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Li Z, Wang W, Yu X, Zhao P, Li W, Zhang X, Peng M, Li S, Ruan M. Integrated analysis of DNA methylome and transcriptome revealing epigenetic regulation of CRIR1-promoted cold tolerance. BMC PLANT BIOLOGY 2024; 24:631. [PMID: 38965467 PMCID: PMC11225538 DOI: 10.1186/s12870-024-05285-0] [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: 03/07/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND DNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance. RESULTS In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance. CONCLUSIONS In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.
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Affiliation(s)
- Zhibo Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Wenjuan Wang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
- College of Tropical Crops, Hainan University, Haikou, 570228, P.R. China
| | - Xiaoling Yu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Pingjuan Zhao
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Wenbin Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Xiuchun Zhang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Ming Peng
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Shuxia Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China.
| | - Mengbin Ruan
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China.
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Venzhik Y, Deryabin A, Zhukova K. Au-Based Nanoparticles Enhance Low Temperature Tolerance in Wheat by Regulating Some Physiological Parameters and Gene Expression. PLANTS (BASEL, SWITZERLAND) 2024; 13:1261. [PMID: 38732476 PMCID: PMC11085431 DOI: 10.3390/plants13091261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
One of the key problems of biology is how plants adapt to unfavorable conditions, such as low temperatures. A special focus is placed on finding ways to increase tolerance in important agricultural crops like wheat. Au-based nanoparticles (Au-NPs) have been employed extensively in this area in recent years. Au-NPs can be produced fast and easily using low-cost chemical reagents. When employed in microdoses, Au-NPs are often non-toxic to plants, animals, and people. In addition, Au-NPs mainly have favorable impacts on plants. In this study, we investigated the effect of Au-NP seed nanopriming (diameter 15.3 nm, Au concentration 5-50 µg mL-1) on cold tolerance, as well as some physiological, biochemical and molecular parameters, of cold-sustainable wheat (Triticum aestivum L.) genotype Zlata. The treatment with Au-NPs improved tolerance to low temperatures in control conditions and after cold hardening. Au-NPs treatment boosted the intensity of growth processes, the quantity of photosynthetic pigments, sucrose in leaves, and the expressions of encoded RuBisCo and Wcor15 genes. The potential mechanisms of Au-NPs' influence on the cold tolerance of wheat varieties were considered.
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Affiliation(s)
- Yuliya Venzhik
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (A.D.); (K.Z.)
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Overlander-Chen M, Carlson CH, Fiedler JD, Yang S. Plastid terminal oxidase is required for chloroplast biogenesis in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1179-1190. [PMID: 37985448 DOI: 10.1111/tpj.16552] [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: 03/01/2022] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Chloroplast biogenesis is critical for crop biomass and economic yield. However, chloroplast development is a very complicated process coordinated by cross-communication between the nucleus and plastids, and the underlying mechanisms have not been fully revealed. To explore the regulatory machinery for chloroplast biogenesis, we conducted map-based cloning of the Grandpa 1 (Gpa1) gene regulating chloroplast development in barley. The spontaneous mutation gpa1.a caused a variegation phenotype of the leaf, dwarfed growth, reduced grain yield, and increased tiller number. Genetic mapping anchored the Gpa1 gene onto 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. One gene (HORVU.MOREX.r3.2HG0213170) in the delimited region encodes a putative plastid terminal oxidase (PTOX) in thylakoid membranes, which is homologous to IMMUTANS (IM) of Arabidopsis. The IM gene is required for chloroplast biogenesis and maintenance of functional thylakoids in Arabidopsis. Using CRISPR technology and gene transformation, we functionally validated that the PTOX-encoding gene, HORVU.MOREX.r3.2HG0213170, is the causal gene of Gpa1. Gene expression and chemical analysis revealed that the carotenoid biosynthesis pathway is suppressed by the gpa1 mutation, rendering mutants vulnerable to photobleaching. Our results showed that the overtillering associated with the gpa1 mutation was caused by the lower accumulation of carotenoid-derived strigolactones (SLs) in the mutant. The cloning of Gpa1 not only improves our understanding of the molecular mechanisms underlying chloroplast biosynthesis but also indicates that the PTOX activity is conserved between monocots and dicots for the establishment of the photosynthesis factory.
