splicing domain (CRM) proteins, pentatricopeptide repeat (PPR) proteins, DEAD-Box RNA helicase (DBRH) proteins, and S1-domain containing proteins (SDPs), have begun to shed light on the role of nCMRBPs in plant growth, development, and stress responses. Here, we review the latest research developments regarding the functional roles of organellar RBPs in RNA metabolism during growth, development, and abiotic stress responses in plants.
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Affiliation(s)
- Kwanuk Lee
- Plant Molecular Biology (Botany), Department of Biology I, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
| | - Hunseung Kang
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
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9
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Christian RW, Hewitt SL, Roalson EH, Dhingra A. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Sci Rep 2020; 10:8281. [PMID: 32427841 PMCID: PMC7237471 DOI: 10.1038/s41598-020-64670-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
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Affiliation(s)
- Ryan W Christian
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Seanna L Hewitt
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Eric H Roalson
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA.
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Kumari K, Rai MP, Bansal N, Prashat GR, Kumari S, Srivathsa R, Dahuja A, Sachdev A, Praveen S, Vinutha T. Study of subcellular localization of Glycine max γ-tocopherol methyl transferase isoforms in N. benthamiana. 3 Biotech 2020; 10:110. [PMID: 32099748 DOI: 10.1007/s13205-020-2086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/21/2020] [Indexed: 10/25/2022] Open
Abstract
Gamma-tocopherol methyltransferase (γ-TMT) converts γ-toc to α-toc-the rate limiting step in toc biosynthesis. Sequencing results revealed that the coding regions of γ-TMT1 and γ-TMT3 were strongly similar to each other (93% at amino acid level). Based on the differences in the N-terminal amino acids, Glycine max-γ-TMT proteins are categorized into three isoforms: γ-TMT1, 2 and 3. In silico structural analysis revealed the presence of chloroplast transit peptide (cTP) in γ-TMT1 and γ-TMT3 protein. However, other properties of transit peptide like presence of hydrophobic amino acids at the first three positions of N-terminal end and lower level of acidic amino acids were revealed only in γ-TMT3 protein. Subcellular localization of GFP fused γ-TMT1 and γ-TMT3 under 35S promoter was studied in Nicotiana benthamiana using confocal microscopy. Results showed that γ-TMT1 was found in the cytosol and γ-TMT3 was found to be localized both in cytosol and chloroplast. Further the presence γ-TMT3 in chloroplast was validated by quantifying α-tocopherol through UPLC. Thus the present study of cytosolic localization of the both γ-TMT1 and γ-TMT3 proteins and chloroplastic localization of γ-TMT3 will help to reveal the importance of γ-TMT encoded α-toc in protecting both chloroplastic and cell membrane from plant oxidative stress.
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Zheng H, Wang Z, Tian Y, Liu L, Lv F, Kong W, Bai W, Wang P, Wang C, Yu X, Liu X, Jiang L, Zhao Z, Wan J. Rice albino 1, encoding a glycyl-tRNA synthetase, is involved in chloroplast development and establishment of the plastidic ribosome system in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:495-503. [PMID: 31015088 DOI: 10.1016/j.plaphy.2019.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
The chloroplast is an important organelle that performs photosynthesis as well as biosynthesis and storage of many metabolites. Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in protein synthesis. However, the relationship between chloroplast development and aaRSs still remains unclear. In this study, we isolated a rice albino 1 (ra1) mutant through methane sulfonate (EMS) mutagenesis of rice japonica cultivar Ningjing 4 (Oryza sativa L.), which displayed albinic leaves in seedling stage due to abnormal chloroplast development. Compared with wild type (WT), ra1 showed significantly decreased levels of chlorophylls (Chl) and carotenoids (Car) in 2-week-old seedlings, which also showed obvious plastidic structural defects including abnormal thylakoid membrane structures and more osmiophilic particles. These defects caused albino phenotypes in seedlings. Map-based cloning revealed that RA1 gene encodes a glycyl-tRNA synthetase (GlyRS), which was confirmed by genetic complementation and knockout by Crispr/Cas9 technology. Sequence analysis showed that a single base mutation (T to A) occurred in the sixth exon of RA1 and resulted in a change from Isoleucine (Ile) to Lysine (Lys). Real-time PCR analyses showed that RA1 expression levels were constitutive in most tissues, but most abundant in the leaves and stems. By transient expression in Nicotiana benthamiana, we found that RA1 protein was localized in the chloroplast. Expression levels of chlorophyll biosynthesis and plastid development related genes were disordered in the ra1 mutant. RNA analysis revealed biogenesis of chloroplast rRNAs was abnormal in ra1. Meanwhile, western blotting showed that synthesis of proteins associated with plastid development was significantly repressed. These results suggest that RA1 is involved in early chloroplast development and establishment of the plastidic ribosome system in rice.
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Affiliation(s)
- Hai Zheng
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhuoran Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - LingLong Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Lv
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyi Kong
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenting Bai
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peiran Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaolong Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaowen Yu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
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12
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Mao M, Yang X, Bennett GM. Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host. Proc Natl Acad Sci U S A 2018; 115:E11691-E11700. [PMID: 30463949 PMCID: PMC6294904 DOI: 10.1073/pnas.1811932115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.
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Affiliation(s)
- Meng Mao
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343;
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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13
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Zhu M, Lin J, Ye J, Wang R, Yang C, Gong J, Liu Y, Deng C, Liu P, Chen C, Cheng Y, Deng X, Zeng Y. A comprehensive proteomic analysis of elaioplasts from citrus fruits reveals insights into elaioplast biogenesis and function. HORTICULTURE RESEARCH 2018; 5:6. [PMID: 29423236 PMCID: PMC5802726 DOI: 10.1038/s41438-017-0014-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 05/02/2023]
Abstract
Elaioplasts of citrus peel are colorless plastids which accumulate significant amounts of terpenes. However, other functions of elaioplasts have not been fully characterized to date. Here, a LC-MS/MS shotgun technology was applied to identify the proteins from elaioplasts that were highly purified from young fruit peel of kumquat. A total of 655 putative plastid proteins were identified from elaioplasts according to sequence homology in silico and manual curation. Based on functional classification via Mapman, ~50% of the identified proteins fall into six categories, including protein metabolism, transport, and lipid metabolism. Of note, elaioplasts contained ATP synthase and ADP, ATP carrier proteins at high abundance, indicating important roles for ATP generation and transport in elaioplast biogenesis. Additionally, a comparison of proteins between citrus chromoplast and elaioplast proteomes suggest a high level of functional conservation. However, some distinctive protein profiles were also observed in both types of plastids notably for isoprene biosynthesis in elaioplasts, and carotenoid metabolism in chromoplasts. In conclusion, this comprehensive proteomic study provides new insights into the major metabolic pathways and unique characteristics of elaioplasts and chromoplasts in citrus fruit.
