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Wang X, Ji D, Ma J, Chi W. Function of plastid translation in plant temperature acclimation: Retrograde signalling or extraribosomal 'moonlighting' functions? PLANT, CELL & ENVIRONMENT 2024. [PMID: 39101459 DOI: 10.1111/pce.15074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Summary StatementSpecific components of the plastid ribosome could act as pivotal limiting factors in plant temperature acclimation. We endeavour to elucidate the molecular nexus between plastid translation and temperature acclimation by incorporating the concept of extraribosomal ‘moonlighting’ functions of plastid ribosome proteins.
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Affiliation(s)
- Xiushun Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daili Ji
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Ma
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Chi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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2
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Yang R, Sun Y, Zhu X, Jiao B, Sun S, Chen Y, Li L, Wang X, Zeng Q, Liang Q, Huang B. The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato. THE NEW PHYTOLOGIST 2024; 241:1676-1689. [PMID: 38044709 DOI: 10.1111/nph.19426] [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: 07/24/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023]
Abstract
In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.
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Affiliation(s)
- Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yuan Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Xiaoling Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Baozhen Jiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Sifan Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yun Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Lizhu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Xue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Qian Zeng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Qiqi Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Binquan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650500, China
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3
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Lu T, Yin W, Zhang Y, Zhu C, Zhong Q, Li S, Wang N, Chen Z, Ye H, Fang Y, Mu D, Wang Y, Rao Y. WLP3 Encodes the Ribosomal Protein L18 and Regulates Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2023; 16:59. [PMID: 38091105 PMCID: PMC10719208 DOI: 10.1186/s12284-023-00674-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Plastid ribosomal proteins play a crucial role in the growth and development of plants, mainly in the gene expression and translation of key genes in chloroplasts. While some information is known about the regulatory processes of plastid ribosomal proteins in various plant species, there is limited knowledge about the underlying mechanisms in rice. In this study, ethyl methanesulfonate (EMS) mutagenesis was used to generate a new mutant called wlp3 (white leaf and panicle3), characterized by white or albino leaves and panicles, which exhibited this phenotype from the second leaf stage until tillering. Furthermore, after a certain period, the newly emerging leaves developed the same phenotype as the rice variety ZH11, while the albino leaves of wlp3 showed an incomplete chloroplast structure and significantly low chlorophyll content. A transition mutation (T to C) at position 380 was identified in the coding region of the LOC_Os03g61260 gene, resulting in the substitution of isoleucine by threonine during translation. WLP3 encodes the ribosomal L18 subunit, which is localized in the chloroplast. Complementation experiments confirmed that LOC_Os03g61260 was responsible for the albino phenotype in rice. WLP3 has high expression in the coleoptile, leaves at the three-leaf stage, and panicles at the heading stage. Compared to the wild-type (WT), wlp3 exhibited reduced chlorophyll synthesis and significantly decreased expression levels of genes associated with plastid development. Yeast two-hybrid (Y2H) analysis revealed that WLP3 interacts with other ribosomal subunits, to influence chloroplast development. These results contribute to a better understanding of the underlying molecular mechanisms of chloroplast development and plastid gene translation.
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Affiliation(s)
- Tao Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Wenjin Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Yinuo Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Chaoyu Zhu
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Sanfeng Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Nuo Wang
- College of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China
| | - Zhengai Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Hanfei Ye
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Yuan Fang
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Dan Mu
- College of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China.
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4
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Pérez de los Cobos F, Coindre E, Dlalah N, Quilot-Turion B, Batlle I, Arús P, Eduardo I, Duval H. Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time. HORTICULTURE RESEARCH 2023; 10:uhad193. [PMID: 37927408 PMCID: PMC10623407 DOI: 10.1093/hr/uhad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023]
Abstract
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | | | | | | | - Ignasi Batlle
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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5
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Li Q, Du J, Qiao Z, Pan C, He W, Zhang L, Li X, Nie Y, Li X, Pan G, Zhang Z, Li G, Ding H. White and green striate leaves 1, predicted to encode a 16S rRNA processing protein, plays a critical role in the processing of chloroplast ribosomes in maize ( Zea mays L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:65. [PMID: 37538809 PMCID: PMC10393919 DOI: 10.1007/s11032-023-01407-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023]
Abstract
Ribosomes play a crucial role in protein biosynthesis and are linked to plant growth and development. The RimM protein has been shown to be involved in the maturation of 30S ribosomal subunits, but its exact function in plants is still unknown. In this study, we discovered a maize mutant with white and green striate leaves (wgsl1) and reduced chlorophyll content. Genetic analysis showed that the wgsl1 mutation was recessive and controlled by a single nuclear gene. Map-based cloning of ZmWGSL1 identified a base substitution (G to A) that generated a missense mutation within the Zm00001d039036 gene in the wgsl1 mutant. Zm00001d039036 encodes a 16S rRNA processing protein containing the RimM motif. Further analysis of transcriptomic data showed that the transcript levels of many ribosomal proteins involved in the small and big ribosomal subunits were dramatically up-regulated in the wgsl1 mutant. Moreover, the level of ribosomal multimers was decreased. This suggests that ZmWGSL1 plays a crucial role in the maturation of the ribosome, leading to abnormal plant growth and development. In addition, subcellular localization results indicate that WGSL1 is localized in chloroplasts. Therefore, we suggest that WGSL1 is a nuclear-encoded protein, is transported to the chloroplast to drive functions, and affects the processing of ribosomes in the chloroplast. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01407-y.
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Affiliation(s)
- Qigui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Jiyuan Du
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Zhenghao Qiao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Chao Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Weiqiang He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Li Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaohu Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yongxin Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Xinzheng Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Zhiming Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
| | - Gaoke Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640 Guangdong Province China
| | - Haiping Ding
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018 Shangdong Province China
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6
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Uribe-López B, Barraza A, Cabrera-Ponce JL. Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions. Genes (Basel) 2023; 14:1463. [PMID: 37510367 PMCID: PMC10379993 DOI: 10.3390/genes14071463] [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: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Braulio Uribe-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC., Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz CP 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
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Tadini L, Jeran N, Domingo G, Zambelli F, Masiero S, Calabritto A, Costantini E, Forlani S, Marsoni M, Briani F, Vannini C, Pesaresi P. Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling. PLoS Genet 2023; 19:e1010344. [PMID: 37418499 PMCID: PMC10355426 DOI: 10.1371/journal.pgen.1010344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/09/2023] [Indexed: 07/09/2023] Open
Abstract
The chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast-quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.
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Affiliation(s)
- Luca Tadini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Nicolaj Jeran
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Anna Calabritto
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Elena Costantini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Sara Forlani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Barraza A, Cabrera-Ponce JL. Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis. Int J Mol Sci 2022; 23:ijms232213835. [PMID: 36430314 PMCID: PMC9696990 DOI: 10.3390/ijms232213835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein-protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs-MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9-may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC. IPN 195, Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
- Correspondence: ; Tel.: +52-462-6239600 (ext. 9421)
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9
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Robles P, Quesada V. Unveiling the functions of plastid ribosomal proteins in plant development and abiotic stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 189:35-45. [PMID: 36041366 DOI: 10.1016/j.plaphy.2022.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Translation of mRNAs into proteins is a universal process and ribosomes are the molecular machinery that carries it out. In eukaryotic cells, ribosomes can be found in the cytoplasm, mitochondria, and also in the chloroplasts of photosynthetic organisms. A number of genetic studies have been performed to determine the function of plastid ribosomal proteins (PRPs). Tobacco has been frequently used as a system to study the ribosomal proteins encoded by the chloroplast genome. In contrast, Arabidopsis thaliana and rice are preferentially used models to study the function of nuclear-encoded PRPs by using direct or reverse genetics approaches. The results of these works have provided a relatively comprehensive catalogue of the roles of PRPs in different plant biology aspects, which highlight that some PRPs are essential, while others are not. The latter ones are involved in chloroplast biogenesis, lateral root formation, leaf morphogenesis, plant growth, photosynthesis or chlorophyll synthesis. Furthermore, small gene families encode some PRPs. In the last few years, an increasing number of findings have revealed a close association between PRPs and tolerance to adverse environmental conditions. Sometimes, the same PRP can be involved in both developmental processes and the response to abiotic stress. The aim of this review is to compile and update the findings hitherto published on the functional analysis of PRPs. The study of the phenotypic effects caused by the disruption of PRPs from different species reveals the involvement of PRPs in different biological processes and highlights the significant impact of plastid translation on plant biology.