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Affiliation(s)
- Megan Overlander-Chen
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, North Dakota, 58102, USA
| | - Craig H Carlson
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, North Dakota, 58102, USA
- Department of Plant Sciences, North Dakota State University, North Dakota, 58102, USA
| | - Jason D Fiedler
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, North Dakota, 58102, USA
- Department of Plant Sciences, North Dakota State University, North Dakota, 58102, USA
| | - Shengming Yang
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, North Dakota, 58102, USA
- Department of Plant Sciences, North Dakota State University, North Dakota, 58102, USA
- Department of Plant Pathology, North Dakota State University, North Dakota, 58102, USA
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4
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Chen H, Zhang S, Du K, Kang X. Genome-wide identification, characterization, and expression analysis of CCT transcription factors in poplar. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108101. [PMID: 37922648 DOI: 10.1016/j.plaphy.2023.108101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
The CCT [CONSTANS (CO), CO-like, and TIMING OF CAB EXPRESSION1 (TOC1)] gene family is involved in photoperiodic flowering and adaptation to different environments. In this study, 39 CCT family genes from the poplar genome were identified and characterized, including 18 COL, 7 PRR, and 14 CMF TFs. Phylogenetics analysis showed that the PtrCCT gene family could be classified into five classes (Classes I-V) that have close relationships with Arabidopsis thaliana. Eight pairs of PtrCCTs had collinear relationships through interchromosomal synteny analysis in poplar, suggesting segmental duplication played a vital role in the expansion of the poplar CCT gene family. Besides, synteny analyses of the CCT members among poplar and different species provided more clues for PtrCCT gene family evolution. Cis-acting elements in the promoters of PtrCCTs predicted their involvement in light responses, hormone responses, biotic/abiotic stress responses, and plant growth and development. Eight members of the PpnCCT gene family were differentially expressed in the apical buds and leaves of triploid poplar compared to diploids. We then focused on PpnCCT39 upregulated in triploid poplars and showed that PpnCCT39 was localized in the nucleus, chloroplast, and cytoplasm and could interact with CLPP1 in the chloroplast. Overexpression of PpnCCT39 in poplar increased chlorophyll contents and enhanced photosynthetic rate. This study provided comprehensive information for the CCT gene family and set up a basis for its function identification in poplar.
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Affiliation(s)
- Hao Chen
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Shuwen Zhang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Kang Du
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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5
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Sun G, Yu H, Wang P, Lopez-Guerrero M, Mural RV, Mizero ON, Grzybowski M, Song B, van Dijk K, Schachtman DP, Zhang C, Schnable JC. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biol 2023; 24:55. [PMID: 36964601 PMCID: PMC10037803 DOI: 10.1186/s13059-023-02891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023] Open
Abstract
Background Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Conclusion Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions. Supplementary information The online version contains supplementary material available at 10.1186/s13059-023-02891-3.
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Affiliation(s)
- Guangchao Sun
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Huihui Yu
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - Peng Wang
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Martha Lopez-Guerrero
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Ravi V. Mural
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Olivier N. Mizero
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Marcin Grzybowski
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Baoxing Song
- grid.5386.8000000041936877XInstitute for Genomic Diversity, Cornell University, Ithaca, USA
| | - Karin van Dijk
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Daniel P. Schachtman
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Chi Zhang
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - James C. Schnable
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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6
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Kendrick R, Chotewutmontri P, Belcher S, Barkan A. Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize. THE PLANT CELL 2022; 34:4897-4919. [PMID: 36073948 PMCID: PMC9709983 DOI: 10.1093/plcell/koac276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 05/09/2023]
Abstract
Signals emanating from chloroplasts influence nuclear gene expression, but roles of retrograde signals during chloroplast development are unclear. To address this gap, we analyzed transcriptomes of non-photosynthetic maize mutants and compared them to transcriptomes of stages of normal leaf development. The transcriptomes of two albino mutants lacking plastid ribosomes resembled transcriptomes at very early stages of normal leaf development, whereas the transcriptomes of two chlorotic mutants with thylakoid targeting or plastid transcription defects resembled those at a slightly later stage. We identified ∼2,700 differentially expressed genes, which fall into six major categories based on the polarity and mutant-specificity of the change. Downregulated genes were generally expressed late in normal development and were enriched in photosynthesis genes, whereas upregulated genes act early and were enriched for functions in chloroplast biogenesis and cytosolic translation. We showed further that target-of-rapamycin (TOR) signaling was elevated in mutants lacking plastid ribosomes and declined in concert with plastid ribosome buildup during normal leaf development. Our results implicate three plastid signals as coordinators of photosynthetic differentiation. One signal requires plastid ribosomes and activates photosynthesis genes. A second signal reflects attainment of chloroplast maturity and represses chloroplast biogenesis genes. A third signal, the consumption of nutrients by developing chloroplasts, represses TOR, promoting termination of cell proliferation during leaf development.