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Affiliation(s)
- Man Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jiajia Lin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Rui Wang
- Shanghai Applied Protein Technology Co. Ltd, Shanghai, 200233 China
| | - Chao Yang
- Shanghai Applied Protein Technology Co. Ltd, Shanghai, 200233 China
| | - Jinli Gong
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chongling Deng
- Guangxi Citrus Research Institute, Guangxi, 541004 China
| | - Ping Liu
- Guangxi Citrus Research Institute, Guangxi, 541004 China
| | - Chuanwu Chen
- Guangxi Citrus Research Institute, Guangxi, 541004 China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Citrus Science, Huazhong Agricultural University, Wuhan, 430070 China
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14
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Zhang N, Rao RSP, Salvato F, Havelund JF, Møller IM, Thelen JJ, Xu D. MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:634. [PMID: 29875778 PMCID: PMC5974146 DOI: 10.3389/fpls.2018.00634] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/23/2018] [Indexed: 05/19/2023]
Abstract
Targeting and translocation of proteins to the appropriate subcellular compartments are crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of complex targeting sequences containing either an N-terminal pre-sequence or a multitude of internal signals. Compared with experimental approaches, computational predictions provide an efficient way to infer subcellular localization of a protein. However, it is still challenging to predict plant mitochondrially localized proteins accurately due to various limitations. Consequently, the performance of current tools can be improved with new data and new machine-learning methods. We present MU-LOC, a novel computational approach for large-scale prediction of plant mitochondrial proteins. We collected a comprehensive dataset of plant subcellular localization, extracted features including amino acid composition, protein position weight matrix, and gene co-expression information, and trained predictors using deep neural network and support vector machine. Benchmarked on two independent datasets, MU-LOC achieved substantial improvements over six state-of-the-art tools for plant mitochondrial targeting prediction. In addition, MU-LOC has the advantage of predicting plant mitochondrial proteins either possessing or lacking N-terminal pre-sequences. We applied MU-LOC to predict candidate mitochondrial proteins for the whole proteome of Arabidopsis and potato. MU-LOC is publicly available at http://mu-loc.org.
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Affiliation(s)
- Ning Zhang
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - R. S. P. Rao
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Fernanda Salvato
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Jesper F. Havelund
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jay J. Thelen
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- *Correspondence: Dong Xu,
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15
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Gruber A, Kroth PG. Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160402. [PMID: 28717012 PMCID: PMC5516111 DOI: 10.1098/rstb.2016.0402] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2017] [Indexed: 11/12/2022] Open
Abstract
Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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16
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Zhang YY, Hao YY, Wang YH, Wang CM, Wang YL, Long WH, Wang D, Liu X, Jiang L, Wan JM. Lethal albinic seedling, encoding a threonyl-tRNA synthetase, is involved in development of plastid protein synthesis system in rice. PLANT CELL REPORTS 2017; 36:1053-1064. [PMID: 28405745 DOI: 10.1007/s00299-017-2136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/27/2017] [Indexed: 05/26/2023]
Abstract
An albinic rice is caused by mutation of threonyl-tRNA synthetase, which is essential for plant development by stabilizing of NEP and PEP gene expressions and chloroplast protein synthesis. Chloroplast biogenesis and development depend on complex genetic mechanisms. Apart from their function in translation, aminoacyl-tRNA synthetases (aaRSs) play additional role in gene expression regulation, RNA splicing, and cytokine activity. However, their detailed functions in plant development are still poorly understood. We isolated a lethal albinic seedling (las) mutant in rice. Physiological and ultrastructural analysis of las mutant plants revealed weak chlorophyll fluorescence, negligible chlorophyll accumulation, and defective thylakoid membrane development. By map based cloning we determined that the LAS allele gene encodes threonyl-tRNA synthetase (ThrRS). LAS was constitutively expressed with relatively high level in leaves. NEP-dependent gene transcripts accumulated in the developing chloroplasts, while PEP-dependent transcripts were reduced in the las mutant. This result indicated that PEP activity was impaired. Chloroplast-encoded protein levels were sharply reduced in the las mutant. Biogenesis of chloroplast rRNAs (16S and 23S rRNA) was arrested, leading to impaired translation and protein synthesis. Together, our findings indicated that LAS is essential not only for chloroplast development by stabilizing the NEP and PEP gene expression, but also for protein synthesis and construction of the ribosome system in rice chloroplasts.
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Affiliation(s)
- Yuan-Yan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Yuan Hao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi-Hua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chun-Ming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yun-Long Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wu-Hua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Min Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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17
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Lee K, Han JH, Park YI, Colas des Francs-Small C, Small I, Kang H. The mitochondrial pentatricopeptide repeat protein PPR19 is involved in the stabilization of NADH dehydrogenase 1 transcripts and is crucial for mitochondrial function and Arabidopsis thaliana development. THE NEW PHYTOLOGIST 2017; 215:202-216. [PMID: 28332713 DOI: 10.1111/nph.14528] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/19/2017] [Indexed: 05/06/2023]
Abstract
Despite the importance of pentatricopeptide repeat (PPR) proteins in organellar RNA metabolism and plant development, the functions of many PPR proteins remain unknown. Here, we determined the role of a mitochondrial PPR protein (At1g52620) comprising 19 PPR motifs, thus named PPR19, in Arabidopsis thaliana. The ppr19 mutant displayed abnormal seed development, reduced seed yield, delayed seed germination, and retarded growth, indicating that PPR19 is indispensable for normal growth and development of Arabidopsis thaliana. Splicing pattern analysis of mitochondrial genes revealed that PPR19 specifically binds to the specific sequence in the 3'-terminus of the NADH dehydrogenase 1 (nad1) transcript and stabilizes transcripts containing the second and third exons of nad1. Loss of these transcripts in ppr19 leads to multiple secondary effects on accumulation and splicing of other nad1 transcripts, from which we can infer the order in which cis- and trans-spliced nad1 transcripts are normally processed. Improper splicing of nad1 transcripts leads to the absence of mitochondrial complex I and alteration of the nuclear transcriptome, notably influencing the alternative splicing of a variety of nuclear genes. Our results indicate that the mitochondrial PPR19 is an essential component in the splicing of nad1 transcripts, which is crucial for mitochondrial function and plant development.
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Affiliation(s)
- Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Ji Hoon Han
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 306-764, Korea
| | - Catherine Colas des Francs-Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
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18
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Taskin AA, Kücükköse C, Burger N, Mossmann D, Meisinger C, Vögtle FN. The novel mitochondrial matrix protease Ste23 is required for efficient presequence degradation and processing. Mol Biol Cell 2017; 28:997-1002. [PMID: 28228553 PMCID: PMC5391191 DOI: 10.1091/mbc.e16-10-0732] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/08/2017] [Accepted: 02/13/2017] [Indexed: 11/15/2022] Open
Abstract
Approximately 70% of mitochondrial precursor proteins are imported from the cytosol via N-terminal presequences, which are cleaved upon exposure to the mitochondrial processing protease MPP in the matrix. Cleaved presequence peptides then need to be efficiently degraded, and impairment of this clearance step, for example, by amyloid β peptides, causes feedback inhibition of MPP, leading ultimately to accumulation of immature precursor proteins within mitochondria. Degradation of mitochondrial peptides is performed by Cym1 in yeast and its homologue, PreP, in humans. Here we identify the novel mitochondrial matrix protease Ste23 in yeast, a homologue of human insulin-degrading enzyme, which is required for efficient peptide degradation. Ste23 and Cym1 tightly cooperate to ensure the correct functioning of the essential presequence processing machinery.