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Affiliation(s)
- Pedro Robles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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10
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Chen S, Zeng X, Li Y, Qiu S, Peng X, Xie X, Liu Y, Liao C, Tang X, Wu J. The nuclear-encoded plastid ribosomal protein L18s are essential for plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:949897. [PMID: 36212366 PMCID: PMC9538462 DOI: 10.3389/fpls.2022.949897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Plastid ribosomal proteins (PRPs) are necessary components for plastid ribosome biogenesis, playing essential roles in plastid development. The ribosomal protein L18 involved in the assemble of 5S rRNA and 23S rRNA, is vital for E. coli viability, but the functions of its homologs in plant plastid remain elusive. Here, we characterized the functions of the plant plastid ribosomal protein L18s (PRPL18s) in Arabidopsis and rice. AtPRPL18 was ubiquitously expressed in most of the plant tissues, but with higher expression levels in seedling shoots, leaves, and flowers. AtPRPL18 was localized in chloroplast. Genetic and cytological analyses revealed that a loss of function of AtPRPL18 resulted in embryo development arrest at globular stage. However, overexpression of AtPRPL18 did not show any visible phenotypical changes in Arabidopsis. The rice OsPRPL18 was localized in chloroplast. In contrast to AtPRPL18, knockout of OsPRPL18 did not affect embryo development, but led to an albino lethal phenotype at the seedling stage. Cytological analyses showed that chloroplast development was impaired in the osprpl18-1 mutant. Moreover, a loss-function of OsPRPL18 led to defects in plastid ribosome biogenesis and a serious reduction in the efficiency of plastid intron splicing. In all, these results suggested that PRPL18s play critical roles in plastid ribosome biogenesis, plastid intron splicing, and chloroplast development, and are essential for plant survival.
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Affiliation(s)
- Shujing Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinhuang Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yiqi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shijun Qiu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoqun Peng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinjue Xie
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yujie Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chancan Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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11
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Dupouy G, McDermott E, Cashell R, Scian A, McHale M, Ryder P, de Groot J, Lucca N, Brychkova G, McKeown PC, Spillane C. Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana. PLANT REPRODUCTION 2022; 35:189-204. [PMID: 35247095 PMCID: PMC9352626 DOI: 10.1007/s00497-022-00440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for early embryo development in A. thaliana, as homozygous loss-of-function mutations in the PRPL5 gene impairs chloroplast development and leads to embryo failure to develop past the globular stage. We confirmed the prpl5 embryo-lethal phenotype by generating a mutant CRISPR/Cas9 line and by genetic complementation. As PRPL5 underwent transfer to the nuclear genome early in the evolution of Embryophyta, PRPL5 can be expected to have acquired a chloroplast transit peptide. We identify and validate the presence of an N-terminal chloroplast transit peptide, but unexpectedly also confirm the presence of a conserved and functional Nuclear Localization Signal on the protein C-terminal end. This study highlights the fundamental role of the plastid translation machinery during the early stages of embryo development in plants and raises the possibility of additional roles of plastid ribosomal proteins in the nucleus.
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Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Emma McDermott
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Anna Scian
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Marcus McHale
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Joelle de Groot
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Noel Lucca
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
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12
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Protein Markers for the Identification of Cork Oak Plants Infected with Phytophthora cinnamomi by Applying an (α, β)-k-Feature Set Approach. FORESTS 2022. [DOI: 10.3390/f13060940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cork oak decline in Mediterranean forests is a complex phenomenon, observed with remarkable frequency in the southern part of the Iberian Peninsula, causing the weakening and death of these woody plants. The defoliation of the canopy, the presence of dry peripheral branches, and exudations on the trunk are visible symptoms used for the prognosis of decline, complemented by the presence of Phytophthora cinnamomi identified in the rhizosphere of the trees and adjacent soils. Recently, a large proteomic dataset obtained from the leaves of cork oak plants inoculated and non-inoculated with P. cinnamomi has become available. We explored it to search for an optimal set of proteins, markers of the biological pattern of interaction with the oomycete. Thus, using published data from the cork oak leaf proteome, we mathematically modelled the problem as an α, β-k-Feature Set Problem to select molecular markers. A set of proteins (features) that represent dominant effects on the host metabolism resulting from pathogen action on roots was found. These results contribute to an early diagnosis of biochemical changes occurring in cork oak associated with P. cinnamomi infection. We hypothesize that these markers may be decisive in identifying trees that go into decline due to interactions with the pathogen, assisting the management of cork oak forest ecosystems.
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13
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Yavari N, Gazestani VH, Wu BS, MacPherson S, Kushalappa A, Lefsrud MG. Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm. J Proteomics 2022; 265:104635. [PMID: 35659537 DOI: 10.1016/j.jprot.2022.104635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022]
Abstract
Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), or red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SIGNIFICANCE: Understanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution labeling proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. These multi-wavelengths lights function in a complex signaling network, which provide major challenges in inference of wavelength-specific molecular processes that underly the plant response. Besides, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further compare the changes to one another, rather than comparing plants proteome to FL, is thus necessary to gain the clear insights to specific underlying biological pathways and their effect consequences in plant response. Here, we employed narrow wavelength LED lights in our design to eliminate the potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the associates of proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant physiological processes particularly because of the tremendous increase in the amount of identified proteins which outreach the other biological data.
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Affiliation(s)
- Nafiseh Yavari
- Department of Bioresource Engineering, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-De-Bellevue, Quebec, Canada; Department of Electro-Chemistry Engineering, Dexcom, Inc., 6340 Sequence Dr., San Diego, CA, USA.
| | - Vahid H Gazestani
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA, USA
| | - Bo-Sen Wu
- Department of Bioresource Engineering, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-De-Bellevue, Quebec, Canada
| | - Sarah MacPherson
- Department of Bioresource Engineering, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-De-Bellevue, Quebec, Canada
| | - Ajjamada Kushalappa
- Department of Plant Science, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-De-Bellevue, Quebec, Canada
| | - Mark G Lefsrud
- Department of Bioresource Engineering, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-De-Bellevue, Quebec, Canada
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14
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Choudhury AR, Roy SK, Trivedi P, Choi J, Cho K, Yun SH, Walitang DI, Park JH, Kim K, Sa T. Label-free proteomics approach reveals candidate proteins in rice (Oryza sativa L.) important for ACC deaminase producing bacteria-mediated tolerance against salt stress. Environ Microbiol 2022; 24:3612-3624. [PMID: 35191581 DOI: 10.1111/1462-2920.15937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
The omics-based studies are important for identifying characteristic proteins in plants to elucidate the mechanism of ACC deaminase producing bacteria-mediated salt tolerance. This study evaluates the changes in the proteome of rice inoculated with ACC deaminase producing bacteria under salt stress conditions. Salt stress resulted in a significant decrease in photosynthetic pigments, whereas inoculation of Methylobacterium oryzae CBMB20 had significantly increased pigment contents under normal and salt stress conditions. A total of 76, 51 and 33 differentially abundant proteins (DAPs) were identified in non-inoculated salt stressed plants, bacteria inoculated plants under normal and salt stress conditions, respectively. The abundances of proteins responsible for ethylene emission and programmed cell death were increased, and that of photosynthesis-related proteins were decreased in non-inoculated plants under salt stress. Whereas, bacteria-inoculated plants had shown higher abundance of antioxidant proteins, RuBisCo and ribosomal proteins that are important for enhancing stress tolerance and improving plant physiological traits. Collectively, salt stress might affect plant physiological traits by impairing photosynthetic machinery and accelerating apoptosis leading to a decline in biomass. However, inoculation of plants with bacteria can assist in enhancing photosynthetic activity, antioxidant activities and ethylene regulation related proteins for attenuating salt induced apoptosis and sustaining growth and development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Aritra Roy Choudhury
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Republic of Korea.,Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Swapan Kumar Roy
- College of Agricultural Sciences, IUBAT-International University of Business Agriculture and Technology, Dhaka, Bangladesh
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeongyun Choi
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Republic of Korea.,Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Kun Cho
- Bio-chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Sung Ho Yun
- Bio-chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Denver I Walitang
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Republic of Korea.,College of Agriculture, Fisheries and Forestry, Romblon State University, Philippines
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Republic of Korea
| | - Kiyoon Kim
- National Forest Seed Variety Center, Chungju, Republic of Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Republic of Korea.,The Korean Academy of Science and Technology, Seongnam, Republic of Korea
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15
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Yang R, Yang Z, Peng Z, He F, Shi L, Dong Y, Ren M, Zhang Q, Geng G, Zhang S. Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance. PeerJ 2022; 9:e12683. [PMID: 35036157 PMCID: PMC8710252 DOI: 10.7717/peerj.12683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Background Soil salinity is a major environmental stress that restricts crop growth and yield. Methods Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism. Results In total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.