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Affiliation(s)
- Rennie Kendrick
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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7
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Yang C, Yan W, Chang H, Sun C. Arabidopsis CIA2 and CIL have distinct and overlapping functions in regulating chloroplast and flower development. PLANT DIRECT 2022; 6:e380. [PMID: 35106435 PMCID: PMC8786619 DOI: 10.1002/pld3.380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/14/2021] [Accepted: 12/26/2021] [Indexed: 05/05/2023]
Abstract
Arabidopsis CHLOROPLAST IMPORT APPARATUS 2 (CIA2) and its paralogous protein CIA2-LIKE (CIL) are nuclear transcription factors containing a C-terminal CCT motif. CIA2 promotes the expression of nuclear genes encoding chloroplast-localized translocons and ribosomal proteins, thereby increasing the efficiency of protein import and synthesis in chloroplasts. We have previously reported that CIA2 and CIL form a homodimer or heterodimer through their C-terminal sequences and interact with other nuclear proteins, such as CONSTANS (CO), via their N-terminal sequences, but the function of CIL had remained unclear. In this study, we verified through transgenic cia2 mutant plants expressing the CIL coding sequence that CIL is partially functionally redundant to CIA2 during vegetative growth. We also compared phenotypes and gene expression profiles of wildtype Col-0, cia2, cil, and cia2/cil mutants. Our results indicate that CIA2 and CIL coordinate chloroplast biogenesis and function mainly by upregulating the expression of the nuclear factor GOLDEN2-LIKE 1 (GLK1) and chloroplast transcription-, translation-, protein import-, and photosynthesis-related genes, with CIA2 playing a more crucial role. Furthermore, we compared flowering phenotypes in single, double, and triple mutant plants of co, cia2, and cil. We found that CIA2 and CIL participate in modulating long-day floral development. Notably, CIA2 increases flower number and height of the inflorescence main axis, whereas CIL promotes flowering.
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Affiliation(s)
- Chun‐Yen Yang
- Department of Life SciencesNational Taiwan Normal UniversityTaipeiTaiwan
| | - Wen‐You Yan
- Department of Life SciencesNational Taiwan Normal UniversityTaipeiTaiwan
| | - Hsin‐Yen Chang
- Department of Life SciencesNational Taiwan Normal UniversityTaipeiTaiwan
| | - Chih‐Wen Sun
- Department of Life SciencesNational Taiwan Normal UniversityTaipeiTaiwan
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8
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Xu X, Legay S, Sergeant K, Zorzan S, Leclercq CC, Charton S, Giarola V, Liu X, Challabathula D, Renaut J, Hausman JF, Bartels D, Guerriero G. Molecular insights into plant desiccation tolerance: transcriptomics, proteomics and targeted metabolite profiling in Craterostigma plantagineum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:377-398. [PMID: 33901322 PMCID: PMC8453721 DOI: 10.1111/tpj.15294] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/05/2021] [Accepted: 04/19/2021] [Indexed: 05/31/2023]
Abstract
The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and targeted metabolite profiling was carried out on leaves collected from different stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 39 metabolites were differentially abundant across the different sampling points. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants for desiccation and recovery. The integrative analysis of all three data sets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The maintenance of cyclic electron flow and photorespiration, and the switch from C3 to crassulacean acid metabolism photosynthesis, may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. Transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid shunt may all play a role in energy management, together conferring bioenergetic advantages to meet energy demands upon rehydration. This study provides a high-resolution map of the changes occurring in primary metabolism during dehydration and rehydration and enriches our understanding of the molecular mechanisms underpinning plant desiccation tolerance. The data sets provided here will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.
