1
|
Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
Collapse
Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
2
|
Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
Collapse
Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| |
Collapse
|
3
|
Liao Z, Ghanizadeh H, Zhang X, Yang H, Zhou Y, Huang L, Zhang X, Jiang Y, Nie G. Exogenous Methyl Jasmonate Mediated MiRNA-mRNA Network Improves Heat Tolerance of Perennial Ryegrass. Int J Mol Sci 2023; 24:11085. [PMID: 37446266 DOI: 10.3390/ijms241311085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Heat stress can hinder the growth of perennial ryegrass (Lolium perenne L.). Methyl jasmonate (MeJA) applied exogenously can increase heat stress tolerance in plants; however, the regulatory mechanisms involved in heat tolerance mediated by MeJA are poorly understood in perennial ryegrass. Here, the microRNA (miRNA) expression profiles of perennial ryegrass were assessed to elucidate the regulatory pathways associated with heat tolerance induced by MeJA. Plants were subjected to four treatments, namely, control (CK), MeJA pre-treatment (T), heat stress treatment (H), and MeJA pre-treatment + heat stress (TH). According to the results, 102 miRNAs were up-regulated in all treatments, with 20, 27, and 33 miRNAs being up-regulated in the T, H, and TH treatment groups, respectively. The co-expression network analysis between the deferentially expressed miRNAs and their corresponding target genes showed that 20 miRNAs modulated 51 potential target genes. Notably, the miRNAs that targeted genes related to with regards to heat tolerance were driven by MeJA, and they were involved in four pathways: novel-m0258-5p mediated signal transduction, novel-m0350-5p mediated protein homeostasis, miR397-z, miR5658-z, and novel-m0008-5p involved in cell wall component, and miR1144-z and miR5185-z dominated chlorophyll degradation. Overall, the findings of this research paved the way for more research into the heat tolerance mechanism in perennial ryegrass and provided a theoretical foundation for developing cultivars with enhanced heat tolerance.
Collapse
Affiliation(s)
- Zongchao Liao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hossein Ghanizadeh
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Xin Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hechuan Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
4
|
Hall ND, Patel JD, McElroy JS, Goertzen LR. Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet). BMC Genomics 2021; 22:175. [PMID: 33706694 PMCID: PMC7953713 DOI: 10.1186/s12864-021-07447-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/16/2021] [Indexed: 01/15/2023] Open
Abstract
Background Finger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A, 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Conclusion The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07447-y.
Collapse
Affiliation(s)
- Nathan D Hall
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA.
| | - Jinesh D Patel
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Science Auburn University, Auburn, AL, USA
| | - Leslie R Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| |
Collapse
|
5
|
Griffin JHC, Prado K, Sutton P, Toledo-Ortiz G. Coordinating light responses between the nucleus and the chloroplast, a role for plant cryptochromes and phytochromes. PHYSIOLOGIA PLANTARUM 2020; 169:515-528. [PMID: 32519399 DOI: 10.1111/ppl.13148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
To promote photomorphogenesis, including plastid development and metabolism, the phytochrome (phy) and the cryptochrome (cry) photoreceptors orchestrate genome-wide changes in gene expression in response to Red (R)- and Blue (B)-light cues. While phys and crys have a clear role in modulating photosynthesis, their role in the coordination of the nuclear genome and the plastome, essential for functional chloroplasts, remains underexplored. Using publicly available genome datasets for WT and phyABCDE or cry1cry2 Arabidopsis seedlings, grown, respectively, under R- or B-light, we bioinformatically analyzed the influence of light inputs and photoreceptors in the control of nuclear genes with a function in the chloroplast, and evaluated the role of phyB in the modulation of plastome-encoded genes. We show gene co-induction by R-phys and B-crys for genes with a chloroplastic function, and also apparent photoreceptor-driven preferential responses. Evidence from phyB in Arabidopsis together with published evidence from CRY2 in tomato also supports the participation of both photoreceptor families in the global modulation of the plastome genes. To begin addressing how these light-sensors orchestrate changes in an organellar genome, we evaluated their effect over genes with potential functions in plastid gene-expression regulation based on their TAIR annotation. Results indicate that both crys and phys modulate 'plastome-regulatory genes' with enrichment in the contribution of crys to all processes and of phys to post-transcription and transcription. Furthermore, we identified a new role for HY5 as a relevant light-signaling component in photoreceptor-based anterograde signaling leading to plastome gene regulation.