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Affiliation(s)
- Rui Yang
- Guizhou University, Guiyang, China
| | | | - Ze Peng
- Guizhou University, Guiyang, China
| | - Fang He
- Guizhou University, Guiyang, China
| | - Luxi Shi
- Guizhou University, Guiyang, China
| | | | - Mingjian Ren
- Guizhou University, Guiyang, China.,Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
| | | | | | - Suqin Zhang
- Guizhou University, Guiyang, China.,Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
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16
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Tang X, Shi F, Wang Y, Huang S, Zhao Y, Feng H. Proteomic analysis of a plastid gene encoding RPS4 mutant in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Funct Integr Genomics 2021; 22:113-130. [PMID: 34881421 DOI: 10.1007/s10142-021-00808-6] [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: 12/04/2020] [Revised: 02/20/2021] [Accepted: 09/18/2021] [Indexed: 10/19/2022]
Abstract
Plastids are important plant cell organelles containing a genome and bacterial-type 70S ribosomes-primarily composed of plastid ribosomal proteins and ribosomal RNAs. In this study, a chlorophyll-deficient mutant (cdm) obtained from double-haploid Chinese cabbage 'FT' was identified as a plastome mutant with an A-to-C base substitution in the plastid gene encoding the ribosomal protein RPS4. To further elucidate the function and regulatory mechanisms of RPS4, a comparative proteomic analysis was conducted between cdm and its wild-type 'FT' plants by isobaric tags and a relative and absolute quantitation (iTRAQ)-based strategy. A total of 6,245 proteins were identified, 540 of which were differentially abundant proteins (DAPs) in the leaves of cdm as compared to those of 'FT'-including 233 upregulated and 307 downregulated proteins. Upregulated DAPs were mainly involved in translation, organonitrogen compound biosynthetic process, ribosomes, and spliceosomes. Meanwhile, downregulated DAPs were mainly involved in photosynthesis, photosynthetic reaction centres, photosynthetic light harvesting, carbon fixation, and chlorophyll binding. These results indicated an important role of RPS4 in the regulation of growth and development of Chinese cabbage, possibly by regulating plastid translation activity by affecting the expression of specific photosynthesis- and cold stress-related proteins. Moreover, a multiple reaction monitoring (MRM) test and quantitative real-time polymerase chain reaction analysis confirmed our iTRAQ results. Quantitative proteomic analysis allowed us to confirm diverse changes in the metabolic pathways between cdm and 'FT' plants. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in Chinese cabbage.
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Affiliation(s)
- Xiaoyan Tang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding College of Horticulture, Anhui Agricultural University, 130 Changjiang West Road, Shushan District, Hefei, China
| | - Fengyan Shi
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yiheng Wang
- Biotechnology Research Institute, Xiqing District, Tianjin Academy of Agricultural Sciences, Jinjing Road 17 km, Tianjin, 300384, China
| | - Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Ying Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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17
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Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes. Genome Biol Evol 2021; 12:1841-1857. [PMID: 32722748 PMCID: PMC7586853 DOI: 10.1093/gbe/evaa155] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.
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Affiliation(s)
- Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Maria Imaculada Zucchi
- Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, SP, Brazil
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Cássio van den Berg
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BA, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
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18
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Zhou K, Zhang C, Xia J, Yun P, Wang Y, Ma T, Li Z. Albino seedling lethality 4; Chloroplast 30S Ribosomal Protein S1 is Required for Chloroplast Ribosome Biogenesis and Early Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2021; 14:47. [PMID: 34046768 PMCID: PMC8160077 DOI: 10.1186/s12284-021-00491-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Ribosomes responsible for transcription and translation of plastid-encoded proteins in chloroplasts are essential for chloroplast development and plant growth. Although most ribosomal proteins in plastids have been identified, the molecular mechanisms regulating chloroplast biogenesis remain to be investigated. RESULTS Here, we identified albinic seedling mutant albino seedling lethality 4 (asl4) caused by disruption of 30S ribosomal protein S1 that is targeted to the chloroplast. The mutant was defective in early chloroplast development and chlorophyll (Chl) biosynthesis. A 2855-bp deletion in the ASL4 allele was verified as responsible for the mutant phenotype by complementation tests. Expression analysis revealed that the ASL4 allele was highly expressed in leaf 4 sections and newly expanded leaves during early leaf development. Expression levels were increased by exposure to light following darkness. Some genes involved in chloroplast biogenesis were up-regulated and others down-regulated in asl4 mutant tissues compared to wild type. Plastid-encoded plastid RNA polymerase (PEP)-dependent photosynthesis genes and nuclear-encoded phage-type RNA polymerase (NEP)-dependent housekeeping genes were separately down-regulated and up-regulated, suggesting that plastid transcription was impaired in the mutant. Transcriptome and western blot analyses showed that levels of most plastid-encoded genes and proteins were reduced in the mutant. The decreased contents of chloroplast rRNAs and ribosomal proteins indicated that chloroplast ribosome biogenesis was impaired in the asl4 mutant. CONCLUSIONS Rice ASL4 encodes 30S ribosomal protein S1, which is targeted to the chloroplast. ASL4 is essential for chloroplast ribosome biogenesis and early chloroplast development. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.
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Affiliation(s)
- Kunneng Zhou
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Caijuan Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Jiafa Xia
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Peng Yun
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Yuanlei Wang
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Tingchen Ma
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Zefu Li
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China.
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19
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Gawroński P, Burdiak P, Scharff LB, Mielecki J, Górecka M, Zaborowska M, Leister D, Waszczak C, Karpiński S. CIA2 and CIA2-LIKE are required for optimal photosynthesis and stress responses in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:619-638. [PMID: 33119927 DOI: 10.1111/tpj.15058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 05/22/2023]
Abstract
Chloroplast-to-nucleus retrograde signaling is essential for cell function, acclimation to fluctuating environmental conditions, plant growth and development. The vast majority of chloroplast proteins are nuclear-encoded, and must be imported into the organelle after synthesis in the cytoplasm. This import is essential for the development of fully functional chloroplasts. On the other hand, functional chloroplasts act as sensors of environmental changes and can trigger acclimatory responses that influence nuclear gene expression. Signaling via mobile transcription factors (TFs) has been recently recognized as a way of communication between organelles and the nucleus. In this study, we performed a targeted reverse genetic screen to identify dual-localized TFs involved in chloroplast retrograde signaling during stress responses. We found that CHLOROPLAST IMPORT APPARATUS 2 (CIA2) has a functional plastid transit peptide, and can be located both in chloroplasts and the nucleus. Further, we found that CIA2, along with its homolog CIA2-like (CIL) are involved in the regulation of Arabidopsis responses to UV-AB, high light and heat shock. Finally, our results suggest that both CIA2 and CIL are crucial for chloroplast translation. Our results contribute to a deeper understanding of signaling events in the chloroplast-nucleus cross-talk.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Paweł Burdiak
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Lars B Scharff
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Jakub Mielecki
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Magdalena Górecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Magdalena Zaborowska
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, Planegg-Martinsried, 82152, Germany
| | - Cezary Waszczak
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
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20
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Dong X, Duan S, Wang H, Jin H. Plastid ribosomal protein LPE2 is involved in photosynthesis and the response to C/N balance in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1418-1432. [PMID: 31944575 PMCID: PMC7540278 DOI: 10.1111/jipb.12907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 01/09/2020] [Indexed: 05/31/2023]
Abstract
The balance between cellular carbon (C) and nitrogen (N) must be tightly coordinated to sustain optimal growth and development in plants. In chloroplasts, photosynthesis converts inorganic C to organic C, which is important for maintenance of C content in plant cells. However, little is known about the role of chloroplasts in C/N balance. Here, we identified a nuclear-encoded protein LOW PHOTOSYNTHETIC EFFICIENCY2 (LPE2) that it is required for photosynthesis and C/N balance in Arabidopsis. LPE2 is specifically localized in the chloroplast. Both loss-of-function mutants, lpe2-1 and lpe2-2, showed lower photosynthetic activity, characterized by slower electron transport and lower PSII quantum yield than the wild type. Notably, LPE2 is predicted to encode the plastid ribosomal protein S21 (RPS21). Deficiency of LPE2 significantly perturbed the thylakoid membrane composition and plastid protein accumulation, although the transcription of plastid genes is not affected obviously. More interestingly, transcriptome analysis indicated that the loss of LPE2 altered the expression of C and N response related genes in nucleus, which is confirmed by quantitative real-time-polymerase chain reaction. Moreover, deficiency of LPE2 suppressed the response of C/N balance in physiological level. Taken together, our findings suggest that LPE2 plays dual roles in photosynthesis and the response to C/N balance.
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Affiliation(s)
- Xiaoxiao Dong
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Sujuan Duan
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- School of Pharmaceutical SciencesGuangzhou University of Chinese MedicineGuangzhou510006China
| | - Hong‐Bin Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Hong‐Lei Jin
- School of Pharmaceutical SciencesGuangzhou University of Chinese MedicineGuangzhou510006China
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21
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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22
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OsCpn60β1 is Essential for Chloroplast Development in Rice ( Oryza sativa L.). Int J Mol Sci 2020; 21:ijms21114023. [PMID: 32512821 PMCID: PMC7313468 DOI: 10.3390/ijms21114023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/03/2023] Open
Abstract
The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types—Cpn60α and Cpn60β and the rice genome encodes three α and three β plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60β1, we attempted to disrupt the OsCpn60β1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60β1 knockout rice plants. The OsCpn60β1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60β1 mutant. In addition, OsCpn60β1 was located in the chloroplast and OsCpn60β1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60β1 mutants. These results indicate that OsCpn60β1 is essential for chloroplast development in rice.
