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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. THE PLANT CELL 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University,
Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of
Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of
Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and
Technology, Socorro, NM, USA
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2
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Kan S, Liao X, Lan L, Kong J, Wang J, Nie L, Zou J, An H, Wu Z. Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U. Mol Biol Evol 2024; 41:msae043. [PMID: 38391484 PMCID: PMC10919925 DOI: 10.1093/molbev/msae043] [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: 10/24/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.
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Affiliation(s)
- Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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3
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Lian Q, Li S, Kan S, Liao X, Huang S, Sloan DB, Wu Z. Association Analysis Provides Insights into Plant Mitonuclear Interactions. Mol Biol Evol 2024; 41:msae028. [PMID: 38324417 PMCID: PMC10875325 DOI: 10.1093/molbev/msae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear and organelle genetic polymorphisms that are involved in these interactions within a species remains relatively rare. The recent surge in whole genome sequencing has provided us an opportunity to explore cytonuclear interaction from a population perspective. In this study, we analyzed a total of 3,439 genomes from 7 species to identify signals of cytonuclear interactions by association (linkage disequilibrium) analysis of variants in both the mitochondrial and nuclear genomes across flowering plants. We also investigated examples of nuclear loci identified based on these association signals using subcellular localization assays, gene editing, and transcriptome sequencing. Our study provides a novel perspective on the investigation of cytonuclear coevolution, thereby enriching our understanding of plant fitness and offspring sterility.
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Affiliation(s)
- Qun Lian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuai Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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4
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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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5
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Gao LL, Hong ZH, Wang Y, Wu GZ. Chloroplast proteostasis: A story of birth, life, and death. PLANT COMMUNICATIONS 2023; 4:100424. [PMID: 35964157 PMCID: PMC9860172 DOI: 10.1016/j.xplc.2022.100424] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/02/2023]
Abstract
Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.
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Affiliation(s)
- Lin-Lin Gao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zheng-Hui Hong
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yinsong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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6
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Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proc Natl Acad Sci U S A 2022; 119:e2204187119. [PMID: 35858449 PMCID: PMC9335225 DOI: 10.1073/pnas.2204187119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
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7
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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8
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Sharbrough J, Conover JL, Fernandes Gyorfy M, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms. Mol Biol Evol 2022; 39:msac074. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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9
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Woodson JD. Control of chloroplast degradation and cell death in response to stress. Trends Biochem Sci 2022; 47:851-864. [DOI: 10.1016/j.tibs.2022.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/16/2022]
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10
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Alamdari K, Fisher KE, Tano DW, Rai S, Palos K, Nelson ADL, Woodson JD. Chloroplast quality control pathways are dependent on plastid DNA synthesis and nucleotides provided by cytidine triphosphate synthase two. THE NEW PHYTOLOGIST 2021; 231:1431-1448. [PMID: 33993494 DOI: 10.1111/nph.17467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Reactive oxygen species (ROS) produced in chloroplasts cause oxidative damage, but also signal to initiate chloroplast quality control pathways, cell death, and gene expression. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant produces the ROS singlet oxygen in chloroplasts that activates such signaling pathways, but the mechanisms are largely unknown. Here we characterize one fc2 suppressor mutation and map it to CYTIDINE TRIPHOSPHATE SYNTHASE TWO (CTPS2), which encodes one of five enzymes in Arabidopsis necessary for de novo cytoplasmic CTP (and dCTP) synthesis. The ctps2 mutation reduces chloroplast transcripts and DNA content without similarly affecting mitochondria. Chloroplast nucleic acid content and singlet oxygen signaling are restored by exogenous feeding of the dCTP precursor deoxycytidine, suggesting ctps2 blocks signaling by limiting nucleotides for chloroplast genome maintenance. An investigation of CTPS orthologs in Brassicaceae showed CTPS2 is a member of an ancient lineage distinct from CTPS3. Complementation studies confirmed this analysis; CTPS3 was unable to compensate for CTPS2 function in providing nucleotides for chloroplast DNA and signaling. Our studies link cytoplasmic nucleotide metabolism with chloroplast quality control pathways. Such a connection is achieved by a conserved clade of CTPS enzymes that provide nucleotides for chloroplast function, thereby allowing stress signaling to occur.
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Affiliation(s)
- Kamran Alamdari
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Karen E Fisher
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - David W Tano
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Snigdha Rai
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Kyle Palos
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Jesse D Woodson
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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11
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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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12
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Razi K, Muneer S. Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops. Crit Rev Biotechnol 2021; 41:669-691. [PMID: 33525946 DOI: 10.1080/07388551.2021.1874280] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Drought stress is one of the most adverse abiotic stresses that hinder plants' growth and productivity, threatening sustainable crop production. It impairs normal growth, disturbs water relations and reduces water-use efficiency in plants. However, plants have evolved many physiological and biochemical responses at the cellular and organism levels, in order to cope with drought stress. Photosynthesis, which is considered one of the most crucial biological processes for survival of plants, is greatly affected by drought stress. A gradual decrease in CO2 assimilation rates, reduced leaf size, stem extension and root proliferation under drought stress, disturbs plant water relations, reducing water-use efficiency, disrupts photosynthetic pigments and reduces the gas exchange affecting the plants adversely. In such conditions, the chloroplast, organelle responsible for photosynthesis, is found to counteract the ill effects of drought stress by its critical involvement as a sensor of changes occurring in the environment, as the first process that drought stress affects is photosynthesis. Beside photosynthesis, chloroplasts carry out primary metabolic functions such as the biosynthesis of starch, amino acids, lipids, and tetrapyroles, and play a central role in the assimilation of nitrogen and sulfur. Because the chloroplasts are central organelles where the photosynthetic reactions take place, modifications in their physiology and protein pools are expected in response to the drought stress-induced variations in leaf gas exchanges and the accumulation of ROS. Higher expression levels of various transcription factors and other proteins including heat shock-related protein, LEA proteins seem to be regulating the heat tolerance mechanisms. However, several aspects of plastid alterations, following a water deficit environment are still poorly characterized. Since plants adapt to various stress tolerance mechanisms to respond to drought stress, understanding mechanisms of drought stress tolerance in plants will lead toward the development of drought tolerance in crop plants. This review throws light on major droughts stress-induced molecular/physiological mechanisms in response to severe and prolonged drought stress and addresses the molecular response of chloroplasts in common vegetable crops. It further highlights research gaps, identifying unexplored domains and suggesting recommendations for future investigations.