Collapse
Affiliation(s)
| | - Karine Prado
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Phoebe Sutton
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | |
Collapse
|
6
|
Cheng B, Smyth HE, Furtado A, Henry RJ. Slower development of lower canopy beans produces better coffee. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4201-4214. [PMID: 32206798 PMCID: PMC7337091 DOI: 10.1093/jxb/eraa151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.
Collapse
Affiliation(s)
- Bing Cheng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Heather E Smyth
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| |
Collapse
|
7
|
Liu S, Zheng L, Jia J, Guo J, Zheng M, Zhao J, Shao J, Liu X, An L, Yu F, Qi Y. Chloroplast Translation Elongation Factor EF-Tu/SVR11 Is Involved in var2-Mediated Leaf Variegation and Leaf Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:295. [PMID: 30915096 PMCID: PMC6423176 DOI: 10.3389/fpls.2019.00295] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/22/2019] [Indexed: 05/02/2023]
Abstract
Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.
Collapse
|
8
|
Wang J, Xia H, Zhao SZ, Hou L, Zhao CZ, Ma CL, Wang XJ, Li PC. A role of GUNs-Involved retrograde signaling in regulating Acetyl-CoA carboxylase 2 in Arabidopsis. Biochem Biophys Res Commun 2018; 505:712-719. [PMID: 30292412 DOI: 10.1016/j.bbrc.2018.09.144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/21/2018] [Indexed: 01/01/2023]
Abstract
In Arabidopsis thaliana (Arabidopsis), Acetyl-CoA Carboxylase 2 (ACC2) is a nuclear DNA-encoded and plastid-targeted enzyme that catalyzes the conversion of acetyl-CoA to malonyl-CoA. ACC2 improves plant growth and development when chloroplast translation is impaired. However, little is known about the upstream signals that regulate ACC2. Here, through analyzing the transcriptome changes in brz-insensitive-pale green (bpg) 2-2, a pale-green mutant with impaired chloroplast gene expression resulting from loss of the BPG2 function, we found that the level of ACC2 was significantly up-regulated. Through performing genetic analysis, we further demonstrated that loss of the GENOMES UNCOUPLED 1 (GUN1) or GUN5 function partly perturbed the up-regulation of ACC2 in the bpg2-2 mutant, whereas ABA INSENSITIVE 4 (ABI4)-function-loss had no clear effect on the ACC2 expression. Furthermore, when plants were treated with plastid translation inhibitors, such as lincomycin and spectinomycin, the ACC2 transcriptional level was also markedly increased in a GUN-dependent manner. In conclusion, our results suggested that the GUN-involved plastid-to-nucleus retrograde communication played a role in regulating ACC2 in Arabidopsis.
Collapse
Affiliation(s)
- Juan Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China; College of Life Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China
| | - Shu-Zhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China
| | - Chuan-Zhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China
| | - Chang-Le Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Xing-Jun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Peng-Cheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| |
Collapse
|
9
|
Janowski M, Zoschke R, Scharff LB, Martinez Jaime S, Ferrari C, Proost S, Ng Wei Xiong J, Omranian N, Musialak-Lange M, Nikoloski Z, Graf A, Schöttler MA, Sampathkumar A, Vaid N, Mutwil M. AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:404-420. [PMID: 30044525 DOI: 10.1111/tpj.14040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 05/24/2023]
Abstract
Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.