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23
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Hu S, Ding Y, Zhu C. Sensitivity and Responses of Chloroplasts to Heat Stress in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:375. [PMID: 32300353 PMCID: PMC7142257 DOI: 10.3389/fpls.2020.00375] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Increased temperatures caused by global warming threaten agricultural production, as warmer conditions can inhibit plant growth and development or even destroy crops in extreme circumstances. Extensive research over the past several decades has revealed that chloroplasts, the photosynthetic organelles of plants, are highly sensitive to heat stress, which affects a variety of photosynthetic processes including chlorophyll biosynthesis, photochemical reactions, electron transport, and CO2 assimilation. Important mechanisms by which plant cells respond to heat stress to protect these photosynthetic organelles have been identified and analyzed. More recent studies have made it clear that chloroplasts play an important role in inducing the expression of nuclear heat-response genes during the heat stress response. In this review, we summarize these important advances in plant-based research and discuss how the sensitivity, responses, and signaling roles of chloroplasts contribute to plant heat sensitivity and tolerance.
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Affiliation(s)
| | | | - Cheng Zhu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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24
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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25
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Nagashima Y, Ohshiro K, Iwase A, Nakata MT, Maekawa S, Horiguchi G. The bRPS6-Family Protein RFC3 Prevents Interference by the Splicing Factor CFM3b during Plastid rRNA Biogenesis in Arabidopsis thaliana. PLANTS 2020; 9:plants9030328. [PMID: 32143506 PMCID: PMC7154815 DOI: 10.3390/plants9030328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/24/2020] [Accepted: 03/03/2020] [Indexed: 01/03/2023]
Abstract
Plastid ribosome biogenesis is important for plant growth and development. REGULATOR OF FATTY ACID COMPOSITION3 (RFC3) is a member of the bacterial ribosomal protein S6 family and is important for lateral root development. rfc3-2 dramatically reduces the plastid rRNA level and produces lateral roots that lack stem cells. In this study, we isolated a suppressor of rfc three2 (sprt2) mutant that enabled recovery of most rfc3 mutant phenotypes, including abnormal primary and lateral root development and reduced plastid rRNA level. Northern blotting showed that immature and mature plastid rRNA levels were reduced, with the exception of an early 23S rRNA intermediate, in rfc3-2 mutants. These changes were recovered in rfc3-2 sprt2-1 mutants, but a second defect in the processing of 16S rRNA appeared in this line. The results suggest that rfc3 mutants may be defective in at least two steps of plastid rRNA processing, one of which is specifically affected by the sprt2-1 mutation. sprt2-1 mutants had a mutation in CRM FAMILY MEMBER 3b (CFM3b), which encodes a plastid-localized splicing factor. A bimolecular fluorescence complementation (BiFC) assay suggested that RFC3 and SPRT2/CFM3b interact with each other in plastids. These results suggest that RFC3 suppresses the nonspecific action of SPRT2/CFM3b and improves the accuracy of plastid rRNA processing.
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Affiliation(s)
- Yumi Nagashima
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Katsutomo Ohshiro
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Akiyasu Iwase
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Miyuki T Nakata
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
- Current address: Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shugo Maekawa
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
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26
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Marino G, Naranjo B, Wang J, Penzler JF, Kleine T, Leister D. Relationship of GUN1 to FUG1 in chloroplast protein homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:521-535. [PMID: 31002470 DOI: 10.1111/tpj.14342] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/23/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
GUN1 integrates retrograde signals in chloroplasts but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcriptional level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and system-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transiently more pronounced phenotypes regarding photosynthesis, leaf colouration, growth and cold acclimation. The gun1-103 mutation also enhances variegation in the var2 mutant, increasing the fraction of white sectors, while fug1-3 suppresses the var2 phenotype. The transcriptomes of fug1-3 and gun1-103 plants are very similar, but absence of GUN1 alone has almost no effect on protein levels, whereas steady-state levels of chloroplast proteins are markedly decreased in fug1-3. In fug1 gun1 double mutants, effects on transcriptomes and particularly on proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased rates of synthesis (fug1) or degradation (var2) of chloroplast proteins, or by low temperatures. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 helps to maintain chloroplast protein homeostasis (proteostasis).
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Affiliation(s)
- Giada Marino
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Jing Wang
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Jan-Ferdinand Penzler
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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27
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Pesaresi P, Kim C. Current understanding of GUN1: a key mediator involved in biogenic retrograde signaling. PLANT CELL REPORTS 2019; 38:819-823. [PMID: 30671650 DOI: 10.1007/s00299-019-02383-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/16/2019] [Indexed: 05/21/2023]
Abstract
Chloroplast-nucleus communication takes place via processes called anterograde and retrograde signaling pathways. Discovery of the retrograde signaling pathways from the chloroplasts to the nucleus also raised an intriguing proposition that chloroplasts may serve as environmental sensors since multitudes of environmental factors disturb chloroplastic homeostasis. Certain chloroplastic perturbations, mostly impairing transcription/translation, are coupled to the repression of photosynthesis-associated nuclear genes (PhANGs), thus finely coordinating photosynthetic and chloroplastic homeostasis. The unbiased forward genetic screen in Arabidopsis leads to the identification of six independent loci called GENOMES UNCOUPLED (GUN), whose inactivation was found to de-repress the expression of PhANGs under certain conditions promoting retrograde signaling. Of the six GUNs, five encode proteins associated with tetrapyrrole biosynthesis and one, namely GUN1, encodes a member of the pentatricopeptide repeat protein family. Despite the fact that GUN1 plays a role as a central signaling mediator for retrograde communication, the molecular details of GUN1 protein still remain to be elucidated. Here, we recapitulate our current understanding of the GUN1-mediated retrograde signaling pathway and propose a possible mode of action of GUN1 in the chloroplasts together with different aspects of GUN1 protein activity that deserve further investigation.
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Affiliation(s)
- Paolo Pesaresi
- Department of Biosciences, University of Milano, 20133, Milan, Italy
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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28
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Cheng R, Gong L, Li Z, Liang YK. Rice BIG gene is required for seedling viability. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:39-50. [PMID: 30530202 DOI: 10.1016/j.jplph.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/04/2018] [Accepted: 11/04/2018] [Indexed: 05/07/2023]
Abstract
Arabidopsis BIG (AtBIG) gene encodes an enormous protein that is required for auxin transport. Loss of AtBIG function not only profoundly changes plant architecture but also alters plant adaptability to environmental stimuli. A putative homolog of AtBIG exists in the rice genome, but no function has been ascribed to it. In this study, we focus on the characterization of the gene structure and function of OsBIG. Sequence and phylogenetic analysis shows that the homologs of OsBIG have high amino acid conservation in several domains across species. Transgenic rice plants in which the expression of OsBIG was disrupted through the CRISPR/Cas9 system-mediated genome editing were used for phenotypic analysis. The Osbig/- plants show high levels of cell death, enhanced electrolyte leakage and membrane lipid peroxidation, and reduced chlorophyll content, which likely accounted for the seedling lethality. Moreover, gene expression between Osbig/- and wild-type plants analyzed by RNA-seq indicates that a number of metabolic and hormonal pathways including ribosome, DNA replication, photosynthesis, and chlorophyll metabolism were significantly perturbed by OsBIG deficiency. In summary, OsBIG gene is integral to the normal growth and development in rice.
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Affiliation(s)
- Rui Cheng
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Luping Gong
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhengzheng Li
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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29
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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.
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30
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Ng SM, Lee XW, Mat-Isa MN, Aizat-Juhari MA, Adam JH, Mohamed R, Wan KL, Firdaus-Raih M. Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. Sci Rep 2018; 8:17258. [PMID: 30467394 PMCID: PMC6250676 DOI: 10.1038/s41598-018-35173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the holoparasitic genus well-known for producing the largest single flower in the world. Our analyses of three transcriptome datasets, two holoparasites (R. cantleyi and Phelipanche aegyptiaca) and one photosynthetic plant (Arabidopsis thaliana), suggest that holoparasites, such as R. cantleyi, retain some common plastid associated processes such as biosynthesis of amino acids and lipids, but are missing photosynthesis components that can be extensions of these pathways. The reconstruction of two selected biosynthetic pathways involving plastids correlates the trend of plastid retention to pathway complexity - transcriptome evidence for R. cantleyi suggests alternate mechanisms in regulating the plastidial heme and terpenoid backbone biosynthesis pathways. The evolution to holoparasitism from autotrophy trends towards devolving the plastid genes to the nuclear genome despite the functional sites remaining in the plastid, or maintaining non-photosynthetic processes in the plastid, before the eventual loss of the plastid and any site dependent functions.