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Affiliation(s)
- Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Burger
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Dirk Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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19
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Senkler J, Senkler M, Eubel H, Hildebrandt T, Lengwenus C, Schertl P, Schwarzländer M, Wagner S, Wittig I, Braun HP. The mitochondrial complexome of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1079-1092. [PMID: 27943495 DOI: 10.1111/tpj.13448] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 05/19/2023]
Abstract
Mitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes relies on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines. There has been a strong interest in the makeup and function of mitochondrial protein complexes and protein-protein interactions in plants, but the experimental approaches used typically suffer from selectivity or bias. Here, we present a complexome profiling analysis for leaf mitochondria of the model plant Arabidopsis thaliana for the systematic characterization of protein assemblies. Purified organelle extracts were separated by 1D Blue native (BN) PAGE, a resulting gel lane was dissected into 70 slices (complexome fractions) and proteins in each slice were identified by label free quantitative shot-gun proteomics. Overall, 1359 unique proteins were identified, which were, on average, present in 17 complexome fractions each. Quantitative profiles of proteins along the BN gel lane were aligned by similarity, allowing us to visualize protein assemblies. The data allow re-annotating the subunit compositions of OXPHOS complexes, identifying assembly intermediates of OXPHOS complexes and assemblies of alternative respiratory oxidoreductases. Several protein complexes were discovered that have not yet been reported in plants, such as a 530 kDa Tat complex, 460 and 1000 kDa SAM complexes, a calcium ion uniporter complex (150 kDa) and several PPR protein complexes. We have set up a tailored online resource (https://complexomemap.de/at_mito_leaves) to deposit the data and to allow straightforward access and custom data analyses.
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Affiliation(s)
- Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Michael Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Tatjana Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Christian Lengwenus
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Peter Schertl
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Markus Schwarzländer
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, Bonn, 53113, Germany
| | - Stephan Wagner
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, Bonn, 53113, Germany
| | - Ilka Wittig
- Functional Proteomics, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt, 60590, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
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20
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Nawaz G, Kang H. Chloroplast- or Mitochondria-Targeted DEAD-Box RNA Helicases Play Essential Roles in Organellar RNA Metabolism and Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:871. [PMID: 28596782 PMCID: PMC5442247 DOI: 10.3389/fpls.2017.00871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/10/2017] [Indexed: 05/04/2023]
Abstract
The yields and productivity of crops are greatly diminished by various abiotic stresses, including drought, cold, heat, and high salinity. Chloroplasts and mitochondria are cellular organelles that can sense diverse environmental stimuli and alter gene expression to cope with adverse environmental stresses. Organellar gene expression is mainly regulated at posttranscriptional levels, including RNA processing, intron splicing, RNA editing, RNA turnover, and translational control, during which a variety of nucleus-encoded RNA-binding proteins (RBPs) are targeted to chloroplasts or mitochondria where they play essential roles in organellar RNA metabolism. DEAD-box RNA helicases (RHs) are enzymes that can alter RNA structures and affect RNA metabolism in all living organisms. Although a number of DEAD-box RHs have been found to play important roles in RNA metabolism in the nucleus and cytoplasm, our understanding on the roles of DEAD-box RHs in the regulation of RNA metabolism in chloroplasts and mitochondria is only at the beginning. Considering that organellar RNA metabolism and gene expression are tightly regulated by anterograde signaling from the nucleus, it is imperative to determine the functions of nucleus-encoded organellar RBPs. In this review, we summarize the emerging roles of nucleus-encoded chloroplast- or mitochondria-targeted DEAD-box RHs in organellar RNA metabolism and plant response to diverse abiotic stresses.
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21
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Daher Z, Recorbet G, Solymosi K, Wienkoop S, Mounier A, Morandi D, Lherminier J, Wipf D, Dumas-Gaudot E, Schoefs B. Changes in plastid proteome and structure in arbuscular mycorrhizal roots display a nutrient starvation signature. PHYSIOLOGIA PLANTARUM 2017; 159:13-29. [PMID: 27558913 DOI: 10.1111/ppl.12505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/17/2016] [Accepted: 07/18/2016] [Indexed: 05/21/2023]
Abstract
During arbuscular mycorrhizal symbiosis, arbuscule-containing root cortex cells display a proliferation of plastids, a feature usually ascribed to an increased plant anabolism despite the lack of studies focusing on purified root plastids. In this study, we investigated mycorrhiza-induced changes in plastidic pathways by performing a label-free comparative subcellular quantitative proteomic analysis targeted on plastid-enriched fractions isolated from Medicago truncatula roots, coupled to a cytological analysis of plastid structure. We identified 490 root plastid protein candidates, among which 79 changed in abundance upon mycorrhization, as inferred from spectral counting. According to cross-species sequence homology searches, the mycorrhiza-responsive proteome was enriched in proteins experimentally localized in thylakoids, whereas it was depleted of proteins ascribed predominantly to amyloplasts. Consistently, the analysis of plastid morphology using transmission electron microscopy indicated that starch depletion associated with the proliferation of membrane-free and tubular membrane-containing plastids was a feature specific to arbusculated cells. The loss of enzymes involved in carbon/nitrogen assimilation and provision of reducing power, coupled to macromolecule degradation events in the plastid-enriched fraction of mycorrhizal roots that paralleled lack of starch accumulation in arbusculated cells, lead us to propose that arbuscule functioning elicits a nutrient starvation and an oxidative stress signature that may prime arbuscule breakdown.
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Affiliation(s)
- Zeina Daher
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Ghislaine Recorbet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Katalin Solymosi
- Department of Plant Anatomy, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Stefanie Wienkoop
- Department of Molecular System Biology, University of Vienna, Vienna 1090, Austria
| | - Arnaud Mounier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Dominique Morandi
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Jeannine Lherminier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Eliane Dumas-Gaudot
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Benoît Schoefs
- MicroMar, Mer, Molécules, Santé, UBL, Université du Maine, Le Mans Cedex 9 72085, France
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Hofstatter PG, Tice AK, Kang S, Brown MW, Lahr DJG. Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages. Proc Biol Sci 2016; 283:20161453. [PMID: 27708147 PMCID: PMC5069510 DOI: 10.1098/rspb.2016.1453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/12/2016] [Indexed: 11/12/2022] Open
Abstract
Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria-eukaryote) and/or secondary (eukaryote-eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.
