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Tang Q, Xu D, Lenzen B, Brachmann A, Yapa MM, Doroodian P, Schmitz-Linneweber C, Masuda T, Hua Z, Leister D, Kleine T. GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation. PLANT COMMUNICATIONS 2024:101069. [PMID: 39169625 DOI: 10.1016/j.xplc.2024.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 08/23/2024]
Abstract
Plastid biogenesis and the coordination of plastid and nuclear genome expression through anterograde and retrograde signaling are essential for plant development. GENOMES UNCOUPLED1 (GUN1) plays a central role in retrograde signaling during early plant development. The putative function of GUN1 has been extensively studied, but its molecular function remains controversial. Here, we evaluate published transcriptome data and generate our own data from gun1 mutants grown under signaling-relevant conditions to show that editing and splicing are not relevant for GUN1-dependent retrograde signaling. Our study of the plastid (post)transcriptome of gun1 seedlings with white and pale cotyledons demonstrates that GUN1 deficiency significantly alters the entire plastid transcriptome. By combining this result with a pentatricopeptide repeat code-based prediction and experimental validation by RNA immunoprecipitation experiments, we identified several putative targets of GUN1, including tRNAs and RNAs derived from ycf1.2, rpoC1, and rpoC2 and the ndhH-ndhA-ndhI-ndhG-ndhE-psaC-ndhD gene cluster. The absence of plastid rRNAs and the significant reduction of almost all plastid transcripts in white gun1 mutants account for the cotyledon phenotype. Our study provides evidence for RNA binding and maturation as the long-sought molecular function of GUN1 and resolves long-standing controversies. We anticipate that our findings will serve as a basis for subsequent studies on mechanisms of plastid gene expression and will help to elucidate the function of GUN1 in retrograde signaling.
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Affiliation(s)
- Qian Tang
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
| | - Duorong Xu
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
| | - Benjamin Lenzen
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Andreas Brachmann
- Biocenter of the LMU Munich, Genetics Section, Grosshaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Madhura M Yapa
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Paymon Doroodian
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | | | - Tatsuru Masuda
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku 153-8902, Tokyo, Japan
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany.
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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3
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Richter AS, Nägele T, Grimm B, Kaufmann K, Schroda M, Leister D, Kleine T. Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. PLANT COMMUNICATIONS 2023; 4:100511. [PMID: 36575799 PMCID: PMC9860301 DOI: 10.1016/j.xplc.2022.100511] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling, allowing nuclear gene expression to be adjusted appropriately. Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated "biogenic" and "operational" controls, respectively. A prominent example of the investigation of biogenic signaling is the screen for gun (genomes uncoupled) mutants. Although the first five gun mutants were identified 30 years ago, the functions of GUN proteins in retrograde signaling remain controversial, and that of GUN1 is hotly disputed. Here, we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants. Moreover, considering heme as a candidate in retrograde signaling, we revisit the spatial organization of heme biosynthesis and export from plastids. Although this review focuses on GUN pathways, we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants. Here, stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response, which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis. We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1. Finally, a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided, and we discuss future directions of dissection of organelle-nucleus communication.
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Affiliation(s)
- Andreas S Richter
- Physiology of Plant Metabolism, Institute for Biosciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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4
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Mackenzie SA, Mullineaux PM. Plant environmental sensing relies on specialized plastids. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7155-7164. [PMID: 35994779 DOI: 10.1093/jxb/erac334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
In plants, plastids are thought to interconvert to various forms that are specialized for photosynthesis, starch and oil storage, and diverse pigment accumulation. Post-endosymbiotic evolution has led to adaptations and specializations within plastid populations that align organellar functions with different cellular properties in primary and secondary metabolism, plant growth, organ development, and environmental sensing. Here, we review the plastid biology literature in light of recent reports supporting a class of 'sensory plastids' that are specialized for stress sensing and signaling. Abundant literature indicates that epidermal and vascular parenchyma plastids display shared features of dynamic morphology, proteome composition, and plastid-nuclear interaction that facilitate environmental sensing and signaling. These findings have the potential to reshape our understanding of plastid functional diversification.
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Affiliation(s)
- Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip M Mullineaux
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
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Postel Z, Poux C, Gallina S, Varré JS, Godé C, Schmitt E, Meyer E, Van Rossum F, Touzet P. Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities. Mol Phylogenet Evol 2022; 169:107436. [DOI: 10.1016/j.ympev.2022.107436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/26/2022]
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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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7
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Christian RW, Hewitt SL, Nelson G, Roalson EH, Dhingra A. Plastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 2020; 8:e9772. [PMID: 32913678 PMCID: PMC7456531 DOI: 10.7717/peerj.9772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
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Affiliation(s)
- Ryan W. Christian
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Seanna L. Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Eric H. Roalson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- Department of Horticulture, Washington State University, Pullman, WA, USA
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