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Affiliation(s)
- Xuan Xu
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Sylvain Legay
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Kjell Sergeant
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Simone Zorzan
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Céline C Leclercq
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Sophie Charton
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Xun Liu
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Dinakar Challabathula
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Jenny Renaut
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Jean-Francois Hausman
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Gea Guerriero
- GreenTech Innovation Centre, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, L-4362, Luxembourg
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9
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Li M, Ruwe H, Melzer M, Junker A, Hensel G, Tschiersch H, Schwenkert S, Chamas S, Schmitz-Linneweber C, Börner T, Stein N. The Arabidopsis AAC Proteins CIL and CIA2 Are Sub-functionalized Paralogs Involved in Chloroplast Development. FRONTIERS IN PLANT SCIENCE 2021; 12:681375. [PMID: 34163512 PMCID: PMC8215611 DOI: 10.3389/fpls.2021.681375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 05/22/2023]
Abstract
The Arabidopsis gene Chloroplast Import Apparatus 2 (CIA2) encodes a transcription factor that positively affects the activity of nuclear genes for chloroplast ribosomal proteins and chloroplast protein import machineries. CIA2-like (CIL) is the paralogous gene of CIA2. We generated a cil mutant by site-directed mutagenesis and compared it with cia2 and cia2cil double mutant. Phenotype of the cil mutant did not differ from the wild type under our growth conditions, except faster growth and earlier time to flowering. Compared to cia2, the cia2cil mutant showed more impaired chloroplast functions and reduced amounts of plastid ribosomal RNAs. In silico analyses predict for CIA2 and CIL a C-terminal CCT domain and an N-terminal chloroplast transit peptide (cTP). Chloroplast (and potentially nuclear) localization was previously shown for HvCMF3 and HvCMF7, the homologs of CIA2 and CIL in barley. We observed nuclear localization of CIL after transient expression in Arabidopsis protoplasts. Surprisingly, transformation of cia2 with HvCMF3, HvCMF7, or with a truncated CIA2 lacking the predicted cTP could partially rescue the pale-green phenotype of cia2. These data are discussed with respect to potentially overlapping functions between CIA2, CIL, and their barley homologs and to the function of the putative cTPs of CIA2 and CIL.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Rhoda Erdmann Haus, Berlin, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, IPK, Gatersleben, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | - Henning Tschiersch
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, IPK, Gatersleben, Germany
| | - Serena Schwenkert
- Department of Biology I, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Sindy Chamas
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | | | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Rhoda Erdmann Haus, Berlin, Germany
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-Universität Göttingen, Göttingen, Germany
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10
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Loudya N, Mishra P, Takahagi K, Uehara-Yamaguchi Y, Inoue K, Bogre L, Mochida K, López-Juez E. Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf. Genome Biol 2021; 22:151. [PMID: 33975629 PMCID: PMC8111775 DOI: 10.1186/s13059-021-02366-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/26/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. RESULTS Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. CONCLUSIONS Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.
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Affiliation(s)
- Naresh Loudya
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Priyanka Mishra
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | | | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Laszlo Bogre
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan.
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, Japan.