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Affiliation(s)
- Kaukab Razi
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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13
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Li C, Wang X, Xiao Y, Sun X, Wang J, Yang X, Sun Y, Sha Y, Lv R, Yu Y, Ding B, Zhang Z, Li N, Wang T, Wendel JF, Liu B, Gong L. Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum. Mol Biol Evol 2020; 37:3409-3422. [PMID: 32602899 PMCID: PMC7743682 DOI: 10.1093/molbev/msaa158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor; and 2) incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes. Here, we describe coevolution of nuclear rbcS genes encoding the small subunits of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) and nuclear genes encoding plastid translocons, which mediate recognition and translocation of nuclear-encoded proteins into plastids, in allopolyploid wheat species. We demonstrate that intergenomic paternal-to-maternal gene conversion specifically occurred in the genic region of the homoeologous rbcS3 gene from the D-genome progenitor of wheat (abbreviated as rbcS3D) such that it encodes a maternal-like or B-subgenome-like SSU3D transit peptide in allohexaploid wheat but not in allotetraploid wheat. Divergent and limited interaction between SSU3D and the D-subgenomic TOC90D translocon subunit is implicated to underpin SSU3D targeting into the chloroplast of hexaploid wheat. This implicates early selection favoring individuals harboring optimal maternal-like organellar SSU3D targeting in hexaploid wheat. These data represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins.
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Affiliation(s)
- Changping Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yaxian Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xuhan Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xuan Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yuchen Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yanan Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Baoxu Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Alamdari K, Fisher KE, Sinson AB, Chory J, Woodson JD. Roles for the chloroplast-localized pentatricopeptide repeat protein 30 and the 'mitochondrial' transcription termination factor 9 in chloroplast quality control. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:735-751. [PMID: 32779277 DOI: 10.1111/tpj.14963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/20/2020] [Indexed: 05/11/2023]
Abstract
Chloroplasts constantly experience photo-oxidative stress while performing photosynthesis. This is particularly true under abiotic stresses that lead to the accumulation of reactive oxygen species (ROS) which oxidize DNA, proteins and lipids. Reactive oxygen species can also act as signals to induce acclimation through chloroplast degradation, cell death and nuclear gene expression. To better understand the mechanisms behind ROS signaling from chloroplasts, we have used the Arabidopsis thaliana mutant plastid ferrochelatase two (fc2) that conditionally accumulates the ROS singlet oxygen (1 O2 ) leading to chloroplast degradation and eventually cell death. Here we have mapped mutations that suppress chloroplast degradation in the fc2 mutant and demonstrate that they affect two independent loci (PPR30 and mTERF9) encoding chloroplast proteins predicted to be involved in post-transcriptional gene expression. These mutants exhibited broadly reduced chloroplast gene expression, impaired chloroplast development and reduced chloroplast stress signaling. Levels of 1 O2 , however, could be uncoupled from chloroplast degradation, suggesting that PPR30 and mTERF9 are involved in ROS signaling pathways. In the wild-type background, ppr30 and mTERF9 mutants were also observed to be less susceptible to cell death induced by excess light stress. While broad inhibition of plastid transcription with rifampicin was also able to suppress cell death in fc2 mutants, specific reductions in plastid gene expression using other mutations was not always sufficient. Together these results suggest that plastid gene expression, or the expression of specific plastid genes by PPR30 and mTERF0, is a necessary prerequisite for chloroplasts to activate the 1 O2 signaling pathways to induce chloroplast quality control pathways and/or cell death.
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Affiliation(s)
- Kamran Alamdari
- The School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, Tucson, AZ, 85721, USA
| | - Karen E Fisher
- The School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, Tucson, AZ, 85721, USA
| | - Andrew B Sinson
- The Division of Biological Sciences, The University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Plant Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Jesse D Woodson
- The School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, Tucson, AZ, 85721, USA
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15
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Guan X, Okazaki Y, Zhang R, Saito K, Nikolau BJ. Dual-Localized Enzymatic Components Constitute the Fatty Acid Synthase Systems in Mitochondria and Plastids. PLANT PHYSIOLOGY 2020; 183:517-529. [PMID: 32245791 PMCID: PMC7271793 DOI: 10.1104/pp.19.01564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 05/07/2023]
Abstract
Plant fatty acid biosynthesis occurs in both plastids and mitochondria. Here, we report the identification and characterization of Arabidopsis (Arabidopsis thaliana) genes encoding three enzymes shared between the mitochondria- and plastid-localized type II fatty acid synthase systems (mtFAS and ptFAS, respectively). Two of these enzymes, β-ketoacyl-acyl carrier protein (ACP) reductase and enoyl-ACP reductase, catalyze two of the reactions that constitute the core four-reaction cycle of the FAS system, which iteratively elongates the acyl chain by two carbon atoms per cycle. The third enzyme, malonyl-coenzyme A:ACP transacylase, catalyzes the reaction that loads the mtFAS system with substrate by malonylating the phosphopantetheinyl cofactor of ACP. GFP fusion experiments revealed that the these enzymes localize to both chloroplasts and mitochondria. This localization was validated by characterization of mutant alleles, which were rescued by transgenes expressing enzyme variants that were retargeted only to plastids or only to mitochondria. The singular retargeting of these proteins to plastids rescued the embryo lethality associated with disruption of the essential ptFAS system, but these rescued plants displayed phenotypes typical of the lack of mtFAS function, including reduced lipoylation of the H subunit of the glycine decarboxylase complex, hyperaccumulation of glycine, and reduced growth. However, these latter traits were reversible in an elevated-CO2 atmosphere, which suppresses mtFAS-associated photorespiration-dependent chemotypes. Sharing enzymatic components between mtFAS and ptFAS systems constrains the evolution of these nonredundant fatty acid biosynthetic machineries.
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Affiliation(s)
- Xin Guan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
| | - Yozo Okazaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Rwisdom Zhang
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Department of Chemical Engineering, University of Southern California, Los Angeles, California 90007
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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16
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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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17
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Cai Z, Jia P, Zhang J, Gan P, Shao Q, Jin G, Wang L, Jin J, Yang J, Luo J. Genetic analysis and fine mapping of a qualitative trait locus wpb1 for albino panicle branches in rice. PLoS One 2019; 14:e0223228. [PMID: 31557269 PMCID: PMC6763196 DOI: 10.1371/journal.pone.0223228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/15/2019] [Indexed: 12/30/2022] Open
Abstract
Chloroplast plays an important role in the plant life cycle. However, the details of its development remain elusive in rice. In this study, we report the fine-mapping of a novel rice gene wpb1 (white panicle branch 1), which affects chloroplast biogenesis, from a tropical japonica variety that results in an albino panicle branches at and after the heading stage. The wpb1 variety was crossed with Nipponbare to generate the F2 and BC1F2 populations. Green and white panicle branch phenotypes with a 3:1 segregation ratio was observed in the F2 population. Bulked segregant analysis (BSA) based on whole genome resequencing was conducted to determine the wpb1 locus. A candidate interval spanning from 11.35 to 23.79M (physical position) on chromosome 1 was identified. The results of BSA analysis were verified by a 40K rice SNP-array using the BC1F2 population. A large-scale F2 population was used to pinpoint wpb1, and the locus was further narrowed down to a 95-kb interval. Furthermore, our results showed that the expression levels of the majority of the genes involved in Chl biosynthesis, photosynthesis and chloroplast development were remarkably affected in wpb1 variety and in F2 plants with a white panicle branch phenotype. In line with the results mentioned above, anatomical structural examination and chlorophyll (Chl) content measurement suggested that wpb1 might play an important role in the regulation of chloroplast development. Further cloning and functional characterization of the wpb1 gene will shed light on the molecular mechanism underlying chloroplast development in rice.