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Affiliation(s)
- Paulo G Hofstatter
- Department of Zoology, Universidade de São Paulo/USP, Cidade Universitária, São Paulo, Brazil
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Seungho Kang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel J G Lahr
- Department of Zoology, Universidade de São Paulo/USP, Cidade Universitária, São Paulo, Brazil
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Thieulin-Pardo G, Schramm A, Lignon S, Lebrun R, Kojadinovic M, Gontero B. The intriguing CP12-like tail of adenylate kinase 3 fromChlamydomonas reinhardtii. FEBS J 2016; 283:3389-407. [DOI: 10.1111/febs.13814] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/14/2016] [Accepted: 07/13/2016] [Indexed: 01/09/2023]
Affiliation(s)
| | - Antoine Schramm
- Aix Marseille Univ; CNRS; BIP, UMR 7281, IMM; Marseille Cedex 20 France
| | - Sabrina Lignon
- Plate-forme Protéomique; Marseille Protéomique (MaP); Institut de Microbiologie de la Méditerranée; CNRS, FR 3479 Marseille Cedex 20 France
| | - Régine Lebrun
- Plate-forme Protéomique; Marseille Protéomique (MaP); Institut de Microbiologie de la Méditerranée; CNRS, FR 3479 Marseille Cedex 20 France
| | - Mila Kojadinovic
- Aix Marseille Univ; CNRS; BIP, UMR 7281, IMM; Marseille Cedex 20 France
| | - Brigitte Gontero
- Aix Marseille Univ; CNRS; BIP, UMR 7281, IMM; Marseille Cedex 20 France
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Mueller SJ, Hoernstein SNW, Reski R. The mitochondrial proteome of the moss Physcomitrella patens. Mitochondrion 2016; 33:38-44. [PMID: 27450107 DOI: 10.1016/j.mito.2016.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/08/2016] [Accepted: 07/18/2016] [Indexed: 01/08/2023]
Abstract
Extant basal land plants are routinely used to trace plant evolution and to track strategies for high abiotic stress resistance. Whereas the structure of mitochondrial genomes and RNA editing are already well studied, mitochondrial proteome research is restricted to a few data sets. While the mitochondrial proteome of the model moss Physcomitrella patens is covered to an estimated 15-25% by proteomic evidence to date, the available data have already provided insights into the evolution of metabolic compartmentation, dual targeting and mitochondrial heterogeneity. This review summarizes the current knowledge about the mitochondrial proteome of P. patens, and gives a perspective on its use as a mitochondrial model system. Its amenability to gene editing, metabolic labelling as well as fluorescence microscopy provides a unique platform to study open questions in mitochondrial biology, such as regulation of protein stability, responses to stress and connectivity to other organelles. Future challenges will include improving the proteomic resources for P. patens, and to link protein inventories and modifications as well as evolutionary differences to the functional level.
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Affiliation(s)
- Stefanie J Mueller
- INRES-Chemical Signalling University of Bonn, Friedrich-Ebert-Allee 144, DE-53113 Bonn, Germany.
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr.1, DE-79104 Freiburg, Germany.
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr.1, DE-79104 Freiburg, Germany; BIOSS - Centre for Biological Signalling Studies, DE-79104 Freiburg, Germany.
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Møller IM. What is hot in plant mitochondria? PHYSIOLOGIA PLANTARUM 2016; 157:256-63. [PMID: 27094909 DOI: 10.1111/ppl.12456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/04/2016] [Accepted: 03/11/2016] [Indexed: 05/23/2023]
Abstract
In this overview of recent trends in plant mitochondrial research, four questions are considered: (1) How large is the mitochondrial proteome? It appears to be in excess of 1500 proteins in a tissue at any given time. It is proposed that the fusion-fission frequently observed for plant mitochondria provides a vital mixing function ensuring that all low-abundance proteins are present in each mitochondrion at least some of the time. (2) What is the significance of posttranslational modifications (PTM) of proteins? As a result of PTM, many proteins are present in a very large number of slightly different forms. The most well-studied PTMs, such as protein phosphorylation, acetylation and reversible cysteine oxidation, are known to regulate mitochondrial function. Recent studies have provided examples of the importance of this regulation, but it remains a research area with a massive growth potential. (3) What is the role(s) of pentatricopeptide repeat (PPR) proteins in plant mitochondria? There is general agreement that PPR proteins are involved in RNA metabolism such as RNA editing. Recent comprehensive proteomic studies raise the question of how many of the potential 250-300 mitochondrial PPR proteins encoded in the nuclear DNA are required to be present for a mitochondrion to be able to grow and divide. (4) What is the mechanism(s) of retrograde signal transduction from the mitochondria to the nucleus? The nature of the signal transduction molecule is still unknown, but calcium ions, hydrogen peroxide and/or oxidized peptides are potential candidates. Recent results place a receptor for the activation of a group of nuclear genes on the endoplasmic reticulum, possibly close to ER-mitochondrial contact points.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark .
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Leister D. Towards understanding the evolution and functional diversification of DNA-containing plant organelles. F1000Res 2016; 5. [PMID: 26998248 PMCID: PMC4792205 DOI: 10.12688/f1000research.7915.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/27/2022] Open
Abstract
Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).
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Affiliation(s)
- Dario Leister
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-Universität, Planegg-Martinsried, 82152, Germany; Copenhagen Plant Science Center (CPSC), University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Abstract
Eukaryotic cells contain a multitude of membrane structures that are connected through a highly dynamic and complex exchange of their constituents. The vibrant instability of these structures challenges the classical view of defined, static compartments that are connected by different types of vesicles. Despite this astonishing complexity, proteins and lipids are accurately transported into the different intracellular membrane systems. Over the past few decades many factors have been identified that either mediate or regulate intracellular membrane trafficking. Like in a modern parcel sorting system of a logistics center, the cargo typically passes through several sequential sorting stations until it finally reaches the location that is specified by its individual address label. While each membrane system employs specific sets of factors, the transport processes typically operate on common principles. With the advent of genome- and proteome-wide screens, the availability of mutant collections, exciting new developments in microscope technology and sophisticated methods to study their dynamics, the future promises a broad and comprehensive picture of the processes by which eukaryotic cells sort their proteins.
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Liu SL, Pan AQ, Adams KL. Protein subcellular relocalization of duplicated genes in Arabidopsis. Genome Biol Evol 2014; 6:2501-15. [PMID: 25193306 PMCID: PMC4202327 DOI: 10.1093/gbe/evu191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.
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Affiliation(s)
- Shao-Lun Liu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Department of Life Science, Tunghai University, Taichung, Taiwan
| | - An Qi Pan
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Mintec Inc., Vancouver, BC, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Hooper CM, Tanz SK, Castleden IR, Vacher MA, Small ID, Millar AH. SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome. ACTA ACUST UNITED AC 2014; 30:3356-64. [PMID: 25150248 DOI: 10.1093/bioinformatics/btu550] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MOTIVATION Knowing the subcellular location of proteins is critical for understanding their function and developing accurate networks representing eukaryotic biological processes. Many computational tools have been developed to predict proteome-wide subcellular location, and abundant experimental data from green fluorescent protein (GFP) tagging or mass spectrometry (MS) are available in the model plant, Arabidopsis. None of these approaches is error-free, and thus, results are often contradictory. RESULTS To help unify these multiple data sources, we have developed the SUBcellular Arabidopsis consensus (SUBAcon) algorithm, a naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein-protein interaction and co-expression data to derive a consensus call and probability. SUBAcon classifies protein location in Arabidopsis more accurately than single predictors. AVAILABILITY SUBAcon is a useful tool for recovering proteome-wide subcellular locations of Arabidopsis proteins and is displayed in the SUBA3 database (http://suba.plantenergy.uwa.edu.au). The source code and input data is available through the SUBA3 server (http://suba.plantenergy.uwa.edu.au//SUBAcon.html) and the Arabidopsis SUbproteome REference (ASURE) training set can be accessed using the ASURE web portal (http://suba.plantenergy.uwa.edu.au/ASURE).