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
| | - Enrique López-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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11
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Bashyal BM, Parmar P, Zaidi NW, Aggarwal R. Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice ( Oryza sativa L.). Front Microbiol 2021; 12:655165. [PMID: 33927706 PMCID: PMC8076752 DOI: 10.3389/fmicb.2021.655165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
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12
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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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13
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Mengarelli DA, Zanor MI. Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max). PLANTA 2021; 253:15. [PMID: 33392793 DOI: 10.1007/s00425-020-03537-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/11/2020] [Indexed: 05/27/2023]
Abstract
MAIN CONCLUSION Soybean possesses 19 CMF genes which mainly arose from duplication events. Their features and motifs are highly conserved but transcriptional data indicated functional diversity in metabolism and stress responses. CCT [for CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)] domain-containing genes play important roles in regulating flowering, plant growth, and grain yield and are also involved in stress responses. The CMF (CCT motif family) genes, included in the CCT family, contain a single CCT domain as the only identifiable domain in their predicted protein sequence and are interesting targets for breeding programs. In this study, we identified 19 putative GmCMF genes, based on the latest soybean (Glycine max) genome annotation. The predicted GmCMF proteins were characterized based on conserved structural features, and a phylogenetic tree was constructed including all CMF proteins from rice and Arabidopsis as representative examples of the monocotyledonous (monocot) and dicotyledonous (dicot) plants, respectively. High similarities in the conserved motifs of the protein sequences and the gene structures were found. In addition, by analyzing the CMF gene family in soybean, we identified seven pairs of genes that originated from segmental chromosomal duplication events attributable to the most recent whole-genome duplication (WGD) event in the Glycine lineage. Expression analysis of GmCMF genes in various tissues and after specific treatments demonstrated tissue and stress-response specific differential expression. Gene expression analysis was complemented by the identification of putative cis-elements present in the promoter regions of the genes through a bioinformatics approach, using the existing soybean reference genome sequence and gene models. Co-functional networks inferred from distinct types of genomics data-including microarrays and RNA-seq samples from soybean-revealed that GmCMF genes might play crucial roles in metabolism and transport processes. The results of this study, the first systematic analysis of the soybean CCT gene family, can serve as a strong foundation for further elucidation of their physiological functions and biological roles.
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14
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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15
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Yang CY, Sun CW. Sequence analysis and protein interactions of Arabidopsis CIA2 and CIL proteins. BOTANICAL STUDIES 2020; 61:20. [PMID: 32556735 PMCID: PMC7303255 DOI: 10.1186/s40529-020-00297-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/11/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND A previous screening of Arabidopsis thaliana for mutants exhibiting dysfunctional chloroplast protein transport identified the chloroplast import apparatus (cia) gene. The cia2 mutant has a pale green phenotype and reduced rate of protein import into chloroplasts, but leaf shape and size are similar to wild-type plants of the same developmental stage. Microarray analysis showed that nuclear CIA2 protein enhances expression of the Toc75, Toc33, CPN10 and cpRPs genes, thereby up-regulating protein import and synthesis efficiency in chloroplasts. CIA2-like (CIL) shares 65% sequence identity to CIA2, suggesting that CIL and CIA2 are homologous proteins in Arabidopsis. Here, we further assess the protein interactions and sequence features of CIA2 and CIL. RESULTS Subcellular localizations of truncated CIA2 protein fragments in our onion transient assay demonstrate that CIA2 contains two nuclear localization signals (NLS) located at amino acids (aa) 62-65 and 291-308, whereas CIL has only one NLS at aa 47-50. We screened a yeast two-hybrid (Y2H) Arabidopsis cDNA library to search for putative CIA2-interacting proteins and identified 12 nuclear proteins, including itself, CIL, and flowering-control proteins (such as CO, NF-YB1, NF-YC1, NF-YC9 and ABI3). Additional Y2H experiments demonstrate that CIA2 and CIL mainly interact with flowering-control proteins via their N-termini, but preferentially form homo- or hetero-dimers through their C-termini. Moreover, sequence alignment showed that the N-terminal sequences of CIA2, CIL and NF-YA are highly conserved. Therefore, NF-YA in the NF-Y complex could be substituted by CIA2 or CIL. CONCLUSIONS We show that Arabidopsis CIA2 and CIL can interact with CO and NF-Y complex, so not only may they contribute to regulate chloroplast function but also to modulate flower development.
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Affiliation(s)
- Chun-Yen Yang
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Chih-Wen Sun
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan.