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Affiliation(s)
- Zhongquan Cai
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Institute for New Rural Development, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Peilong Jia
- Institute for New Rural Development, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Jiaqiang Zhang
- Research and Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ping Gan
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Qi Shao
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Gang Jin
- Guangxi Subtropical Crops Research Institute, Nanning, China
| | - Liping Wang
- Guangxi Subtropical Crops Research Institute, Nanning, China
| | - Jian Jin
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- * E-mail: (JL); (JY); (JJ)
| | - Jiangyi Yang
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- * E-mail: (JL); (JY); (JJ)
| | - Jijing Luo
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- * E-mail: (JL); (JY); (JJ)
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18
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Füssy Z, Faitová T, Oborník M. Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol Evol 2019; 11:1765-1779. [PMID: 31192348 PMCID: PMC6668581 DOI: 10.1093/gbe/evz123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
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Affiliation(s)
- Zoltán Füssy
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Tereza Faitová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Engineering and Natural Sciences, Department of Computer Science, Johannes Kepler University, Linz, Austria
| | - Miroslav Oborník
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
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19
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Li C, Sun X, Conover JL, Zhang Z, Wang J, Wang X, Deng X, Wang H, Liu B, Wendel JF, Gong L. Cytonuclear Coevolution following Homoploid Hybrid Speciation in Aegilops tauschii. Mol Biol Evol 2019; 36:341-349. [PMID: 30445640 PMCID: PMC6367959 DOI: 10.1093/molbev/msy215] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The diploid D-genome lineage of the Triticum/Aegilops complex has an evolutionary history involving genomic contributions from ancient A- and B/S-genome species. We explored here the possible cytonuclear evolutionary responses to this history of hybridization. Phylogenetic analysis of chloroplast DNAs indicates that the D-genome lineage has a maternal origin of the A-genome or some other closely allied lineage. Analyses of the nuclear genome in the D-genome species Aegilops tauschii indicate that accompanying and/or following this ancient hybridization, there has been biased maintenance of maternal A-genome ancestry in nuclear genes encoding cytonuclear enzyme complexes (CECs). Our study provides insights into mechanisms of cytonuclear coevolution accompanying the evolution and eventual stabilization of homoploid hybrid species. We suggest that this coevolutionary process includes likely rapid fixation of A-genome CEC orthologs as well as biased retention of A-genome nucleotides in CEC homologs following population level recombination during the initial generations.
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Affiliation(s)
- Changping Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xuhan Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xin Deng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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20
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Sharma M, Kretschmer C, Lampe C, Stuttmann J, Klösgen RB. Targeting specificity of nuclear-encoded organelle proteins with a self-assembling split-fluorescent protein toolkit. J Cell Sci 2019; 132:jcs230839. [PMID: 31085714 DOI: 10.1242/jcs.230839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022] Open
Abstract
A large number of nuclear-encoded proteins are targeted to the organelles of endosymbiotic origin, namely mitochondria and plastids. To determine the targeting specificity of these proteins, fluorescent protein tagging is a popular approach. However, ectopic expression of fluorescent protein fusions commonly results in considerable background signals and often suffers from the large size and robust folding of the reporter protein, which may perturb membrane transport. Among the alternative approaches that have been developed in recent years, the self-assembling split-fluorescent protein (sasplit-FP) technology appears particularly promising to analyze protein targeting specificity in vivo Here, we improved the sensitivity of this technology and systematically evaluated its utilization to determine protein targeting to plastids and mitochondria. Furthermore, to facilitate high-throughput screening of candidate proteins we developed a Golden Gate-based vector toolkit (PlaMinGo). As a result of these improvements, dual targeting could be detected for a number of proteins that had earlier been characterized as being targeted to a single organelle only. These results were independently confirmed with a plant phenotype complementation approach based on the immutans mutant.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Mayank Sharma
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Carola Kretschmer
- Institute of Biology-Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Christina Lampe
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Johannes Stuttmann
- Institute of Biology-Genetics, 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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21
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de Luna-Valdez LA, Villaseñor-Salmerón CI, Cordoba E, Vera-Estrella R, León-Mejía P, Guevara-García AA. Functional analysis of the Chloroplast GrpE (CGE) proteins from Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:293-306. [PMID: 30927692 DOI: 10.1016/j.plaphy.2019.03.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/26/2019] [Accepted: 03/17/2019] [Indexed: 05/20/2023]
Abstract
The function of proteins depends on specific partners that regulate protein folding, degradation and protein-protein interactions, such partners are the chaperones and cochaperones. In chloroplasts, proteins belonging to several families of chaperones have been identified: chaperonins (Cpn60s), Hsp90s (Hsp90-5/Hsp90C), Hsp100s (Hsp93/ClpC) and Hsp70s (cpHsc70s). Several lines of evidence have demonstrated that cpHsc70 chaperones are involved in molecular processes like protein import, protein folding and oligomer formation that impact important physiological aspects in plants such as thermotolerance and thylakoid biogenesis. Despite the vast amount of data existing around the function of cpHcp70s chaperones, very little attention has been paid to the roles of DnaJ and GrpE cochaperones in the chloroplast. In this study, we performed a phylogenetic analysis of the chloroplastic GrpE (CGE) proteins from 71 species. Based on their phylogenetic relationships and on a motif enrichment analysis, we propose a classification system for land plants' CGEs, which include two independent groups with specific primary structure traits. Furthermore, using in vivo assays we determined that the two CGEs from A. thaliana (AtCGEs) complement the mutant phenotype displayed by a knockout E. coli strain defective in the bacterial grpE gene. Moreover, we determined in planta that the two AtCGEs are bona fide chloroplastic proteins, which form the essential homodimers needed to establish direct physical interactions with the cpHsc70-1 chaperone. Finally, we found evidence suggesting that AtCGE1 is involved in specific physiological phenomena in A. thaliana, such as the chloroplastic response to heat stress, and the correct oligomerization of the photosynthesis-related LHCII complex.
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Affiliation(s)
- L A de Luna-Valdez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
| | - C I Villaseñor-Salmerón
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
| | - E Cordoba
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
| | - R Vera-Estrella
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
| | - P León-Mejía
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
| | - A A Guevara-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, CP 62210, Mexico.