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Affiliation(s)
- Cornelia M Hooper
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Sandra K Tanz
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Ian R Castleden
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Michael A Vacher
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Ian D Small
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - A Harvey Millar
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
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Daras G, Rigas S, Tsitsekian D, Zur H, Tuller T, Hatzopoulos P. Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease. MOLECULAR PLANT 2014; 7:989-1005. [PMID: 24646630 DOI: 10.1093/mp/ssu030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cellular homeostasis relies on components of protein quality control including chaperones and proteases. In bacteria and eukaryotic organelles, Lon proteases play a critical role in removing irreparably damaged proteins and thereby preventing the accumulation of deleterious degradation-resistant aggregates. Gene expression, live-cell imaging, immunobiochemical, and functional complementation approaches provide conclusive evidence for Lon1 dual-targeting to chloroplasts and mitochondria. Dual-organellar deposition of Lon1 isoforms depends on both transcriptional regulation and alternative translation initiation via leaky ribosome scanning from the first AUG sequence context that deviates extensively from the optimum Kozak consensus. Organelle-specific Lon1 targeting results in partial complementation of Arabidopsis lon1-1 mutants, whereas full complementation is solely accomplished by dual-organellar targeting. Both the optimal and non-optimal AUG sequence contexts are functional in yeast and facilitate leaky ribosome scanning complementing the pim1 phenotype when the mitochondrial presequence is used. Bioinformatic search identified a limited number of Arabidopsis genes with Lon1-type dual-targeting sequence organization. Lon4, the paralog of Lon1, has an ambiguous presequence likely evolved from the twin presequences of an ancestral Lon1-like gene, generating a single dual-targeted protein isoform. We postulate that Lon1 and its subfunctional paralog Lon4 evolved complementary subsets of transcriptional and posttranscriptional regulatory components responsive to environmental cues for dual-organellar targeting.
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Affiliation(s)
- Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Hadas Zur
- School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Polydefkis Hatzopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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Salvato F, Havelund JF, Chen M, Rao RSP, Rogowska-Wrzesinska A, Jensen ON, Gang DR, Thelen JJ, Møller IM. The potato tuber mitochondrial proteome. PLANT PHYSIOLOGY 2014; 164:637-53. [PMID: 24351685 PMCID: PMC3912095 DOI: 10.1104/pp.113.229054] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/16/2013] [Indexed: 05/17/2023]
Abstract
Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.
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Affiliation(s)
| | - Jesper F. Havelund
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Mingjie Chen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - R. Shyama Prasad Rao
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Ole N. Jensen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - David R. Gang
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
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Baudisch B, Langner U, Garz I, Klösgen RB. The exception proves the rule? Dual targeting of nuclear-encoded proteins into endosymbiotic organelles. THE NEW PHYTOLOGIST 2014; 201:80-90. [PMID: 24024706 DOI: 10.1111/nph.12482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 08/05/2013] [Indexed: 05/17/2023]
Abstract
Plant cells harbor two types of endosymbiotic organelle: mitochondria and chloroplasts. As a consequence of endosymbiotic gene transfer, the majority of their proteins are encoded in the nucleus and post-translationally 're'-imported into the respective target organelle. The corresponding transport signals are usually selective for a single organelle, but several proteins are transported into both the mitochondria and chloroplasts. To estimate the number of proteins with such dual targeting properties in Arabidopsis, we classified the proteins encoded by nuclear genes of endosymbiotic origin according to the respective targeting specificity of their N-terminal transport signals as predicted by the TargetP software package. Selected examples of the resulting protein classes were subsequently analyzed by transient transformation assays as well as by in organello protein transport experiments. It was found that most proteins with high prediction values for both organelles show dual targeting with both experimental approaches. Unexpectedly, however, dual targeting was even found among those proteins that are predicted to be localized solely in one of the two endosymbiotic organelles. In total, among the 16 candidate proteins analyzed, we identified 10 proteins with dual targeting properties. This unexpectedly high proportion suggests that such transport properties are much more abundant than anticipated.
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Affiliation(s)
- Bianca Baudisch
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Uwe Langner
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Ingo Garz
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Ralf Bernd Klösgen
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
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Tanz SK, Castleden I, Hooper CM, Small I, Millar AH. Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family. FRONTIERS IN PLANT SCIENCE 2014; 5:396. [PMID: 25161662 PMCID: PMC4130198 DOI: 10.3389/fpls.2014.00396] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/24/2014] [Indexed: 05/20/2023]
Abstract
Sub-functionalization during the expansion of gene families in eukaryotes has occurred in part through specific subcellular localization of different family members. To better understand this process in plants, compiled records of large-scale proteomic and fluorescent protein localization datasets can be explored and bioinformatic predictions for protein localization can be used to predict the gaps in experimental data. This process can be followed by targeted experiments to test predictions. The SUBA3 database is a free web-service at http://suba.plantenergy.uwa.edu.au that helps users to explore reported experimental data and predictions concerning proteins encoded by gene families and to define the experiments required to locate these homologous sets of proteins. Here we show how SUBA3 can be used to explore the subcellular location of the Deg protease family of ATP-independent serine endopeptidases (Deg1-Deg16). Combined data integration and new experiments refined location information for Deg1 and Deg9, confirmed Deg2, Deg5, and Deg8 in plastids and Deg 15 in peroxisomes and provide substantial experimental evidence for mitochondrial localized Deg proteases. Two of these, Deg3 and Deg10, additionally localized to the plastid, revealing novel dual-targeted Deg proteases in the plastid and the mitochondrion. SUBA3 is continually updated to ensure that researchers can use the latest published data when planning the experimental steps remaining to localize gene family functions.