Collapse
Affiliation(s)
- Marcin Janowski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Lars B Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Silvia Martinez Jaime
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Jonathan Ng Wei Xiong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | | | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl- Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| |
Collapse
|
10
|
Jiang T, Zhang J, Rong L, Feng Y, Wang Q, Song Q, Zhang L, Ouyang M. ECD1 functions as an RNA-editing trans-factor of rps14-149 in plastids and is required for early chloroplast development in seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3037-3051. [PMID: 29648606 PMCID: PMC5972661 DOI: 10.1093/jxb/ery139] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/29/2018] [Indexed: 05/18/2023]
Abstract
Chloroplast development is a highly complex process and the regulatory mechanisms have not yet been fully characterized. In this study, we identified Early Chloroplast Development 1 (ECD1), a chloroplast-localized pentatricopeptide repeat protein (PPR) belonging to the PLS subfamily. Inactivation of ECD1 in Arabidopsis led to embryo lethality, and abnormal embryogenesis occurred in ecd1/+ heterozygous plants. A decrease in ECD1 expression induced by RNAi resulted in seedlings with albino cotyledons but normal true leaves. The aberrant morphology and under-developed thylakoid membrane system in cotyledons of RNAi seedlings suggests a role of ECD1 specifically in chloroplast development in seedlings. In cotyledons of ECD1-RNAi plants, RNA-editing of rps14-149 (encoding ribosomal protein S14) was seriously impaired. In addition, dramatically decreased plastid-encoded RNA polymerase-dependent gene expression and abnormal chloroplast rRNA processing were also observed. Taken together, our results indicate that ECD1 is indispensable for chloroplast development at the seedling stage in Arabidopsis.
Collapse
Affiliation(s)
- Tian Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjiang Feng
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qi Wang
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiulai Song
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence:
| |
Collapse
|
11
|
Arabidopsis YL1/BPG2 Is Involved in Seedling Shoot Response to Salt Stress through ABI4. Sci Rep 2016; 6:30163. [PMID: 27444988 PMCID: PMC4957093 DOI: 10.1038/srep30163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/29/2016] [Indexed: 12/17/2022] Open
Abstract
The chloroplast-localized proteins play roles in plant salt stress response, but their mechanisms remain largely unknown. In this study, we screened a yellow leaf mutant, yl1-1, whose shoots exhibited hypersensitivity to salt stress. We mapped YL1 to AT3G57180, which encodes a YqeH-type GTPase. YL1, as a chloroplast stroma-localized protein, could be markedly reduced by high salinity. Upon exposure to high salinity, seedling shoots of yl1-1 and yl1-2 accumulated significantly higher levels of Na+ than wild type. Expression analysis of factors involved in plant salt stress response showed that the expression of ABI4 was increased and HKT1 was evidently suppressed in mutant shoots compared with the wild type under normal growth conditions. Moreover, salinity effects on ABI4 and HKT1 were clearly weakened in the mutant shoots, suggesting that the loss of YL1 function impairs ABI4 and HKT1 expression. Notably, the shoots of yl1-2 abi4 double mutant exhibited stronger resistance to salt stress and accumulated less Na+ levels after salt treatment compared with the yl1-2 single mutant, suggesting the salt-sensitive phenotype of yl1-2 seedlings could be rescued via loss of ABI4 function. These results reveal that YL1 is involved in the salt stress response of seedling shoots through ABI4.