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22
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Li H, Ji G, Wang Y, Qian Q, Xu J, Sodmergen, Liu G, Zhao X, Chen M, Zhai W, Li D, Zhu L. WHITE PANICLE3, a Novel Nucleus-Encoded Mitochondrial Protein, Is Essential for Proper Development and Maintenance of Chloroplasts and Mitochondria in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:762. [PMID: 29928286 PMCID: PMC5997807 DOI: 10.3389/fpls.2018.00762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/17/2018] [Indexed: 09/11/2023]
Abstract
Mitochondria and chloroplasts are interacting organelles that play important roles in plant development. In addition to a small number proteins encoded by their own genomes, the majority of mitochondrial and chloroplast proteins are encoded in the cell nucleus and imported into the organelle. As a consequence, coordination between mitochondria, chloroplasts, and the nucleus is of crucial importance to plant cells. Variegated mutants are chloroplast-defective mutants and are considered to be ideal models for studying the intercommunication between these organelles. Here, we report the isolation of WHITE PANICLE3 (WP3), a nuclear gene involved in variegation, from a naturally occurring white panicle rice mutant. Disrupted expression of WP3 in the mutant leads to severe developmental defects in both chloroplasts and mitochondria, and consequently causes the appearance of white-striped leaves and white panicles in the mutant plants. Further investigation showed that WP3 encodes a protein most likely targeted to mitochondria and is specifically expressed in rice panicles. Interestingly, we demonstrate that the recessive white-panicle phenotype in the wp3 mutant is inherited in a typical Mendelian manner, while the white-striped leaf phenotype in wp3 is maternally inherited. Our data collectively suggest that the nucleus-encoded mitochondrial protein, WP3, plays an essential role in the regulation of chloroplast development in rice panicles by maintaining functional mitochondria. Therefore, the wp3 mutant is an excellent model in which to explore the communication between the nucleus, mitochondria, and chloroplasts in plant cells.
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Affiliation(s)
- Hongchang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guobiao Ji
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yun Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qian Qian
- China National Rice Research Institute, Hangzhou, China
| | - Jichen Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Sodmergen
- School of Life Sciences, Peking University, Beijing, China
| | - Guozhen Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, China
| | - Xianfeng Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenxue Zhai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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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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25
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Aroca A, Benito JM, Gotor C, Romero LC. Persulfidation proteome reveals the regulation of protein function by hydrogen sulfide in diverse biological processes in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4915-4927. [PMID: 28992305 PMCID: PMC5853657 DOI: 10.1093/jxb/erx294] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/28/2017] [Indexed: 05/20/2023]
Abstract
Hydrogen sulfide-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the post-translational modification of cysteine residues to form a persulfidated thiol motif, a process called protein persulfidation. We have developed a comparative and quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in wild-type Arabidopsis and L-CYSTEINE DESULFHYDRASE 1 mutant leaves using the tag-switch method. The 2015 identified persulfidated proteins were isolated from plants grown under controlled conditions, and therefore, at least 5% of the entire Arabidopsis proteome may undergo persulfidation under baseline conditions. Bioinformatic analysis revealed that persulfidated cysteines participate in a wide range of biological functions, regulating important processes such as carbon metabolism, plant responses to abiotic and biotic stresses, plant growth and development, and RNA translation. Quantitative analysis in both genetic backgrounds reveals that protein persulfidation is mainly involved in primary metabolic pathways such as the tricarboxylic acid cycle, glycolysis, and the Calvin cycle, suggesting that this protein modification is a new regulatory component in these pathways.
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Affiliation(s)
| | - Juan M Benito
- Instituto de Investigaciones Química, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Avenida Américo Vespucio, Sevilla, Spain
| | | | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis
- Correspondence:
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Fristedt R. Chloroplast function revealed through analysis of GreenCut2 genes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2111-2120. [PMID: 28369575 DOI: 10.1093/jxb/erx082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chloroplasts are the green plastids responsible for light-powered photosynthetic reactions and carbon assimilation in the plant cell. Our knowledge of chloroplast functions is constantly increasing and we now know this plastid is predicted to house around 3000 proteins. However, even with generous estimates, we do not know the function of more than 10-15% of these proteins. The next frontier in chloroplast research is to identify and characterize the function of the whole chloroplast proteome, a challenging task due to the inherent complexity a proteome possesses. A logical starting point is to identify and study proteins that have been determined experimentally to be localized in the chloroplast, conserved only among the photosynthetic lineage. These are the proteins with the most probable and important roles in chloroplast function. This review gives an introduction to the GreenCut2, a collection of proteins present only in photosynthetic organisms. By using recent large scale proteomics data, this cut was narrowed to include only those proteins experimentally verified to be localized in the chloroplast, and more specifically to the photosynthetic thylakoid membrane. By using highly informative bioinformatic approaches, the theoretical functional prediction for several of these uncharacterized GreenCut2 proteins is discussed.
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Affiliation(s)
- Rikard Fristedt
- Biophysics of Photosynthesis, Faculty of Sciences, VU University Amsterdam,Amsterdam,the Netherlands
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27
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Mueller SJ, Hoernstein SNW, Reski R. Approaches to Characterize Organelle, Compartment, or Structure Purity. Methods Mol Biol 2017; 1511:13-28. [PMID: 27730599 DOI: 10.1007/978-1-4939-6533-5_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The function of subcellular structures is defined by their specific sets of proteins, making subcellular protein localization one of the most important topics in organelle research. To date, many organelle proteomics workflows involve the (partial) purification of the desired subcellular structure and the subsequent analysis of the proteome using tandem mass spectrometry (MS/MS). This chapter gives an overview of the methods that have been used to assay the purity and enrichment of subcellular structures, with an emphasis on quantitative proteomics using differently enriched subcellular fractions. We introduce large-scale-based criteria for assignment of proteins to subcellular structures and describe in detail the use of 15N metabolic labeling in moss to characterize plastid and mitochondrial proteomes.
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Affiliation(s)
- Stefanie J Mueller
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
- FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany.
- TIP Trinational Institute for Plant Research, University of Freiburg, Freiburg, Germany.
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28
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Köhler D, Helm S, Agne B, Baginsky S. Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. PLANT PHYSIOLOGY 2016; 172:2429-2444. [PMID: 27733515 PMCID: PMC5129725 DOI: 10.1104/pp.16.01393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins. In the tic56-1 mutant, the assembly of functional ribosomes is furthermore hampered by a processing defect of the plastid 23S rRNA. Spectinomycin-treatment of wild-type plants phenocopies the molecular phenotype of plastid proteome accumulation in tic56-1 and to a smaller degree also ppi2 plastids, suggesting that a defect in plastid translation is largely responsible for the phenotype of both import mutants. Import experiments with the tic56-3 mutant revealed no significant defect in the import of small ribosomal protein 16 in the absence of full-length Tic56, suggesting that the defect in ribosome assembly in tic56-1 may be independent of a function of Tic56 in protein import. Our data establish a previously unknown link between plastid protein import, the processing of plastid rRNAs, and the assembly of plastid ribosomes and provide further knowledge on the function of the translocon components and the molecular basis for their albino phenotype.
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Affiliation(s)
- Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
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29
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Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L. Int J Mol Sci 2016; 17:ijms17111794. [PMID: 27801782 PMCID: PMC5133795 DOI: 10.3390/ijms17111794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.