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Affiliation(s)
- Sandra K. Tanz
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- *Correspondence: Sandra K. Tanz, The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia e-mail:
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Ian Small
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - A. Harvey Millar
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
- Centre for Comparative Analysis on Biomolecular Networks, The University of Western AustraliaPerth, WA, Australia
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Rigas S, Daras G, Tsitsekian D, Alatzas A, Hatzopoulos P. Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:145. [PMID: 24782883 PMCID: PMC3990055 DOI: 10.3389/fpls.2014.00145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/26/2014] [Indexed: 05/18/2023]
Abstract
Lon is the first identified ATP-dependent protease highly conserved across all kingdoms. Model plant species Arabidopsis thaliana has a small Lon gene family of four members. Although these genes share common structural features, they have distinct properties in terms of gene expression profile, subcellular targeting and substrate recognition motifs. This supports the notion that their functions under different environmental conditions are not necessarily redundant. This article intends to unravel the biological role of Lon proteases in energy metabolism and plant growth through an evolutionary perspective. Given that plants are sessile organisms exposed to diverse environmental conditions and plant organelles are semi-autonomous, it is tempting to suggest that Lon genes in Arabidopsis are paralogs. Adaptive evolution through repetitive gene duplication events of a single archaic gene led to Lon genes with complementing sets of subfunctions providing to the organism rapid adaptability for canonical development under different environmental conditions. Lon1 function is adequately characterized being involved in mitochondrial biogenesis, modulating carbon metabolism, oxidative phosphorylation and energy supply, all prerequisites for seed germination and seedling establishment. Lon is not a stand-alone proteolytic machine in plant organelles. Lon in association with other nuclear-encoded ATP-dependent proteases builds up an elegant nevertheless, tight interconnected circuit. This circuitry channels properly and accurately, proteostasis and protein quality control among the distinct subcellular compartments namely mitochondria, chloroplasts, and peroxisomes.
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Affiliation(s)
| | | | | | | | - Polydefkis Hatzopoulos
- *Correspondence: Polydefkis Hatzopoulos, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece e-mail:
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Grimaud F, Renaut J, Dumont E, Sergeant K, Lucau-Danila A, Blervacq AS, Sellier H, Bahrman N, Lejeune-Hénaut I, Delbreil B, Goulas E. Exploring chloroplastic changes related to chilling and freezing tolerance during cold acclimation of pea (Pisum sativum L.). J Proteomics 2013; 80:145-59. [PMID: 23318888 DOI: 10.1016/j.jprot.2012.12.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/22/2012] [Accepted: 12/29/2012] [Indexed: 01/10/2023]
Abstract
Pea (Pisum sativum L.) productivity is linked to its ability to cope with abiotic stresses such as low temperatures during fall and winter. In this study, we investigate the chloroplast-related changes occurring during pea cold acclimation, in order to further lead to genetic improvement of its field performance. Champagne and Térèse, two pea lines with different acclimation capabilities, were studied by physiological measurements, sub-cellular fractionation followed by relative protein quantification and two-dimensional DIGE. The chilling tolerance might be related to an increase in protein related to soluble sugar synthesis, antioxidant potential, regulation of mRNA transcription and translation through the chloroplast. Freezing tolerance, only observed in Champagne, seems to rely on a higher inherent photosynthetic potential at the beginning of the cold exposure, combined with an early ability to start metabolic processes aimed at maintaining the photosynthetic capacity, optimizing the stoichiometry of the photosystems and inducing dynamic changes in carbohydrate and protein synthesis and/or turnover.
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Affiliation(s)
- Florent Grimaud
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France; Centre de Recherche Public, Gabriel Lippmann, Department of Environment and Agrobiotechnologies (EVA), 4422, Belvaux, Luxembourg.
| | - Jenny Renaut
- Centre de Recherche Public, Gabriel Lippmann, Department of Environment and Agrobiotechnologies (EVA), 4422, Belvaux, Luxembourg.
| | - Estelle Dumont
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Kjell Sergeant
- Centre de Recherche Public, Gabriel Lippmann, Department of Environment and Agrobiotechnologies (EVA), 4422, Belvaux, Luxembourg.
| | - Anca Lucau-Danila
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Anne-Sophie Blervacq
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Hélène Sellier
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Nasser Bahrman
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Isabelle Lejeune-Hénaut
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Bruno Delbreil
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
| | - Estelle Goulas
- Université Lille 1/INRA, UMR 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, 59650 Villeneuve d'Ascq Cedex/Estrées-Mons, 80200 cedex, France.
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Havelund JF, Thelen JJ, Møller IM. Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells. FRONTIERS IN PLANT SCIENCE 2013; 4:51. [PMID: 23494127 PMCID: PMC3595712 DOI: 10.3389/fpls.2013.00051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/26/2013] [Indexed: 05/24/2023]
Abstract
Mitochondria fulfill some basic roles in all plant cells. They supply the cell with energy in the form of ATP and reducing equivalents [NAD(P)H] and they provide the cell with intermediates for a range of biosynthetic pathways. In addition to this, mitochondria contribute to a number of specialized functions depending on the tissue and cell type, as well as environmental conditions. We will here review the biochemistry and proteomics of mitochondria from non-green cells and organs, which differ from those of photosynthetic organs in a number of respects. We will briefly cover purification of mitochondria and general biochemical properties such as oxidative phosphorylation. We will then mention a few adaptive properties in response to water stress, seed maturation and germination, and the ability to function under hypoxic conditions. The discussion will mainly focus on Arabidopsis cell cultures, etiolated germinating rice seedlings and potato tubers as model plants. It will cover the general proteome as well as the posttranslational modification protein phosphorylation. To date 64 phosphorylated mitochondrial proteins with a total of 103 phosphorylation sites have been identified.
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Affiliation(s)
- Jesper F. Havelund
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-ColumbiaColumbia, MO, USA
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
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Stoll B, Stoll K, Steinhilber J, Jonietz C, Binder S. Mitochondrial transcript length polymorphisms are a widespread phenomenon in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2013; 81:221-233. [PMID: 23225154 DOI: 10.1007/s11103-012-9993-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/27/2012] [Indexed: 05/27/2023]
Abstract
Natural genetic variation affects development, physiology, biochemical properties as well as mitochondrial transcripts of the model species Arabidopsis thaliana (Arabidopsis). In a previous study, we identified mitochondrial transcript end polymorphisms in Arabidopsis accessions Columbia, C24 and Landsberg erecta. The polymorphic transcript species could either be assigned to differences in the mitochondrial DNA or to natural genetic variation in the nucleus. To analyze the distribution and to identify additional 5' end polymorphisms we now analyzed 19 mitochondrial transcription units in 26 different accessions. We found additional 5' end polymorphisms indicating that such transcript length differences are a widespread phenomenon in Arabidopsis. The new polymorphisms affect cox1, cox2, nad2 as well nad3-rps12 transcript species. While the cox2 polymorphism can be attributed to a recombination event in the mitochondrial DNA, the nad2 transcript polymorphism is linked to differences in the nuclear DNA. A complex pattern is found for nad3-rps12 mRNA whose 5' ends differ between several accessions. These new polymorphisms provide an important basis for a more detailed characterization of mitochondrial 5' end processing.