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16
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Dong Z, Li J, Chen L, Wang S, Liu Q, Shao T. Using proteomics to decipher the effect of tissue damage on the fate of red clover proteins during ensiling. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2019.114271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize. Genomics 2019; 112:1233-1244. [PMID: 31323298 DOI: 10.1016/j.ygeno.2019.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/26/2019] [Accepted: 07/15/2019] [Indexed: 11/23/2022]
Abstract
AT-hook motif nuclear localized (AHL) genes have diverse but poorly understood biological functions. We identified and analyzed 37 AHL genes in maize. We also discovered four and one additional AHLs in rice and sorghum, respectively, besides those reported earlier. The maize AHLs were classified into two clades (A and B) and three distinct types (I, II, and III) as also reported in Arabidopsis. Phylogenetic and ortholog analyses showed that, while the evolutionary classification was conserved in plants, expansion of the AHL gene family in maize was accompanied with new biological functions. Gene structure analysis showed that, while all but one Type-I AHLs lacked an intron, origin of Type-II and Type-III AHLs was associated with the gain of introns suggesting evolutionarily distinct temporal and spatial expression patterns and, likely, neofunctionalization. Gene duplication analysis revealed that AHLs in maize expanded via dispersive duplication further supporting their functional diversity. To discern these functions, we analyzed 71 transcriptomes from diverse tissues and developmental stages of maize and classified AHLs into eight groups with distinct temporal/spatial expression profiles. Coexpression analysis implicated 5 AHLs and 33 novel genes in networks specific to endosperm, seed, root, leaf, and reproductive tissues indicating their role in the development of these organs. Major processes coregulated by AHLs include pollen development, drought response, senescence, and wound response. We also identified interactions of AHL proteins in coregulating important processes including stress response. These novel insights into the role of AHLs in plant development provide a platform for functional analyses in maize and related grasses.
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18
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Li M, Hensel G, Mascher M, Melzer M, Budhagatapalli N, Rutten T, Himmelbach A, Beier S, Korzun V, Kumlehn J, Börner T, Stein N. Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain Gene in albostrians Barley. THE PLANT CELL 2019; 31:1430-1445. [PMID: 31023840 PMCID: PMC6635869 DOI: 10.1105/tpc.19.00132] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/23/2019] [Indexed: 05/17/2023]
Abstract
Chloroplasts fuel plant development and growth by converting solar energy into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley (Hordeum vulgare) has greatly broadened the field of chloroplast biology, including the discovery of retrograde signaling. Here, we report identification of the ALBOSTRIANS gene HvAST (also known as Hordeum vulgare CCT Motif Family gene 7, HvCMF7) by positional cloning as well as its functional validation based on independently induced mutants by Targeting Induced Local Lesions in Genomes (TILLING) and RNA-guided clustered regularly interspaced short palindromic repeats-associated protein 9 endonuclease-mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvCMF7 in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvCMF7 is a homolog of the Arabidopsis (Arabidopsis thaliana) CONSTANS, CO-like, and TOC1 (CCT) Motif transcription factor gene CHLOROPLAST IMPORT APPARATUS2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Notably, in barley we localized HvCMF7 to the chloroplast, without any clear evidence for nuclear localization.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Molecular Genetics Group, Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Goetz Hensel
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Martin Mascher
- Domestication Genomics Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Nagaveni Budhagatapalli
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Twan Rutten
- Structural Cell Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Axel Himmelbach
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Sebastian Beier
- Bioinformatics and Information Technology Group, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | | | - Jochen Kumlehn
- Plant Reproductive Biology Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Thomas Börner
- Molecular Genetics Group, Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Nils Stein
- Genomics of Genetic Resources Group, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
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19
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Osella AV, Mengarelli DA, Mateos J, Dong S, Yanovsky MJ, Balazadeh S, Valle EM, Zanor MI. FITNESS, a CCT domain-containing protein, deregulates reactive oxygen species levels and leads to fine-tuning trade-offs between reproductive success and defence responses in Arabidopsis. PLANT, CELL & ENVIRONMENT 2018; 41:2328-2341. [PMID: 29852518 DOI: 10.1111/pce.13354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/18/2018] [Indexed: 05/22/2023]
Abstract
Environmental stresses are the major factors that limit productivity in plants. Here, we report on the function of an uncharacterized gene At1g07050, encoding a CCT domain-containing protein, from Arabidopsis thaliana. At1g07050 expression is highly repressed by oxidative stress. We used metabolomics, biochemical, and genomic approaches to analyse performance of transgenic lines with altered expression of At1g07050 under normal and oxidative stress conditions. At1g07050 overexpressing lines showed increased levels of reactive oxygen species (ROS), whereas knock-out mutants exhibited decreased levels of ROS and higher tolerance to oxidative stress generated in the chloroplast. Our results uncover a role for At1g07050 in cellular redox homeostasis controlling H2 O2 levels, due to changes in enzymes, metabolites, and transcripts related to ROS detoxification. Therefore, we call this gene FITNESS. Additionally, several genes such as ACD6, PCC1, and ICS1 related to salicylic acid signalling and defence were found differentially expressed among the lines. Notably, FITNESS absence significantly improved seed yield suggesting an effective fine-tuning trade-off between reproductive success and defence responses.