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30
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Cole LW. The Evolution of Per-cell Organelle Number. Front Cell Dev Biol 2016; 4:85. [PMID: 27588285 PMCID: PMC4988970 DOI: 10.3389/fcell.2016.00085] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Organelles with their own distinct genomes, such as plastids and mitochondria, are found in most eukaryotic cells. As these organelles and their host cells have evolved, the partitioning of metabolic processes and the encoding of interacting gene products have created an obligate codependence. This relationship has played a role in shaping the number of organelles in cells through evolution. Factors such as stochastic evolutionary forces acting on genes involved in organelle biogenesis, organelle-nuclear gene interactions, and physical limitations may, to varying degrees, dictate the selective constraint that per-cell organelle number is under. In particular, coordination between nuclear and organellar gene expression may be important in maintaining gene product stoichiometry, which may have a significant role in constraining the evolution of this trait.
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Affiliation(s)
- Logan W Cole
- Department of Biology, Indiana University Bloomington, IN, USA
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31
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Baginsky S. Protein phosphorylation in chloroplasts - a survey of phosphorylation targets. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3873-82. [PMID: 26969742 DOI: 10.1093/jxb/erw098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.
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Affiliation(s)
- Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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32
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Li X, Jackson A, Xie M, Wu D, Tsai WC, Zhang S. Proteomic insights into floral biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1050-60. [PMID: 26945514 DOI: 10.1016/j.bbapap.2016.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/25/2016] [Accepted: 02/24/2016] [Indexed: 12/17/2022]
Abstract
The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou 310021, PR China; International Atomic Energy Agency Collaborating Center, Zhejiang University, Hangzhou 310029, PR China.
| | | | - Ming Xie
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou 310021, PR China.
| | - Dianxing Wu
- International Atomic Energy Agency Collaborating Center, Zhejiang University, Hangzhou 310029, PR China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Cornell University, New York 14853, USA
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Pfannschmidt T, Blanvillain R, Merendino L, Courtois F, Chevalier F, Liebers M, Grübler B, Hommel E, Lerbs-Mache S. Plastid RNA polymerases: orchestration of enzymes with different evolutionary origins controls chloroplast biogenesis during the plant life cycle. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6957-73. [PMID: 26355147 DOI: 10.1093/jxb/erv415] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Chloroplasts are the sunlight-collecting organelles of photosynthetic eukaryotes that energetically drive the biosphere of our planet. They are the base for all major food webs by providing essential photosynthates to all heterotrophic organisms including humans. Recent research has focused largely on an understanding of the function of these organelles, but knowledge about the biogenesis of chloroplasts is rather limited. It is known that chloroplasts develop from undifferentiated precursor plastids, the proplastids, in meristematic cells. This review focuses on the activation and action of plastid RNA polymerases, which play a key role in the development of new chloroplasts from proplastids. Evolutionarily, plastids emerged from the endosymbiosis of a cyanobacterium-like ancestor into a heterotrophic eukaryote. As an evolutionary remnant of this process, they possess their own genome, which is expressed by two types of plastid RNA polymerase, phage-type and prokaryotic-type RNA polymerase. The protein subunits of these polymerases are encoded in both the nuclear and plastid genomes. Their activation and action therefore require a highly sophisticated regulation that controls and coordinates the expression of the components encoded in the plastid and nucleus. Stoichiometric expression and correct assembly of RNA polymerase complexes is achieved by a combination of developmental and environmentally induced programmes. This review highlights the current knowledge about the functional coordination between the different types of plastid RNA polymerases and provides working models of their sequential expression and function for future investigations.
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Affiliation(s)
- Thomas Pfannschmidt
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Robert Blanvillain
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Livia Merendino
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Florence Courtois
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Fabien Chevalier
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Monique Liebers
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Björn Grübler
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Elisabeth Hommel
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Silva Lerbs-Mache
- Université Grenoble-Alpes, F-38000 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
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34
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Reyes-Prieto A. The basic genetic toolkit to move in with your photosynthetic partner. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Figueroa‐Martinez F, Nedelcu AM, Smith DR, Reyes‐Prieto A. When the lights go out: the evolutionary fate of free-living colorless green algae. THE NEW PHYTOLOGIST 2015; 206:972-82. [PMID: 26042246 PMCID: PMC5024002 DOI: 10.1111/nph.13279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/10/2014] [Indexed: 05/22/2023]
Abstract
The endosymbiotic origin of plastids was a launching point for eukaryotic evolution. The autotrophic abilities bestowed by plastids are responsible for much of the eukaryotic diversity we observe today. But despite its many advantages, photosynthesis has been lost numerous times and in disparate lineages throughout eukaryote evolution. For example, among green algae, several groups have lost photosynthesis independently and in response to different selective pressures; these include the parasitic/pathogenic trebouxiophyte genera Helicosporidium and Prototheca, and the free-living chlamydomonadalean genera Polytomella and Polytoma. Here, we examine the published data on colorless green algae and argue that investigations into the different evolutionary routes leading to their current nonphotosynthetic lifestyles provide exceptional opportunities to understand the ecological and genomic factors involved in the loss of photosynthesis.
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Affiliation(s)
| | - Aurora M. Nedelcu
- Biology DepartmentUniversity of New BrunswickFrederictonNBE3B 5A3Canada
| | - David R. Smith
- Biology DepartmentUniversity of Western OntarioLondonONN6A 5B7Canada
| | - Adrian Reyes‐Prieto
- Biology DepartmentUniversity of New BrunswickFrederictonNBE3B 5A3Canada
- Integrated Microbiology ProgramCanadian Institute for Advanced ResearchTorontoON M5G 1Z8Canada
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Köhler D, Montandon C, Hause G, Majovsky P, Kessler F, Baginsky S, Agne B. Characterization of chloroplast protein import without Tic56, a component of the 1-megadalton translocon at the inner envelope membrane of chloroplasts. PLANT PHYSIOLOGY 2015; 167:972-90. [PMID: 25588737 PMCID: PMC4348784 DOI: 10.1104/pp.114.255562] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/14/2015] [Indexed: 05/17/2023]
Abstract
We report on the characterization of Tic56, a unique component of the recently identified 1-MD translocon at the inner envelope membrane of chloroplasts (TIC) in Arabidopsis (Arabidopsis thaliana) comprising Tic20, Tic100, and Tic214. We isolated Tic56 by copurification with Tandem Affinity Purification-tagged Toc159 in the absence of precursor protein, indicating spontaneous and translocation-independent formation of the translocon at the outer envelope membrane of chloroplasts (TOC) and TIC supercomplexes. Tic56 mutant plants have an albino phenotype and are unable to grow without an external carbon source. Using specific enrichment of protein amino termini, we analyzed the tic56-1 and plastid protein import2 (toc159) mutants to assess the in vivo import capacity of plastids in mutants of an outer and inner envelope component of the anticipated TOC-TIC supercomplex. Inboth mutants, we observed processing of several import substrates belonging to various pathways. Our results suggest that despite the severe developmental defects, protein import into Tic56-deficient plastids is functional to a considerable degree, indicating the existence of alternative translocases at the inner envelope membrane.