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MESH Headings
- 5' Untranslated Regions/genetics
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Cell Nucleus/genetics
- Cells, Cultured
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Genetic Variation
- Genotype
- Mitochondria/genetics
- Mitochondria/metabolism
- Polymorphism, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombination, Genetic
- Seedlings/genetics
- Seedlings/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. J Comput Aided Mol Des 2013; 27:91-103. [PMID: 23283513 DOI: 10.1007/s10822-012-9628-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/17/2012] [Indexed: 01/25/2023]
Abstract
The function of a protein is generally related to its subcellular localization. Therefore, knowing its subcellular localization is helpful in understanding its potential functions and roles in biological processes. This work develops a hybrid method for computationally predicting the subcellular localization of eukaryotic protein. The method is called EuLoc and incorporates the Hidden Markov Model (HMM) method, homology search approach and the support vector machines (SVM) method by fusing several new features into Chou's pseudo-amino acid composition. The proposed SVM module overcomes the shortcoming of the homology search approach in predicting the subcellular localization of a protein which only finds low-homologous or non-homologous sequences in a protein subcellular localization annotated database. The proposed HMM modules overcome the shortcoming of SVM in predicting subcellular localizations using few data on protein sequences. Several features of a protein sequence are considered, including the sequence-based features, the biological features derived from PROSITE, NLSdb and Pfam, the post-transcriptional modification features and others. The overall accuracy and location accuracy of EuLoc are 90.5 and 91.2 %, respectively, revealing a better predictive performance than obtained elsewhere. Although the amounts of data of the various subcellular location groups in benchmark dataset differ markedly, the accuracies of 12 subcellular localizations of EuLoc range from 82.5 to 100 %, indicating that this tool is much more balanced than other tools. EuLoc offers a high, balanced predictive power for each subcellular localization. EuLoc is now available on the web at http://euloc.mbc.nctu.edu.tw/.
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40
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Barsan C, Zouine M, Maza E, Bian W, Egea I, Rossignol M, Bouyssie D, Pichereaux C, Purgatto E, Bouzayen M, Latché A, Pech JC. Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components. PLANT PHYSIOLOGY 2012; 160:708-25. [PMID: 22908117 PMCID: PMC3461550 DOI: 10.1104/pp.112.203679] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/16/2012] [Indexed: 05/18/2023]
Abstract
A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.
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Affiliation(s)
| | | | | | | | - Isabel Egea
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Michel Rossignol
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - David Bouyssie
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Carole Pichereaux
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Eduardo Purgatto
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Mondher Bouzayen
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Alain Latché
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Jean-Claude Pech
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
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Misra N, Panda PK, Parida BK, Mishra BK. Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses. Evol Bioinform Online 2012; 8:545-64. [PMID: 23032611 PMCID: PMC3460774 DOI: 10.4137/ebo.s10159] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Optimizing microalgal biofuel production using metabolic engineering tools requires an in-depth understanding of the structure-function relationship of genes involved in lipid biosynthetic pathway. In the present study, genome-wide identification and characterization of 398 putative genes involved in lipid biosynthesis in Arabidopsis thaliana Chlamydomonas reinhardtii, Volvox carteri, Ostreococcus lucimarinus, Ostreococcus tauri and Cyanidioschyzon merolae was undertaken on the basis of their conserved motif/domain organization and phylogenetic profile. The results indicated that the core lipid metabolic pathways in all the species are carried out by a comparable number of orthologous proteins. Although the fundamental gene organizations were observed to be invariantly conserved between microalgae and Arabidopsis genome, with increased order of genome complexity there seems to be an association with more number of genes involved in triacylglycerol (TAG) biosynthesis and catabolism. Further, phylogenomic analysis of the genes provided insights into the molecular evolution of lipid biosynthetic pathway in microalgae and confirm the close evolutionary proximity between the Streptophyte and Chlorophyte lineages. Together, these studies will improve our understanding of the global lipid metabolic pathway and contribute to the engineering of regulatory networks of algal strains for higher accumulation of oil.
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Affiliation(s)
- Namrata Misra
- Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology (Formerly Regional Research Laboratory), Bhubaneswar, Odisha, India
| | - Prasanna Kumar Panda
- Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology (Formerly Regional Research Laboratory), Bhubaneswar, Odisha, India
| | - Bikram Kumar Parida
- Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology (Formerly Regional Research Laboratory), Bhubaneswar, Odisha, India
| | - Barada Kanta Mishra
- Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology (Formerly Regional Research Laboratory), Bhubaneswar, Odisha, India
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A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:253-9. [PMID: 22683762 DOI: 10.1016/j.bbamcr.2012.05.029] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/26/2012] [Accepted: 05/28/2012] [Indexed: 01/08/2023]
Abstract
Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Lee CP, Eubel H, Solheim C, Millar AH. Mitochondrial proteome heterogeneity between tissues from the vegetative and reproductive stages of Arabidopsis thaliana development. J Proteome Res 2012. [PMID: 22540835 DOI: 10.1021/pr3001157 [epub ahead of print]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Specialization of the mitochondrial proteome in Arabidopsis has the potential to underlie the roles of these organelles at different developmental time points and in specific organs; however, most research to date has been limited to studies of mitochondrial composition from a few vegetative tissue types. To provide further insight into the extent of mitochondrial heterogeneity in Arabidopsis, mitochondria isolated from six organ/cell types, leaf, root, cell culture, flower, bolt stem, and silique, were analyzed. Of the 286 protein spots on a 2-D gel of the mitochondrial proteome, the abundance of 237 spots was significantly varied between different samples. Identification of these spots revealed a nonredundant set of 83 proteins which were differentially expressed between organ/cell types, and the protein identification information can be analyzed in an integrated manner in an interactive fashion online. A number of mitochondrial protein spots were identified as being derived from the same genes in Arabidopsis but differed in their pI, indicating organ-specific variation in the post-translational modifications, or in their MW, suggesting differences in truncated mitochondrial products accumulating in different tissues. Comparisons of the proteomic data for the major isoforms with microarray analysis showed a positive correlation between mRNA and mitochondrial protein abundance and 60-90% concordance between changes in protein and transcript abundance. These analyses demonstrate that, while mitochondrial proteins are controlled transcriptionally by the nucleus, post-transcriptional regulation and/or post-translational modifications play a vital role in modulating the state or regulation of proteins in key biochemical pathways in plant mitochondria for specific functions. The integration of protein abundance and protein modification data with respiratory measurements, enzyme assays, and transcript data sets has allowed the identification of organ-enhanced differences in central carbon and amino acid metabolism pathways and provides ranked lists of mitochondrial proteins that are strongly transcriptionally regulated vs those whose abundance or activity is strongly influenced by a variety of post-transcriptional processes.