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Affiliation(s)
- Ana Virginia Osella
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Ocampo y Esmeralda PREDIO CCT-Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR), Rosario, Argentina
| | - Diego Alberto Mengarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Ocampo y Esmeralda PREDIO CCT-Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR), Rosario, Argentina
| | - Julieta Mateos
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Shuchao Dong
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Salma Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Estela Marta Valle
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Ocampo y Esmeralda PREDIO CCT-Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR), Rosario, Argentina
| | - María Inés Zanor
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Ocampo y Esmeralda PREDIO CCT-Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR), Rosario, Argentina
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20
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Rizal G, Karki S, Thakur V, Wanchana S, Alonso-Cantabrana H, Dionora J, Sheehy JE, Furbank R, von Caemmerer S, Quick WP. A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio. PLoS One 2017. [PMID: 28640841 PMCID: PMC5480886 DOI: 10.1371/journal.pone.0179567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent efforts to engineer C4 photosynthetic traits into C3 plants such as rice demand an understanding of the genetic elements that enable C4 plants to outperform C3 plants. As a part of the C4 Rice Consortium’s efforts to identify genes needed to support C4 photosynthesis, EMS mutagenized sorghum populations were generated and screened to identify genes that cause a loss of C4 function. Stable carbon isotope ratio (δ13C) of leaf dry matter has been used to distinguishspecies with C3 and C4 photosynthetic pathways. Here, we report the identification of a sorghum (Sorghum bicolor) mutant with a low δ13C characteristic. A mutant (named Mut33) with a pale phenotype and stunted growth was identified from an EMS treated sorghum M2 population. The stable carbon isotope analysis of the mutants showed a decrease of 13C uptake capacity. The noise of random mutation was reduced by crossing the mutant and its wildtype (WT). The back-cross (BC1F1) progenies were like the WT parent in terms of 13C values and plant phenotypes. All the BC1F2 plants with low δ13C died before they produced their 6th leaf. Gas exchange measurements of the low δ13C sorghum mutants showed a higher CO2 compensation point (25.24 μmol CO2.mol-1air) and the maximum rate of photosynthesis was less than 5μmol.m-2.s-1. To identify the genetic determinant of this trait, four DNA pools were isolated; two each from normal and low δ13C BC1F2 mutant plants. These were sequenced using an Illumina platform. Comparison of allele frequency of the single nucleotide polymorphisms (SNPs) between the pools with contrasting phenotype showed that a locus in Chromosome 10 between 57,941,104 and 59,985,708 bps had an allele frequency of 1. There were 211 mutations and 37 genes in the locus, out of which mutations in 9 genes showed non-synonymous changes. This finding is expected to contribute to future research on the identification of the causal factor differentiating C4 from C3 species that can be used in the transformation of C3 to C4 plants.