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Köhler D, Dobritzsch D, Hoehenwarter W, Helm S, Steiner JM, Baginsky S. Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation. FRONTIERS IN PLANT SCIENCE 2015; 6:559. [PMID: 26257763 PMCID: PMC4510345 DOI: 10.3389/fpls.2015.00559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 05/06/2023]
Abstract
Glaucophyta, rhodophyta, and chloroplastida represent the three main evolutionary lineages that diverged from a common ancestor after primary endosymbiosis. Comparative analyses between members of these three lineages are a rich source of information on ancestral plastid features. We analyzed the composition and the cleavage site of cyanelle transit peptides from the glaucophyte Cyanophora paradoxa by terminal amine labeling of substrates (TAILS), and compared their characteristics to those of representatives of the chloroplastida. Our data show that transit peptide architecture is similar between members of these two lineages. This entails a comparable modular structure, an overrepresentation of serine or alanine and similarities in the amino acid composition around the processing peptidase cleavage site. The most distinctive difference is the overrepresentation of phenylalanine in the N-terminal 1-10 amino acids of cyanelle transit peptides. A quantitative proteome analysis with periplasm-free cyanelles identified 42 out of 262 proteins without the N-terminal phenylalanine, suggesting that the requirement for phenylalanine in the N-terminal region is not absolute. Proteins in this set are on average of low abundance, suggesting that either alternative import pathways are operating specifically for low abundance proteins or that the gene model annotation is incorrect for proteins with fewer EST sequences. We discuss these two possibilities and provide examples for both interpretations.
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Affiliation(s)
- Daniel Köhler
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Dirk Dobritzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | | | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Jürgen M. Steiner
- Plant Physiology, Institute of Biology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
- *Correspondence: Sacha Baginsky, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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38
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Lu Q, Ding S, Reiland S, Rödiger A, Roschitzki B, Xue P, Gruissem W, Lu C, Baginsky S. Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice). JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:175-87. [PMID: 25316064 DOI: 10.1093/jxb/eru405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plastid casein kinase II is an important regulator of transcription, posttranscriptional processes, and, most likely, different metabolic functions in dicotyledonous species. Here we report the identification and characterization of pCKII from the monocotyledonous species Oryza sativa. OspCKII activity was enriched from isolated rice chloroplasts using heparin-Sepharose chromatography, in which it co-elutes with the transcriptionally active chromosome (TAC) and several ribosomal proteins. Inclusion mass scanning of the kinase-active fraction identified the gene model for OspCKII. Transient expression of GFP fused to the 184 N-terminal amino acids of the OspCKII sequence in rice confirmed the chloroplastic localization of the kinase. OspCKII activity shows the characteristic features of casein kinase II, such as the utilization of GTP as phosphate donor, inhibition by low concentrations of heparin and poly-lysine, and utilization of the canonical pCKII motif E-S-E-G-E in the model substrate RNP29. Phosphoproteome analysis of a protein extract from rice leaves combined with a meta-analysis with published phosphoproteomics data revealed differences in the target protein spectrum between rice and Arabidopsis. Consistently, several pCKII phosphorylation sites in dicotyledonous plants are not conserved in monocots and algae, suggesting that details of pCKII regulation in plastids have changed during evolution.
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Affiliation(s)
- Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shunhua Ding
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Sonja Reiland
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anja Rödiger
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich \ ETH Zurich, 8057 Zurich, Switzerland
| | - Peng Xue
- Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland Functional Genomics Center Zurich, University of Zurich \ ETH Zurich, 8057 Zurich, Switzerland
| | - Congming Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Sacha Baginsky
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland
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Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PLoS One 2014; 9:e112870. [PMID: 25393533 PMCID: PMC4231079 DOI: 10.1371/journal.pone.0112870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids.
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Schönberg A, Bergner E, Helm S, Agne B, Dünschede B, Schünemann D, Schutkowski M, Baginsky S. The peptide microarray "ChloroPhos1.0" identifies new phosphorylation targets of plastid casein kinase II (pCKII) in Arabidopsis thaliana. PLoS One 2014; 9:e108344. [PMID: 25295873 PMCID: PMC4189921 DOI: 10.1371/journal.pone.0108344] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
We report the development of a peptide microarray based on previously determined phosphorylation sites in chloroplast proteins. Altogether, 905 peptides were spotted as 15mers in nine replicates onto glass slides. We used the microarray for in vitro phosphorylation experiments and specifically assessed the peptide substrate spectrum of chloroplast casein kinase II (pCKII). To this end, native pCKII from Arabidopsis thaliana and Sinapis alba chloroplasts was enriched by Heparin-Sepharose chromatography and its activity on the microarray was compared to the activity of a recombinant Arabidopsis pCKII. All three kinase preparations phosphorylated a similar set of peptides that were clearly distinct from those phosphorylated by bovine heart protein kinase A (PKA) in control experiments. The majority of the pCKII phosphorylation targets are involved in plastid gene expression, supporting the earlier denomination of pCKII as plastid transcription kinase (PTK). In addition we identified Alb3 as pCKII substrate that is essential for the integration of light-harvesting complex subunits (LHC) into the thylakoid membrane. Plastid CKII phosphorylation activity was characterized in greater detail in vitro with recombinant wildtype Alb3 and phosphorylation site mutants as substrates, establishing S424 as the pCKII phosphorylation site. Our data show that the peptide microarray ChloroPhos1.0 is a suitable tool for the identification of new kinase downstream targets in vitro that can be validated subsequently by in vivo experiments.
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Affiliation(s)
- Anna Schönberg
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Elena Bergner
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Mike Schutkowski
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Steinbeis-Forschungszentrum, Peptide Microarrays, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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41
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Nelson CJ, Alexova R, Jacoby RP, Millar AH. Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling. PLANT PHYSIOLOGY 2014; 166:91-108. [PMID: 25082890 PMCID: PMC4149734 DOI: 10.1104/pp.114.243014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein turnover is a key component in cellular homeostasis; however, there is little quantitative information on degradation kinetics for individual plant proteins. We have used (15)N labeling of barley (Hordeum vulgare) plants and gas chromatography-mass spectrometry analysis of free amino acids and liquid chromatography-mass spectrometry analysis of proteins to track the enrichment of (15)N into the amino acid pools in barley leaves and then into tryptic peptides derived from newly synthesized proteins. Using information on the rate of growth of barley leaves combined with the rate of degradation of (14)N-labeled proteins, we calculate the turnover rates of 508 different proteins in barley and show that they vary by more than 100-fold. There was approximately a 9-h lag from label application until (15)N incorporation could be reliably quantified in extracted peptides. Using this information and assuming constant translation rates for proteins during the time course, we were able to quantify degradation rates for several proteins that exhibit half-lives on the order of hours. Our workflow, involving a stringent series of mass spectrometry filtering steps, demonstrates that (15)N labeling can be used for large-scale liquid chromatography-mass spectrometry studies of protein turnover in plants. We identify a series of abundant proteins in photosynthesis, photorespiration, and specific subunits of chlorophyll biosynthesis that turn over significantly more rapidly than the average protein involved in these processes. We also highlight a series of proteins that turn over as rapidly as the well-known D1 subunit of photosystem II. While these proteins need further verification for rapid degradation in vivo, they cluster in chlorophyll and thiamine biosynthesis.