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Affiliation(s)
- Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia , 35 Stirling Highway, Crawley WA 6009, Australia
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Lee CP, Eubel H, Solheim C, Millar AH. Mitochondrial Proteome Heterogeneity between Tissues from the Vegetative and Reproductive Stages of Arabidopsis thaliana Development. J Proteome Res 2012; 11:3326-43. [DOI: 10.1021/pr3001157] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Holger Eubel
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Cory Solheim
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
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Schuhmann H, Adamska I. Deg proteases and their role in protein quality control and processing in different subcellular compartments of the plant cell. PHYSIOLOGIA PLANTARUM 2012; 145:224-34. [PMID: 22008015 DOI: 10.1111/j.1399-3054.2011.01533.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Degradation of periplasmic proteins (Deg)/high temperature requirement A (HtrA) proteases are ATP-independent serine endopeptidases found in almost every organism. Database searches revealed that 16 Deg paralogues are encoded by the genome of Arabidopsis thaliana, six of which were experimentally shown to be located in chloroplasts, one in peroxisomes, one in mitochondria and one in the nucleus. Two more Deg proteases are predicted to reside in chloroplasts, five in mitochondria (one of them with a dual chloroplastidial/mitochondrial localization) and the subcellular location of one protein is uncertain. This review summarizes the current knowledge on the role of Deg proteases in maintaining protein homeostasis and protein processing in various subcompartments of the plant cell. The chloroplast Deg proteases are the best examined so far, especially with respect to their role in the degradation of photodamaged photosynthetic proteins and in biogenesis of photosystem II (PSII). A combined action of thylakoid lumen and stroma Deg proteases in the primary cleavage of photodamaged D1 protein from PSII reaction centre is discussed on the basis of a recently resolved crystal structure of plant Deg1. The peroxisomal Deg protease is a processing enzyme responsible for the cleavage of N-terminal peroxisomal targeting signals (PTSs). A. thaliana mutants lacking this enzyme show reduced peroxisomal β-oxidation, indicating for the first time the impact of protein processing on peroxisomal functions in plants. Much less data is available for mitochondrial and nuclear Deg proteases. Based on the available expression data we hypothesize a role in general protein quality control and during acquired heat resistance.
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Affiliation(s)
- Holger Schuhmann
- Department of Plant Biology, University of Konstanz, D-78457 Konstanz, Germany
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Prihoda J, Tanaka A, de Paula WBM, Allen JF, Tirichine L, Bowler C. Chloroplast-mitochondria cross-talk in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1543-57. [PMID: 22268145 DOI: 10.1093/jxb/err441] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Diatoms are unicellular, mainly photosynthetic, eukaryotes living within elaborate silicified cell walls and believed to be responsible for around 40% of global primary productivity in the oceans. Their abundance in aquatic ecosystems is such that they have on different occasions been described as the insects, the weeds, or the cancer cells of the ocean. In contrast to higher plants and green algae which derive from a primary endosymbiosis, diatoms are now believed to originate from a serial secondary endosymbiosis involving both green and red algae and a heterotrophic exosymbiont host. As a consequence of their dynamic evolutionary history, they appear to have red algal-derived chloroplasts empowered largely by green algal proteins, working alongside mitochondria derived from the non-photosynthetic exosymbiont. This review will discuss the evidence for such an unusual assemblage of organelles in diatoms, and will present the evidence implying that it has enabled them with unorthodox metabolisms that may have contributed to their profound ecological success.
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Affiliation(s)
- Judit Prihoda
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, Paris, 46 rue d'Ulm, 75230 Paris Cedex 05, France
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Waller JC, Ellens KW, Alvarez S, Loizeau K, Ravanel S, Hanson AD. Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron-sulphur cluster metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:403-11. [PMID: 21984653 PMCID: PMC3245475 DOI: 10.1093/jxb/err286] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/04/2011] [Accepted: 08/12/2011] [Indexed: 05/07/2023]
Abstract
COG0354 proteins have been implicated in synthesis or repair of iron/sulfur (Fe/S) clusters in all domains of life, and those of bacteria, animals, and protists have been shown to require a tetrahydrofolate to function. Two COG0354 proteins were identified in Arabidopsis and many other plants, one (At4g12130) related to those of α-proteobacteria and predicted to be mitochondrial, the other (At1g60990) related to those of cyanobacteria and predicted to be plastidial. Grasses and poplar appear to lack the latter. The predicted subcellular locations of the Arabidopsis proteins were validated by in vitro import assays with purified pea organelles and by targeting assays in Arabidopsis and tobacco protoplasts using green fluorescent protein fusions. The At4g12130 protein was shown to be expressed mainly in flowers, siliques, and seeds, whereas the At1g60990 protein was expressed mainly in young leaves. The folate dependence of both Arabidopsis proteins was established by functional complementation of an Escherichia coli COG0354 (ygfZ) deletant; both plant genes restored in vivo activity of the Fe/S enzyme MiaB but restoration was abrogated when folates were eliminated by deleting folP. Insertional inactivation of At4g12130 was embryo lethal; this phenotype was reversed by genetic complementation of the mutant. These data establish that COG0354 proteins have a folate-dependent function in mitochondria and plastids, and that the mitochondrial protein is essential. That plants retain mitochondrial and plastidial COG0354 proteins with distinct phylogenetic origins emphasizes how deeply the extant Fe/S cluster assembly machinery still reflects the ancient endosymbioses that gave rise to plants.
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Affiliation(s)
- Jeffrey C. Waller
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Kenneth W. Ellens
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Sophie Alvarez
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Karen Loizeau
- Laboratoire de Physiologie Cellulaire Végétale, CNRS/CEA/INRA/Université Joseph Fourier, CEA-Grenoble, F-38054 Grenoble cedex 9, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire Végétale, CNRS/CEA/INRA/Université Joseph Fourier, CEA-Grenoble, F-38054 Grenoble cedex 9, France
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Lloyd AH, Rousseau-Gueutin M, Timmis JN, Sheppard AE, Ayliffe MA. Promiscuous Organellar DNA. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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The mitochondrial proteome of the model legume Medicago truncatula. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1658-68. [DOI: 10.1016/j.bbapap.2011.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 08/08/2011] [Accepted: 08/15/2011] [Indexed: 11/23/2022]
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50
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Zeng Y, Pan Z, Ding Y, Zhu A, Cao H, Xu Q, Deng X. A proteomic analysis of the chromoplasts isolated from sweet orange fruits [Citrus sinensis (L.) Osbeck]. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5297-309. [PMID: 21841170 PMCID: PMC3223033 DOI: 10.1093/jxb/err140] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 05/18/2023]
Abstract
Here, a comprehensive proteomic analysis of the chromoplasts purified from sweet orange using Nycodenz density gradient centrifugation is reported. A GeLC-MS/MS shotgun approach was used to identify the proteins of pooled chromoplast samples. A total of 493 proteins were identified from purified chromoplasts, of which 418 are putative plastid proteins based on in silico sequence homology and functional analyses. Based on the predicted functions of these identified plastid proteins, a large proportion (∼60%) of the chromoplast proteome of sweet orange is constituted by proteins involved in carbohydrate metabolism, amino acid/protein synthesis, and secondary metabolism. Of note, HDS (hydroxymethylbutenyl 4-diphosphate synthase), PAP (plastid-lipid-associated protein), and psHSPs (plastid small heat shock proteins) involved in the synthesis or storage of carotenoid and stress response are among the most abundant proteins identified. A comparison of chromoplast proteomes between sweet orange and tomato suggested a high level of conservation in a broad range of metabolic pathways. However, the citrus chromoplast was characterized by more extensive carotenoid synthesis, extensive amino acid synthesis without nitrogen assimilation, and evidence for lipid metabolism concerning jasmonic acid synthesis. In conclusion, this study provides an insight into the major metabolic pathways as well as some unique characteristics of the sweet orange chromoplasts at the whole proteome level.
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Affiliation(s)
| | | | | | | | | | | | - Xiuxin Deng
- To whom correspondence should be addressed. E-mail:
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