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Affiliation(s)
- Siuk-Mun Ng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Codon Genomics SB, No 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Xin-Wei Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Afiq Aizat-Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Jumaat Haji Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Rahmah Mohamed
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Mohd Firdaus-Raih
- Centre for Frontier Sciences, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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31
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Qiu Z, Chen D, He L, Zhang S, Yang Z, Zhang Y, Wang Z, Ren D, Qian Q, Guo L, Zhu L. The rice white green leaf 2 gene causes defects in chloroplast development and affects the plastid ribosomal protein S9. RICE (NEW YORK, N.Y.) 2018; 11:39. [PMID: 29995230 PMCID: PMC6041223 DOI: 10.1186/s12284-018-0233-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/04/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plastid ribosomal proteins (PRPs) play important roles in the translation of key proteins involved in chloroplast development and photosynthesis. PRPs have been widely studied in many plant species; however, few studies have investigated their roles in rice. RESULT In the present study, we used ethyl methane sulfonate mutagenesis and obtained a novel rice mutant called white green leaf 2 (wgl2). The wgl2 mutants exhibited an albino phenotype from germination through the three-leaf stage, and then gradually transitioned to green through the later developmental stages. Consistent with this albino phenotype, wgl2 mutants had abnormal chloroplasts and lower levels of photosynthetic pigments. Map-based cloning and DNA sequencing analyses of wgl2 revealed a single-nucleotide substitution (G to T) in the first exon of LOC_Os03g55930, which resulted in a substitution of glycine 92 to valine (G92 V). WGL2 encodes a conserved ribosomal protein, which localizes to the chloroplast. Complementation and targeted deletion experiments confirmed that the point mutation in WGL2 is responsible for the wgl2 mutant phenotype. WGL2 is preferentially expressed in the leaf, and mutating WGL2 led to obvious changes in the expression of genes related to chlorophyll biosynthesis, photosynthesis, chloroplast development, and ribosome development compared with wild-type. CONCLUSIONS WGL2 encodes a conserved ribosomal protein, which localizes to the chloroplast. WGL2 is essential for early chloroplast development in rice. These results facilitate research that will further uncover the molecular mechanism of chloroplast development.
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Affiliation(s)
- Zhennan Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Dongdong Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Lei He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Sen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zenan Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Yu Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhongwei Wang
- Biotechnology Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, 401329 China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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Tadini L, Ferrari R, Lehniger MK, Mizzotti C, Moratti F, Resentini F, Colombo M, Costa A, Masiero S, Pesaresi P. Trans-splicing of plastid rps12 transcripts, mediated by AtPPR4, is essential for embryo patterning in Arabidopsis thaliana. PLANTA 2018; 248:257-265. [PMID: 29687222 DOI: 10.1007/s00425-018-2896-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/17/2018] [Indexed: 05/21/2023]
Abstract
AtPPR4-mediated trans-splicing of plastid rps12 transcripts is essential for key embryo morphogenetic events such as development of cotyledons, determination of provascular tissue, and organization of the shoot apical meristem (SAM), but not for the formation of the protodermal layer. Members of the pentatricopeptide repeat (PPR) containing protein family have emerged as key regulators of the organelle post-transcriptional processing and to be essential for proper plant embryo development. In this study, we report the functional characterization of the AtPPR4 (At5g04810) gene encoding a plastid nucleoid PPR protein. In-situ hybridization analysis reveals the presence of AtPPR4 transcripts already at the transition stage of embryo development. As a consequence, embryos lacking the AtPPR4 protein arrest their development at the transition/early-heart stages and show defects in the determination of the provascular tissue and organization of SAM. This complex phenotype is due to the specific role of AtPPR4 in the trans-splicing of the plastid rps12 transcripts, as shown by northern and slot-blot hybridizations, and the consequent defect in 70S ribosome accumulation and plastid protein synthesis, in agreement with the role proposed for the maize orthologue, ZmPPR4.
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Affiliation(s)
- Luca Tadini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Roberto Ferrari
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Marie-Kristin Lehniger
- Molecular Genetics, Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Chiara Mizzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Fabio Moratti
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Francesca Resentini
- Instituto de Biologıa Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Monica Colombo
- Centro Ricerca e Innovazione, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Alex Costa
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| | - Paolo Pesaresi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli studi di Milano, Milan, Italy.
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Tang X, Wang Y, Zhang Y, Huang S, Liu Z, Fei D, Feng H. A missense mutation of plastid RPS4 is associated with chlorophyll deficiency in Chinese cabbage (Brassica campestris ssp. pekinensis). BMC PLANT BIOLOGY 2018; 18:130. [PMID: 29940850 PMCID: PMC6019835 DOI: 10.1186/s12870-018-1353-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 06/17/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plastome mutants are ideal resources for elucidating the functions of plastid genes. Numerous studies have been conducted for the function of plastid genes in barley and tobacco; however, related information is limited in Chinese cabbage. RESULTS A chlorophyll-deficient mutant of Chinese cabbage that was derived by ethyl methanesulfonate treatment on isolated microspores showed uniformly pale green inner leaves and slow growth compared with that shown by the wild type "Fukuda 50' ('FT'). Genetic analysis revealed that cdm was cytoplasmically inherited. Physiological and ultrastructural analyses of cdm showed impaired photosynthesis and abnormal chloroplast development. Utilizing next generation sequencing, the complete plastomes of cdm and 'FT' were respectively re-mapped to the reference genome of Chinese cabbage, and an A-to-C base substitution with a mutation ratio higher than 99% was detected. The missense mutation of plastid ribosomal protein S4 led to valine substitution for glycine at residue 193. The expression level of rps4 was analyzed using quantitative real-time PCR and found lower in than in 'FT'. RNA gel-blot assays showed that the abundance of mature 23S rRNA, 16S rRNA, 5S rRNA, and 4.5S rRNA significantly decreased and that the processing of 23S, 16S rRNA, and 4.5S rRNA was seriously impaired, affecting the ribosomal function in cdm. CONCLUSIONS These findings indicated that cdm was a plastome mutant and that chlorophyll deficiency might be due to an A-to-C base substitution of the plastome-encoded rps4 that impaired the rRNA processing and affected the ribosomal function.
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Affiliation(s)
- Xiaoyan Tang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yiheng Wang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yun Zhang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Shengnan Huang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Zhiyong Liu
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Danli Fei
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Hui Feng
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
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Nakata MT, Sato M, Wakazaki M, Sato N, Kojima K, Sekine A, Nakamura S, Shikanai T, Toyooka K, Tsukaya H, Horiguchi G. Plastid translation is essential for lateral root stem cell patterning in Arabidopsis thaliana. Biol Open 2018; 7:bio028175. [PMID: 29367414 PMCID: PMC5861355 DOI: 10.1242/bio.028175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/08/2018] [Indexed: 12/29/2022] Open
Abstract
The plastid evolved from a symbiotic cyanobacterial ancestor and is an essential organelle for plant life, but its developmental roles in roots have been largely overlooked. Here, we show that plastid translation is connected to the stem cell patterning in lateral root primordia. The RFC3 gene encodes a plastid-localized protein that is a conserved bacterial ribosomal protein S6 of β/γ proteobacterial origin. The rfc3 mutant developed lateral roots with disrupted stem cell patterning and associated with decreased leaf photosynthetic activity, reduced accumulation of plastid rRNAs in roots, altered root plastid gene expression, and changes in expression of several root stem cell regulators. These results suggest that deficiencies in plastid function affect lateral root stem cells. Treatment with the plastid translation inhibitor spectinomycin phenocopied the defective stem cell patterning in lateral roots and altered plastid gene expression observed in the rfc3 mutant. Additionally, when prps17 defective in a plastid ribosomal protein was treated with low concentrations of spectinomycin, it also phenocopied the lateral root phenotypes of rfc3 The spectinomycin treatment and rfc3 mutation also negatively affected symplasmic connectivity between primary root and lateral root primordia. This study highlights previously unrecognized functions of plastid translation in the stem cell patterning in lateral roots.