Collapse
|
12
|
Qi Y, Zhao J, An R, Zhang J, Liang S, Shao J, Liu X, An L, Yu F. Mutations in circularly permuted GTPase family genes AtNOA1/RIF1/SVR10 and BPG2 suppress var2-mediated leaf variegation in Arabidopsis thaliana. PHOTOSYNTHESIS RESEARCH 2016; 127:355-67. [PMID: 26435530 DOI: 10.1007/s11120-015-0195-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/24/2015] [Indexed: 05/18/2023]
Abstract
Leaf variegation mutants constitute a unique group of chloroplast development mutants and are ideal genetic materials to dissect the regulation of chloroplast development. We have utilized the Arabidopsis yellow variegated (var2) mutant and genetic suppressor analysis to probe the mechanisms of chloroplast development. Here we report the isolation of a new var2 suppressor locus SUPPRESSOR OF VARIEGATION (SVR10). Genetic mapping and molecular complementation indicated that SVR10 encodes a circularly permuted GTPase that has been reported as Arabidopsis thaliana NITRIC OXIDE ASSOCIATED 1 (AtNOA1) and RESISTANT TO INHIBITION BY FOSMIDOMYCIN 1 (RIF1). Biochemical evidence showed that SVR10/AtNOA1/RIF1 likely localizes to the chloroplast stroma. We further demonstrate that the mutant of a close homologue of SVR10/AtNOA1/RIF1, BRASSINAZOLE INSENSITIVE PALE GREEN 2 (BPG2), can also suppress var2 leaf variegation. Mutants of SVR10 and BPG2 are impaired in photosynthesis and the accumulation of chloroplast proteins. Interestingly, two-dimensional blue native gel analysis showed that mutants of SVR10 and BPG2 display defects in the assembly of thylakoid membrane complexes including reduced levels of major photosynthetic complexes and the abnormal accumulation of a chlorophyll-protein supercomplex containing photosystem I. Taken together, our findings suggest that SVR10 and BPG2 are functionally related with VAR2, likely through their potential roles in regulating chloroplast protein homeostasis, and both SVR10 and BPG2 are required for efficient thylakoid protein complex assembly and photosynthesis.
Collapse
Affiliation(s)
- Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Rui An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Juan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuang Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingxia Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
13
|
Li C, Shen Y, Meeley R, McCarty DR, Tan BC. Embryo defective 14 encodes a plastid-targeted cGTPase essential for embryogenesis in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:785-799. [PMID: 26771182 DOI: 10.1111/tpj.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/24/2015] [Indexed: 06/05/2023]
Abstract
The embryo defective (emb) mutants in maize genetically define a unique class of loci that is required for embryogenesis but not endosperm development, allowing dissection of two developmental processes of seed formation. Through characterization of the emb14 mutant, we report here that Emb14 gene encodes a circular permuted, YqeH class GTPase protein that likely functions in 30S ribosome formation in plastids. Loss of Emb14 function in the null mutant arrests embryogenesis at the early transition stage. Emb14 was cloned by transposon tagging and was confirmed by analysis of four alleles. Subcellular localization indicated that the EMB14 is targeted to chloroplasts. Recombinant EMB14 is shown to hydrolyze GTP in vitro (Km = 2.42 ± 0.3 μm). Emb14 was constitutively expressed in all tissues examined and high level of expression was found in transition stage embryos. Comparison of emb14 and WT indicated that loss of EMB14 function severely impairs accumulation of 16S rRNA and several plastid encoded ribosomal genes. We show that an EMB14 transgene complements the pale green, slow growth phenotype conditioned by mutations in AtNOA1, a closely related YqeH GTPase of Arabidopsis. Taken together, we propose that the EMB14/AtNOA1/YqeH class GTPases function in assembly of the 30S subunit of the chloroplast ribosome, and that this function is essential to embryogenesis in plants.
Collapse
Affiliation(s)
- Cuiling Li
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Yun Shen
- State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Robert Meeley
- DuPont Pioneer AgBiotech Research, Johnston, Iowa, 50131-1004, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Bao-Cai Tan
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
- State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| |
Collapse
|
14
|
Bohne AV. The nucleoid as a site of rRNA processing and ribosome assembly. FRONTIERS IN PLANT SCIENCE 2014; 5:257. [PMID: 24926303 PMCID: PMC4046486 DOI: 10.3389/fpls.2014.00257] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/19/2014] [Indexed: 05/08/2023]
|
15
|
Germain A, Hotto AM, Barkan A, Stern DB. RNA processing and decay in plastids. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:295-316. [PMID: 23536311 DOI: 10.1002/wrna.1161] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus-encoded proteins recruited from cyanobacterial or host-cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence-specific RNA-binding proteins (RBPs). Other plastid RBPs, largely members of the helical-repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein-DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation.
Collapse
|