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Affiliation(s)
- Clark J Nelson
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ralitza Alexova
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Richard P Jacoby
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
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42
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Uncovering the protein lysine and arginine methylation network in Arabidopsis chloroplasts. PLoS One 2014; 9:e95512. [PMID: 24748391 PMCID: PMC3991674 DOI: 10.1371/journal.pone.0095512] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/27/2014] [Indexed: 11/28/2022] Open
Abstract
Post-translational modification of proteins by the addition of methyl groups to the side chains of Lys and Arg residues is proposed to play important roles in many cellular processes. In plants, identification of non-histone methylproteins at a cellular or subcellular scale is still missing. To gain insights into the extent of this modification in chloroplasts we used a bioinformatics approach to identify protein methyltransferases targeted to plastids and set up a workflow to specifically identify Lys and Arg methylated proteins from proteomic data used to produce the Arabidopsis chloroplast proteome. With this approach we could identify 31 high-confidence Lys and Arg methylation sites from 23 chloroplastic proteins, of which only two were previously known to be methylated. These methylproteins are split between the stroma, thylakoids and envelope sub-compartments. They belong to essential metabolic processes, including photosynthesis, and to the chloroplast biogenesis and maintenance machinery (translation, protein import, division). Also, the in silico identification of nine protein methyltransferases that are known or predicted to be targeted to plastids provided a foundation to build the enzymes/substrates relationships that govern methylation in chloroplasts. Thereby, using in vitro methylation assays with chloroplast stroma as a source of methyltransferases we confirmed the methylation sites of two targets, plastid ribosomal protein L11 and the β-subunit of ATP synthase. Furthermore, a biochemical screening of recombinant chloroplastic protein Lys methyltransferases allowed us to identify the enzymes involved in the modification of these substrates. The present study provides a useful resource to build the methyltransferases/methylproteins network and to elucidate the role of protein methylation in chloroplast biology.
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43
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Mueller SJ, Lang D, Hoernstein SN, Lang EG, Schuessele C, Schmidt A, Fluck M, Leisibach D, Niegl C, Zimmer AD, Schlosser A, Reski R. Quantitative analysis of the mitochondrial and plastid proteomes of the moss Physcomitrella patens reveals protein macrocompartmentation and microcompartmentation. PLANT PHYSIOLOGY 2014; 164:2081-95. [PMID: 24515833 PMCID: PMC3982764 DOI: 10.1104/pp.114.235754] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/07/2014] [Indexed: 05/22/2023]
Abstract
Extant eukaryotes are highly compartmentalized and have integrated endosymbionts as organelles, namely mitochondria and plastids in plants. During evolution, organellar proteomes are modified by gene gain and loss, by gene subfunctionalization and neofunctionalization, and by changes in protein targeting. To date, proteomics data for plastids and mitochondria are available for only a few plant model species, and evolutionary analyses of high-throughput data are scarce. We combined quantitative proteomics, cross-species comparative analysis of metabolic pathways, and localizations by fluorescent proteins in the model plant Physcomitrella patens in order to assess evolutionary changes in mitochondrial and plastid proteomes. This study implements data-mining methodology to classify and reliably reconstruct subcellular proteomes, to map metabolic pathways, and to study the effects of postendosymbiotic evolution on organellar pathway partitioning. Our results indicate that, although plant morphologies changed substantially during plant evolution, metabolic integration of organelles is largely conserved, with exceptions in amino acid and carbon metabolism. Retargeting or regulatory subfunctionalization are common in the studied nucleus-encoded gene families of organelle-targeted proteins. Moreover, complementing the proteomic analysis, fluorescent protein fusions revealed novel proteins at organelle interfaces such as plastid stromules (stroma-filled tubules) and highlight microcompartments as well as intercellular and intracellular heterogeneity of mitochondria and plastids. Thus, we establish a comprehensive data set for mitochondrial and plastid proteomes in moss, present a novel multilevel approach to organelle biology in plants, and place our findings into an evolutionary context.
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Neuman H, Galpaz N, Cunningham FX, Zamir D, Hirschberg J. The tomato mutation nxd1 reveals a gene necessary for neoxanthin biosynthesis and demonstrates that violaxanthin is a sufficient precursor for abscisic acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:80-93. [PMID: 24506237 DOI: 10.1111/tpj.12451] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 05/20/2023]
Abstract
Carotenoid pigments are indispensable for plant life. They are synthesized within plastids where they provide essential functions in photosynthesis. Carotenoids serve as precursors for the synthesis of the strigolactone phytohormones, which are made from β-carotene, and of abscisic acid (ABA), which is produced from certain xanthophylls. Despite the significant progress that has been made in our understanding of the carotenoid biosynthesis pathway, the synthesis of the xanthophyll neoxanthin has remained unknown. We report here on the isolation of a tomato (Solanum lycopersicum) mutant, neoxanthin-deficient 1 (nxd1), which lacks neoxanthin, and on the cloning of a gene that is necessary for neoxanthin synthesis in both tomato and Arabidopsis. The locus nxd1 encodes a gene of unknown function that is conserved in all higher plants. The activity of NXD1 is essential but cannot solely support neoxanthin synthesis. Lack of neoxanthin does not significantly reduce the fitness of tomato plants in cultivated field conditions and does not impair the synthesis of ABA, suggesting that in tomato violaxanthin is a sufficient precursor for ABA production in vivo.
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Affiliation(s)
- Hadar Neuman
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Jerusalem, 91904, Israel
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45
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Velikova V, Ghirardo A, Vanzo E, Merl J, Hauck SM, Schnitzler JP. Genetic Manipulation of Isoprene Emissions in Poplar Plants Remodels the Chloroplast Proteome. J Proteome Res 2014; 13:2005-18. [DOI: 10.1021/pr401124z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Violeta Velikova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 21, 1113 Sofia, Bulgaria
- Helmholtz
Zentrum München, Institute of Biochemical Plant Pathology, Research Unit, Environmental Simulation, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Andrea Ghirardo
- Helmholtz
Zentrum München, Institute of Biochemical Plant Pathology, Research Unit, Environmental Simulation, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Elisa Vanzo
- Helmholtz
Zentrum München, Institute of Biochemical Plant Pathology, Research Unit, Environmental Simulation, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Juliane Merl
- Helmholtz
Zentrum München, Research Unit Protein Science, Ingolstädter
Landstr. 1, D-85764 Neuherberg, Germany
| | - Stefanie M. Hauck
- Helmholtz
Zentrum München, Research Unit Protein Science, Ingolstädter
Landstr. 1, D-85764 Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Helmholtz
Zentrum München, Institute of Biochemical Plant Pathology, Research Unit, Environmental Simulation, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
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Ito J, Parsons HT, Heazlewood JL. The Arabidopsis cytosolic proteome: the metabolic heart of the cell. FRONTIERS IN PLANT SCIENCE 2014; 5:21. [PMID: 24550929 PMCID: PMC3914213 DOI: 10.3389/fpls.2014.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/19/2014] [Indexed: 05/09/2023]
Abstract
The plant cytosol is the major intracellular fluid that acts as the medium for inter-organellar crosstalk and where a plethora of important biological reactions take place. These include its involvement in protein synthesis and degradation, stress response signaling, carbon metabolism, biosynthesis of secondary metabolites, and accumulation of enzymes for defense and detoxification. This central role is highlighted by estimates indicating that the majority of eukaryotic proteins are cytosolic. Arabidopsis thaliana has been the subject of numerous proteomic studies on its different subcellular compartments. However, a detailed study of enriched cytosolic fractions from Arabidopsis cell culture has been performed only recently, with over 1,000 proteins reproducibly identified by mass spectrometry. The number of proteins allocated to the cytosol nearly doubles to 1,802 if a series of targeted proteomic characterizations of complexes is included. Despite this, few groups are currently applying advanced proteomic approaches to this important metabolic space. This review will highlight the current state of the Arabidopsis cytosolic proteome since its initial characterization a few years ago.