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Affiliation(s)
- Miyuki T Nakata
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Mayuko Sato
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mayumi Wakazaki
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Nozomi Sato
- Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Koji Kojima
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Akihiko Sekine
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Shiori Nakamura
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Toshiharu Shikanai
- Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kiminori Toyooka
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Tsukaya
- Graduate school of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Gorou Horiguchi
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
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35
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Robles P, Núñez-Delegido E, Ferrández-Ayela A, Sarmiento-Mañús R, Micol JL, Quesada V. Arabidopsis mTERF6 is required for leaf patterning. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 266:117-129. [PMID: 29241561 DOI: 10.1016/j.plantsci.2017.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/31/2017] [Accepted: 11/05/2017] [Indexed: 05/21/2023]
Abstract
To enhance our understanding of the roles of mitochondrial transcription termination factors (mTERFs) in plants, we have taken a reverse genetic approach in Arabidopsis thaliana. One of the mutants isolated carried a novel allele of the mTERF6 gene, which we named mterf6-5. mTERF6 is a chloroplast and mitochondrial localised protein required for the maturation of chloroplast isoleucine tRNA. The mterf6-5 plants are pale and exhibit markedly reduced growth, and altered leaf and chloroplast development. Our qRT-PCR analyses revealed mis-expression of several plastid, mitochondrial and nuclear genes in mterf6-5 plants. Synergistic phenotypes were observed in double mutant combinations of mterf6-5 with alleles of other mTERF genes as well as with scabra3-2, affected in the plastid RpoTp RNA polymerase; these observations suggest a functional relationship between mTERF6, other mTERFs and SCA3. The mterf6-5 mutation also enhanced the leaf dorsoventral polarity defects of the asymmetric leaves1-1 (as1-1) mutant, which resulted in radial leaves. This interaction seemed specific of the impaired mTERF6 function because mutations in the mTERF genes MDA1 or TWR-1/mTERF9 did not result in radialised leaves. Furthermore, the mterf6-5 mutation dramatically increased the leaf phenotype of as2-1 and caused lethality early in vegetative development. Our results uncover a new role for mTERF6 in leaf patterning and highlight the importance of mTERFs in plant development.
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Affiliation(s)
- Pedro Robles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Eva Núñez-Delegido
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | | | - Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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36
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Jeon Y, Ahn HK, Kang YW, Pai HS. Functional characterization of chloroplast-targeted RbgA GTPase in higher plants. PLANT MOLECULAR BIOLOGY 2017; 95:463-479. [PMID: 29038916 DOI: 10.1007/s11103-017-0664-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Plant RbgA GTPase is targeted to chloroplasts and co-fractionated with chloroplast ribosomes, and plays a role in chloroplast rRNA processing and/or ribosome biogenesis. Ribosome Biogenesis GTPase A (RbgA) homologs are evolutionarily conserved GTPases that are widely distributed in both prokaryotes and eukaryotes. In this study, we investigated functions of chloroplast-targeted RbgA. Nicotiana benthamiana RbgA (NbRbgA) and Arabidopsis thaliana RbgA (AtRbgA) contained a conserved GTP-binding domain and a plant-specific C-terminal domain. NbRbgA and AtRbgA were mainly localized in chloroplasts, and possessed GTPase activity. Since Arabidopsis rbgA null mutants exhibited an embryonic lethal phenotype, virus-induced gene silencing (VIGS) of NbRbgA was performed in N. benthamiana. NbRbgA VIGS resulted in a leaf-yellowing phenotype caused by disrupted chloroplast development. NbRbgA was mainly co-fractionated with 50S/70S ribosomes and interacted with the chloroplast ribosomal proteins cpRPL6 and cpRPL35. NbRbgA deficiency lowered the levels of mature 23S and 16S rRNAs in chloroplasts and caused processing defects. Sucrose density gradient sedimentation revealed that NbRbgA-deficient chloroplasts contained reduced levels of mature 23S and 16S rRNAs and diverse plastid-encoded mRNAs in the polysomal fractions, suggesting decreased protein translation activity in the chloroplasts. Interestingly, NbRbgA protein was highly unstable under high light stress, suggesting its possible involvement in the control of chloroplast ribosome biogenesis under environmental stresses. Collectively, these results suggest a role for RbgA GTPase in chloroplast rRNA processing/ribosome biogenesis, affecting chloroplast protein translation in higher plants.
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Affiliation(s)
- Young Jeon
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea
| | - Hee-Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea
| | - Yong Won Kang
- R&D Center, Morechem Co., Ltd., Yongin, Gyeonggi-do, 16954, South Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea.
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37
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Ye LS, Zhang Q, Pan H, Huang C, Yang ZN, Yu QB. EMB2738, which encodes a putative plastid-targeted GTP-binding protein, is essential for embryogenesis and chloroplast development in higher plants. PHYSIOLOGIA PLANTARUM 2017; 161:414-430. [PMID: 28675462 DOI: 10.1111/ppl.12603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
In higher plants, chloroplasts carry out many important functions, and normal chloroplast development is required for embryogenesis. Numerous chloroplast-targeted proteins involved in embryogenesis have been identified. Nevertheless, their functions remain unclear. In this study, a chloroplast-localized protein, EMB2738, was reported to be involved in Arabidopsis embryogenesis. EMB2738 knockout led to defective embryos, and the embryo development in emb2738 was interrupted after the globular stage. Complementation experiments identified the AT3G12080 locus as EMB2738. Cellular observation indicated that severely impaired chloroplast development was observed in these aborted embryos. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis showed that chloroplast-encoded photosynthetic genes, which are transcribed by plastid-encoded RNA polymerase (PEP), are predominantly decreased in defective embryogenesis, compared with those in the wild-type. In contrast, genes encoding PEP core subunits, which are transcribed by nucleus-encoded RNA polymerase (NEP), were increased. These results suggested that the knockout of EMB2738 strongly blocked chloroplast-encoded photosynthesis gene expression in embryos. Silencing of the EMB2738 orthologue in tobacco through a virus-induced genome silencing technique resulted in an albinism phenotype, vacuolated chloroplasts and decreased PEP-dependent plastid transcription. These results suggested that NtEMB2738 might be involved in plastid gene expression. Nevertheless, genetic analysis showed that the NtEMB2738 coding sequence could not fully rescue the defective embryogenesis of the emb2738 mutant, which suggested functional divergence between NtEMB2738 and EMB2738 in embryogenesis. Taken together, these results indicated that both EMB2738 and NtEMB2738 are involved in the expression of plastid genes in higher plants, and there is a functional divergence between NtEMB2738 and EMB2738 in embryogenesis.
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Affiliation(s)
- Lin-Shan Ye
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
- College of Tourism, Shanghai Normal University, Shanghai 200234, China
| | - Qin Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hui Pan
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
- College of Tourism, Shanghai Normal University, Shanghai 200234, China
| | - Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
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38
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Lu S, Li C, Zhang Y, Zheng Z, Liu D. Functional Disruption of a Chloroplast Pseudouridine Synthase Desensitizes Arabidopsis Plants to Phosphate Starvation. FRONTIERS IN PLANT SCIENCE 2017; 8:1421. [PMID: 28861101 PMCID: PMC5559850 DOI: 10.3389/fpls.2017.01421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/31/2017] [Indexed: 05/29/2023]
Abstract
Phosphate (Pi) deficiency is a common nutritional stress of plants in both agricultural and natural ecosystems. Plants respond to Pi starvation in the environment by triggering a suite of biochemical, physiological, and developmental changes that increase survival and growth. The key factors that determine plant sensitivity to Pi starvation, however, are unclear. In this research, we identified an Arabidopsis mutant, dps1, with greatly reduced sensitivity to Pi starvation. The dps1 phenotypes are caused by a mutation in the previously characterized SVR1 (SUPPRESSION OF VARIAGATION 1) gene, which encodes a chloroplast-localized pseudouridine synthase. The mutation of SVR1 results in defects in chloroplast rRNA biogenesis, which subsequently reduces chloroplast translation. Another mutant, rps5, which contains a mutation in the chloroplast ribosomal protein RPS5 and has reduced chloroplast translation, also displayed decreased sensitivity to Pi starvation. Furthermore, wild type plants treated with lincomycin, a chemical inhibitor of chloroplast translation, showed similar growth phenotypes and Pi starvation responses as dps1 and rps5. These results suggest that impaired chloroplast translation desensitizes plants to Pi starvation. Combined with previously published results showing that enhanced leaf photosynthesis augments plant responses to Pi starvation, we propose that the decrease in responses to Pi starvation in dps1, rps5, and lincomycin-treated plants is due to their reduced demand for Pi input from the environment.
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Affiliation(s)
| | | | | | | | - Dong Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
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Ahsan N, Chen M, Salvato F, Wilson RS, Shyama Prasad Rao R, Thelen JJ. Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis. J Proteomics 2017; 165:51-60. [DOI: 10.1016/j.jprot.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 01/21/2023]
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40
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Takáč T, Šamajová O, Pechan T, Luptovčiak I, Šamaj J. Feedback Microtubule Control and Microtubule-Actin Cross-talk in Arabidopsis Revealed by Integrative Proteomic and Cell Biology Analysis of KATANIN 1 Mutants. Mol Cell Proteomics 2017; 16:1591-1609. [PMID: 28706004 DOI: 10.1074/mcp.m117.068015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Indexed: 12/20/2022] Open
Abstract
Microtubule organization and dynamics are critical for key developmental processes such as cell division, elongation, and morphogenesis. Microtubule severing is an essential regulator of microtubules and is exclusively executed by KATANIN 1 in Arabidopsis In this study, we comparatively studied the proteome-wide effects in two KATANIN 1 mutants. Thus, shotgun proteomic analysis of roots and aerial parts of single nucleotide mutant fra2 and T-DNA insertion mutant ktn1-2 was carried out. We have detected 42 proteins differentially abundant in both fra2 and ktn1-2 KATANIN 1 dysfunction altered the abundance of proteins involved in development, metabolism, and stress responses. The differential regulation of tubulins and microtubule-destabilizing protein MDP25 implied a feedback microtubule control in KATANIN 1 mutants. Furthermore, deregulation of profilin 1, actin-depolymerizing factor 3, and actin 7 was observed. These findings were confirmed by immunoblotting analysis of actin and by microscopic observation of actin filaments using fluorescently labeled phalloidin. Results obtained by quantitative RT-PCR analysis revealed that changed protein abundances were not a consequence of altered expression levels of corresponding genes in the mutants. In conclusion, we show that abundances of several cytoskeletal proteins as well as organization of microtubules and the actin cytoskeleton are amended in accordance with defective microtubule severing.
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Affiliation(s)
- Tomáš Takáč
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Tibor Pechan
- §Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Starkville, Mississippi 39759
| | - Ivan Luptovčiak
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic;
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41
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Wang WJ, Zheng KL, Gong XD, Xu JL, Huang JR, Lin DZ, Dong YJ. The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:1-11. [PMID: 28483049 DOI: 10.1016/j.plantsci.2017.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 05/20/2023]
Abstract
Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.
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Affiliation(s)
- Wen-Juan Wang
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai-Lun Zheng
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Di Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; Institute of Genetics and Developmental Biology Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 10010, China
| | - Jian-Long Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ji-Rong Huang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong-Zhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Yan-Jun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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42
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Wang X, Chen L, Yang A, Bu C, He Y. Quantitative Proteomics Analysis of Developmental Reprogramming in Protoplasts of the Moss Physcomitrella patens. PLANT & CELL PHYSIOLOGY 2017; 58:946-961. [PMID: 28398533 DOI: 10.1093/pcp/pcx039] [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] [Received: 12/26/2014] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
The moss Physcomitrella patens is a model system for studying Plant developmental processes. To better understand the biochemical and physiological changes involved in developmental reprogramming, we conducted a quantitative proteomics analysis for protonemata, protoplasts made therefrom and protoplasts regenerated for 2 d. Using an iTRAQ peptide labeling strategy and liquid chromatography-tandem mass spectrometry (LC-MS/MS), >3,000 peptides and 1,000 proteins were quantified. Of these, 162 proteins were identified as having differential abundances during developmental reprogramming. These proteins were involved in various biological functions, such as defense, energy production, translation, metabolism, protein destination and storage, transcription, transport, cell growth/division, cell structure and signal transduction. Of these, the proteins involved in energy production and translation increased in abundance, while many of the metabolism and defense proteins decreased in abundance. In addition, most of the cell growth/division, protein stability and cell structure proteins were also down-regulated. This is the first report on the metabolic changes involved in developmental reprogramming in protoplasts. The significance of metabolic networks in developmental programming is beginning to emerge. Our study suggested that stress signals, energy metabolism and ribosomal proteins are pivotal components during developmental programming.
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Affiliation(s)
- Xiaoqin Wang
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit trees, Beijing University of Agriculture, Beijing, China
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Lu Chen
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aizhen Yang
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Chunya Bu
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing, China
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Du L, Zhang J, Qu S, Zhao Y, Su B, Lv X, Li R, Wan Y, Xiao J. The Pentratricopeptide Repeat Protein Pigment-Defective Mutant2 is Involved in the Regulation of Chloroplast Development and Chloroplast Gene Expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:747-759. [PMID: 28158776 DOI: 10.1093/pcp/pcx004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/08/2017] [Indexed: 05/10/2023]
Abstract
The development of functional chloroplasts, which is assisted by a series of nuclear-encoded auxiliary protein factors, is essential for plant autotrophic growth and development. To understand the molecular mechanisms underlying chloroplast development, we isolated and characterized a pigment-defective mutant, pdm2, and its corresponding variegated RNA interference (RNAi) lines in Arabidopsis. Sequence analysis revealed that PDM2 encodes a pentatricopeptide repeat protein that belongs to the P subgroup. Confocal microscopic analysis and immunoblotting of the chloroplast protein fraction showed that PDM2 was located in the stroma. In RNAi plants, protein-related photosynthesis was severely compromised. Furthermore, analysis of the transcript profile of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nuclear-encoded polymerase-dependent transcript levels were increased, in RNAi plants. In addition, PDM2 affects plastid RNA editing efficiency in most editing sites, apparently by directly interacting with multiple organellar RNA editing factor 2 (MORF2) and MORF9. Thus, our results demonstrate that PDM2 is probably involved in the regulation of plastid gene expression required for normal chloroplast development.
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Affiliation(s)
- Liang Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jian Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shaofeng Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Bodan Su
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xueqin Lv
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ruili Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jianwei Xiao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Ferrari R, Tadini L, Moratti F, Lehniger MK, Costa A, Rossi F, Colombo M, Masiero S, Schmitz-Linneweber C, Pesaresi P. CRP1 Protein: (dis)similarities between Arabidopsis thaliana and Zea mays. FRONTIERS IN PLANT SCIENCE 2017; 8:163. [PMID: 28261232 PMCID: PMC5309229 DOI: 10.3389/fpls.2017.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/26/2017] [Indexed: 05/25/2023]
Abstract
Biogenesis of chloroplasts in higher plants is initiated from proplastids, and involves a series of processes by which a plastid able to perform photosynthesis, to synthesize amino acids, lipids, and phytohormones is formed. All plastid protein complexes are composed of subunits encoded by the nucleus and chloroplast genomes, which require a coordinated gene expression to produce the correct concentrations of organellar proteins and to maintain organelle function. To achieve this, hundreds of nucleus-encoded factors are imported into the chloroplast to control plastid gene expression. Among these factors, members of the Pentatricopeptide Repeat (PPR) containing protein family have emerged as key regulators of the organellar post-transcriptional processing. PPR proteins represent a large family in plants, and the extent to which PPR functions are conserved between dicots and monocots deserves evaluation, in light of differences in photosynthetic metabolism (C3 vs. C4) and localization of chloroplast biogenesis (mesophyll vs. bundle sheath cells). In this work we investigated the role played in the process of chloroplast biogenesis by At5g42310, a member of the Arabidopsis PPR family which we here refer to as AtCRP1 (Chloroplast RNA Processing 1), providing a comparison with the orthologous ZmCRP1 protein from Zea mays. Loss-of-function atcrp1 mutants are characterized by yellow-albinotic cotyledons and leaves owing to defects in the accumulation of subunits of the thylakoid protein complexes. As in the case of ZmCRP1, AtCRP1 associates with the 5' UTRs of both psaC and, albeit very weakly, petA transcripts, indicating that the role of CRP1 as regulator of chloroplast protein synthesis has been conserved between maize and Arabidopsis. AtCRP1 also interacts with the petB-petD intergenic region and is required for the generation of petB and petD monocistronic RNAs. A similar role has been also attributed to ZmCRP1, although the direct interaction of ZmCRP1 with the petB-petD intergenic region has never been reported, which could indicate that AtCRP1 and ZmCRP1 differ, in part, in their plastid RNA targets.
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Affiliation(s)
- Roberto Ferrari
- Dipartimento di Bioscienze, Università degli studi di MilanoMilano, Italy
| | - Luca Tadini
- Dipartimento di Bioscienze, Università degli studi di MilanoMilano, Italy
| | - Fabio Moratti
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | | | - Alex Costa
- Dipartimento di Bioscienze, Università degli studi di MilanoMilano, Italy
| | - Fabio Rossi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli studi di MilanoMilano, Italy
| | - Monica Colombo
- Centro Ricerca e Innovazione, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli studi di MilanoMilano, Italy
| | | | - Paolo Pesaresi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli studi di MilanoMilano, Italy
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Fu S, Shao J, Zhou C, Hartung JS. Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:1419. [PMID: 28912786 PMCID: PMC5583216 DOI: 10.3389/fpls.2017.01419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/31/2017] [Indexed: 05/18/2023]
Abstract
Citrus tristeza is one of the most destructive citrus diseases and is caused by the phloem-restricted Closterovirus, Citrus tristeza virus. Mild strain CTV-B2 does not cause obvious symptoms on indicators whereas severe strain CTV-B6 causes symptoms, including stem pitting, cupping, yellowing, and stiffening of leaves, and vein corking. Our laboratory has previously characterized changes in transcription in sweet orange separately infected with CTV-B2 and CTV-B6. In the present study, transcriptome analysis of Citrus sinensis in response to double infection by CTV-B2 and CTV-B6 was carried out. Four hundred and eleven transcripts were up-regulated and 356 transcripts were down-regulated prior to the onset of symptoms. Repressed genes were overwhelmingly associated with photosynthesis, and carbon and nucleic acid metabolism. Expression of genes related to the glycolytic, oxidative pentose phosphate (OPP), tricarboxylic acid cycle (TCA) pathways, tetrapyrrole synthesis, redox homeostasis, nucleotide metabolism, protein synthesis and post translational protein modification and folding, and cell organization were all reduced. Ribosomal composition was also greatly altered in response to infection by CTV-B2/CTV-B6. Genes that were induced were related to cell wall structure, secondary and hormone metabolism, responses to biotic stress, regulation of transcription, signaling, and secondary metabolism. Transport systems dedicated to metal ions were especially disturbed and ZIPs (Zinc Transporter Precursors) showed different expression patterns in response to co-infection by CTV-B2/CTV-B6 and single infection by CTV-B2. Host plants experienced root decline that may have contributed to Zn, Fe, and other nutrient deficiencies. Though defense responses, such as, strengthening of the cell wall, alteration of hormone metabolism, secondary metabolites, and signaling pathways, were activated, these defense responses did not suppress the spread of the pathogens and the development of symptoms. The mild strain CTV-B2 did not provide a useful level of cross-protection to citrus against the severe strain CTV-B6.