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Affiliation(s)
- Jun Ito
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
| | - Harriet T. Parsons
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
- Department of Plant and Environmental Sciences, University of Copenhagen, CopenhagenDenmark
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
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Jarvis P, López-Juez E. Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol 2014; 14:787-802. [PMID: 24263360 DOI: 10.1038/nrm3702] [Citation(s) in RCA: 403] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chloroplasts are the organelles that define plants, and they are responsible for photosynthesis as well as numerous other functions. They are the ancestral members of a family of organelles known as plastids. Plastids are remarkably dynamic, existing in strikingly different forms that interconvert in response to developmental or environmental cues. The genetic system of this organelle and its coordination with the nucleocytosolic system, the import and routing of nucleus-encoded proteins, as well as organellar division all contribute to the biogenesis and homeostasis of plastids. They are controlled by the ubiquitin-proteasome system, which is part of a network of regulatory mechanisms that integrate plastid development into broader programmes of cellular and organismal development.
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Affiliation(s)
- Paul Jarvis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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48
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Grimmer J, Rödiger A, Hoehenwarter W, Helm S, Baginsky S. The RNA-binding protein RNP29 is an unusual Toc159 transport substrate. FRONTIERS IN PLANT SCIENCE 2014; 5:258. [PMID: 24982663 PMCID: PMC4059279 DOI: 10.3389/fpls.2014.00258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/20/2014] [Indexed: 05/08/2023]
Abstract
The precursors of RNP29 and Ferredoxin (Fd2) were previously identified in the cytosol of ppi2 plant cells with their N-terminal amino acid acetylated. Here, we explore whether precursor accumulation in ppi2 is characteristic for Toc159 client proteins, by characterizing the import properties of the RNP29 precursor in comparison to Fd2 and other Toc159-dependent or independent substrates. We find specific accumulation of the RNP29 precursor in ppi2 but not in wild type or ppi1 protoplasts. With the exception of Lhcb4, precursor accumulation is also detected with all other tested constructs in ppi2. However, RNP29 is clearly different from the other proteins because only precursor but almost no mature protein is detectable in protoplast extracts. Co-transformation of RNP29 with Toc159 complements its plastid import, supporting the hypothesis that RNP29 is a Toc159-dependent substrate. Exchange of the second amino acid in the RNP29 transit peptide to Glu or Asn prevents methionine excision but not N-terminal acetylation, suggesting that different N-acetyltransferases may act on chloroplast precursor proteins in vivo. All different RNP29 constructs are efficiently imported into wild type but not into ppi2 plastids, arguing for a minor impact of the N-terminal amino acid on the import process.
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Affiliation(s)
- Julia Grimmer
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Anja Rödiger
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | | | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
- *Correspondence: Sacha Baginsky, Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany e-mail:
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Schröter Y, Steiner S, Weisheit W, Mittag M, Pfannschmidt T. A purification strategy for analysis of the DNA/RNA-associated sub-proteome from chloroplasts of mustard cotyledons. FRONTIERS IN PLANT SCIENCE 2014; 5:557. [PMID: 25400643 PMCID: PMC4212876 DOI: 10.3389/fpls.2014.00557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/29/2014] [Indexed: 05/20/2023]
Abstract
Plant cotyledons are a tissue that is particularly active in plastid gene expression in order to develop functional chloroplasts from pro-plastids, the plastid precursor stage in plant embryos. Cotyledons, therefore, represent a material being ideal for the study of composition, function and regulation of protein complexes involved in plastid gene expression. Here, we present a pilot study that uses heparin-Sepharose and phospho-cellulose chromatography in combination with isoelectric focussing and denaturing SDS gel electrophoresis (two-dimensional gel electrophoresis) for investigating the nucleic acids binding sub-proteome of mustard chloroplasts purified from cotyledons. We describe the technical requirements for a highly resolved biochemical purification of several hundreds of protein spots obtained from such samples. Subsequent mass spectrometry of peptides isolated out of cut spots that had been treated with trypsin identified 58 different proteins within 180 distinct spots. Our analyses indicate a high enrichment of proteins involved in transcription and translation and, in addition, the presence of massive post-translational modification of this plastid protein sub-fraction. The study provides an extended catalog of plastid proteins from mustard being involved in gene expression and its regulation and describes a suitable purification strategy for further analysis of low abundant gene expression related proteins.
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Affiliation(s)
- Yvonne Schröter
- Lehrstuhl für Pflanzenphysiologie, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität JenaJena, Germany
| | - Sebastian Steiner
- Lehrstuhl für Pflanzenphysiologie, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität JenaJena, Germany
- KWS SAAT AGEinbeck, Germany
| | - Wolfram Weisheit
- Lehrstuhl für Pflanzenphysiologie, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität JenaJena, Germany
- Department of General Botany, Institute of General Botany and Plant Physiology, Friedrich Schiller University JenaJena, Germany
| | - Maria Mittag
- Lehrstuhl für Pflanzenphysiologie, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität JenaJena, Germany
- Department of General Botany, Institute of General Botany and Plant Physiology, Friedrich Schiller University JenaJena, Germany
| | - Thomas Pfannschmidt
- Lehrstuhl für Pflanzenphysiologie, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität JenaJena, Germany
- University of Grenoble-AlpesGrenoble, France
- CNRS, UMR5168Grenoble, France
- Commissariat a L'energie Atomique (CEA), iRTSV, Laboratoire de Physiologie Cellulaire & VégétaleGrenoble, France
- INRA, USC1359Grenoble, France
- *Correspondence: Thomas Pfannschmidt, Commissariat a L'energie Atomique (CEA), iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 17 Rue des Martyrs, 38000 Grenoble, France e-mail:
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