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Affiliation(s)
- Shimin Fu
- Citrus Research Institute, Southwest UniversityChongqing, China
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Changyong Zhou
- Citrus Research Institute, Southwest UniversityChongqing, China
| | - John S. Hartung
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
- *Correspondence: John S. Hartung
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Pedroza-Garcia JA, Domenichini S, Bergounioux C, Benhamed M, Raynaud C. Chloroplasts around the plant cell cycle. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:107-113. [PMID: 27816816 DOI: 10.1016/j.pbi.2016.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 06/06/2023]
Abstract
Plastids arose from an endosymbiosis between a host cell and free-living bacteria. One key step during this evolutionary process has been the establishment of coordinated cell and symbiont division to allow the maintenance of organelles during proliferation of the host. However, surprisingly little is known about the underlying mechanisms. In addition, due to their central role in the cell's energetic metabolism and to their sensitivity to various environmental cues such as light or temperature, plastids are ideally fitted to be the source of signals allowing plants to adapt their development according to external conditions. Consistently, there is accumulating evidence that plastid-derived signals can impinge on cell cycle regulation. In this review, we summarize current knowledge of the dialogue between chloroplasts and the nucleus in the context of the cell cycle.
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Affiliation(s)
- José-Antonio Pedroza-Garcia
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Séverine Domenichini
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.
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47
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Yang J, Suzuki M, McCarty DR. Essential role of conserved DUF177A protein in plastid 23S rRNA accumulation and plant embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5447-5460. [PMID: 27574185 PMCID: PMC5049393 DOI: 10.1093/jxb/erw311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DUF177 proteins are nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, duf177 mutants in bacteria have not established a function. In contrast, duf177a mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize inbred W22, duf177a mutant embryos arrest at an early transition stage, whereas the block is suppressed in the B73 inbred background, conditioning an albino seedling phenotype. Background-dependent embryo lethal phenotypes are characteristic of maize plastid gene expression mutants. Consistent with the plastid gene expression hypothesis, quantitative real-time PCR revealed a significant reduction of 23S rRNA in an Escherichia coli duf177 knockout. Plastid 23S rRNA contents of duf177a mutant tissues were also markedly reduced compared with the wild-type, whereas plastid 16S, 5S, and 4.5S rRNA contents were less affected, indicating that DUF177 is specifically required for accumulation of prokaryote-type 23S rRNA. An AtDUF177A-green fluorescent protein (GFP) transgene controlled by the native AtDUF177A promoter fully complemented the Arabidopsis atduf177a mutant. Transient expression of AtDUF177A-GFP in Nicotiana benthamiana leaves showed that the protein was localized in chloroplasts. The essential role of DUF177A in chloroplast-ribosome formation is reminiscent of IOJAP, another highly conserved ribosome-associated protein, suggesting that key mechanisms controlling ribosome formation in plastids evolved from non-essential pathways for regulation of the prokaryotic ribosome.
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Affiliation(s)
- Jiani Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Masaharu Suzuki
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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48
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Echevarría-Zomeño S, Fernández-Calvino L, Castro-Sanz AB, López JA, Vázquez J, Castellano MM. Dissecting the proteome dynamics of the early heat stress response leading to plant survival or death in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1264-78. [PMID: 26580143 DOI: 10.1111/pce.12664] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 05/18/2023]
Abstract
In many plant species, an exposure to a sublethal temperature triggers an adaptative response called acclimation. This response involves an extensive molecular reprogramming that allows the plant to further survive to an otherwise lethal increase of temperature. A related response is also launched under an abrupt and lethal heat stress that, in this case, is unable to successfully promote thermotolerance and therefore ends up in plant death. Although these molecular programmes are expected to have common players, the overlapping degree and the specific regulators of each process are currently unknown. We have carried out a high-throughput comparative proteomics analysis during acclimation and during the early stages of the plant response to a severe heat stress that lead Arabidopsis seedlings either to survival or death. This analysis dissects these responses, unravels the common players and identifies the specific proteins associated with these different fates. Thermotolerance assays of mutants in genes with an uncharacterized role in heat stress demonstrate the relevance of this study to uncover both positive and negative heat regulators and pinpoint a pivotal role of JR1 and BAG6 in heat tolerance.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | | | - Ana B Castro-Sanz
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Juan Antonio López
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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49
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Zhao DS, Zhang CQ, Li QF, Yang QQ, Gu MH, Liu QQ. A residue substitution in the plastid ribosomal protein L12/AL1 produces defective plastid ribosome and causes early seedling lethality in rice. PLANT MOLECULAR BIOLOGY 2016; 91:161-77. [PMID: 26873698 DOI: 10.1007/s11103-016-0453-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/08/2016] [Indexed: 05/25/2023]
Abstract
The plastid ribosome is essential for chloroplast biogenesis as well as seedling formation. As the plastid ribosome closely resembles the prokaryotic 70S ribosome, many plastid ribosomal proteins (PRPs) have been identified in higher plants. However, their assembly in the chloroplast ribosome in rice remains unclear. In the present study, we identified a novel rice mutant, albino lethal 1 (al1), from a chromosome segment substitution line population. The al1 mutant displayed an albino phenotype at the seedling stage and did not survive past the three-leaf stage. No other apparent differences in plant morphology were observed in the al1 mutant. The albino phenotype of the al1 mutant was associated with decreased chlorophyll content and abnormal chloroplast morphology. Using fine mapping, AL1 was shown to encode the PRPL12, a protein localized in the chloroplasts of rice, and a spontaneous single-nucleotide mutation (C/T), resulting in a residue substitution from leucine in AL1 to phenylalanine in al1, was found to be responsible for the early seedling lethality. This point mutation is located at the L10 interface feature of the L12/AL1 protein. Yeast two-hybrid analysis showed that there was no physical interaction between al1 and PRPL10. In addition, the mutation had little effect on the transcript abundance of al1, but had a remarkable effect on the protein abundance of al1 and transcript abundance of chloroplast biogenesis-related and photosynthesis-related genes. These results provide a first glimpse into the molecular details of L12's function in rice.
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Affiliation(s)
- Dong-Sheng Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Chang-Quan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qian-Feng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qing-Qing Yang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Ming-Hong Gu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qiao-Quan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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50
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Zhang J, Yuan H, Yang Y, Fish T, Lyi SM, Thannhauser TW, Zhang L, Li L. Plastid ribosomal protein S5 is involved in photosynthesis, plant development, and cold stress tolerance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2731-44. [PMID: 27006483 PMCID: PMC4861020 DOI: 10.1093/jxb/erw106] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plastid ribosomal proteins are essential components of protein synthesis machinery and have diverse roles in plant growth and development. Mutations in plastid ribosomal proteins lead to a range of developmental phenotypes in plants. However, how they regulate these processes is not fully understood, and the functions of some individual plastid ribosomal proteins remain unknown. To identify genes responsible for chloroplast development, we isolated and characterized a mutant that exhibited pale yellow inner leaves with a reduced growth rate in Arabidopsis. The mutant (rps5) contained a missense mutation of plastid ribosomal protein S5 (RPS5), which caused a dramatically reduced abundance of chloroplast 16S rRNA and seriously impaired 16S rRNA processing to affect ribosome function and plastid translation. Comparative proteomic analysis revealed that the rps5 mutation suppressed the expression of a large number of core components involved in photosystems I and II as well as many plastid ribosomal proteins. Unexpectedly, a number of proteins associated with cold stress responses were greatly decreased in rps5, and overexpression of the plastid RPS5 improved plant cold stress tolerance. Our results indicate that RPS5 is an important constituent of the plastid 30S subunit and affects proteins involved in photosynthesis and cold stress responses to mediate plant growth and development.
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Affiliation(s)
- Junxiang Zhang
- College of Horticulture, State Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, 712100, China Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hui Yuan
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Sangbom M Lyi
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Theodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Lugang Zhang
- College of Horticulture, State Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, 712100, China
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
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