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Affiliation(s)
- Govinda Rizal
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
| | - Shanta Karki
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
- Government of Nepal, Ministry of Agricultural Development, Kathmandu, Nepal
| | - Vivek Thakur
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Hugo Alonso-Cantabrana
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Jacque Dionora
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
| | - John E. Sheehy
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
- University of Sheffield, Sheffield, United Kingdom
| | - Robert Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - William Paul Quick
- C4 Rice Center, IRRI, Los Banos, Laguna, the Philippines
- University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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van Campen JC, Yaapar MN, Narawatthana S, Lehmeier C, Wanchana S, Thakur V, Chater C, Kelly S, Rolfe SA, Quick WP, Fleming AJ. Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development. PLANT PHYSIOLOGY 2016; 170:1655-74. [PMID: 26813793 PMCID: PMC4775128 DOI: 10.1104/pp.15.01624] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/22/2016] [Indexed: 05/24/2023]
Abstract
Leaves are derived from heterotrophic meristem tissue that, at some point, must make the transition to autotrophy via the initiation of photosynthesis. However, the timing and spatial coordination of the molecular and cellular processes underpinning this switch are poorly characterized. Here, we report on the identification of a specific stage in rice (Oryza sativa) leaf development (P3/P4 transition) when photosynthetic competence is first established. Using a combined physiological and molecular approach, we show that elements of stomatal and vascular differentiation are coordinated with the onset of measurable light absorption for photosynthesis. Moreover, by exploring the response of the system to environmental perturbation, we show that the earliest stages of rice leaf development have significant plasticity with respect to elements of cellular differentiation of relevance for mature leaf photosynthetic performance. Finally, by performing an RNA sequencing analysis targeted at the early stages of rice leaf development, we uncover a palette of genes whose expression likely underpins the acquisition of photosynthetic capability. Our results identify the P3/P4 transition as a highly dynamic stage in rice leaf development when several processes for the initiation of photosynthetic competence are coordinated. As well as identifying gene targets for future manipulation of rice leaf structure/function, our data highlight a developmental window during which such manipulations are likely to be most effective.
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Affiliation(s)
- Julia C van Campen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Muhammad N Yaapar
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Supatthra Narawatthana
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Christoph Lehmeier
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Samart Wanchana
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Vivek Thakur
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Caspar Chater
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Steve Kelly
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - W Paul Quick
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
| | - Andrew J Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom (J.C.v.C., M.N.Y., S.N., C.L., C.C., S.A.R., A.J.F.);International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines (S.W., V.T., W.P.Q.);National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani 12120, Thailand (S.W.);Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Mexico (C.C.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.)
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Baute J, Herman D, Coppens F, De Block J, Slabbinck B, Dell'Acqua M, Pè ME, Maere S, Nelissen H, Inzé D. Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network. PLANT PHYSIOLOGY 2016; 170:1848-67. [PMID: 26754667 PMCID: PMC4775144 DOI: 10.1104/pp.15.01883] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/07/2016] [Indexed: 05/20/2023]
Abstract
Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with in-depth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement.
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Affiliation(s)
- Joke Baute
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dorota Herman
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Frederik Coppens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Jolien De Block
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Bram Slabbinck
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Matteo Dell'Acqua
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Mario Enrico Pè
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Steven Maere
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Hilde Nelissen
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
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Wang Z, Fang B, Chen X, Liao M, Chen J, Zhang X, Huang L, Luo Z, Yao Z, Li Y. Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas). BMC PLANT BIOLOGY 2015; 15:180. [PMID: 26174091 PMCID: PMC4502468 DOI: 10.1186/s12870-015-0567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development. RESULTS Here, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development. CONCLUSIONS The results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality.
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Affiliation(s)
- Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Boping Fang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xinliang Chen
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Minghuan Liao
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jingyi Chen
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xiongjian Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Lifei Huang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Zhongxia Luo
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Zhufang Yao
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Yujun Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Ganguly D, Crisp P, Harter K, Pogson BJ, Albrecht-Borth V. Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways. FUNCTIONAL PLANT BIOLOGY : FPB 2015; 42:676-686. [PMID: 32480711 DOI: 10.1071/fp15026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/02/2015] [Indexed: 06/11/2023]
Abstract
Plant development is regulated by external and internal factors such as light and chloroplast development. A revertant of the Arabidopsis thaliana (L.) Heyhn. chloroplast biogenesis mutant snowy cotyledon 3 (sco3-1) was isolated partially recovering the impaired chloroplast phenotype. The mutation was identified in the Phytochrome B (PhyB) gene and is a result of an amino acid change within the PAS repeat domain required for light-induced nuclear localisation. An independent phyB-9 mutation was crossed into sco3-1 mutants, resulting in the same partial reversion of sco3-1. Further analysis demonstrated that SCO3 and PhyB influence the greening process of seedlings and rosette leaves, embryogenesis, rosette formation and flowering. Interestingly, the functions of these proteins are interwoven in various ways, suggesting a complex genetic interaction. Whole-transcriptome profiling of sco3-1phyB-9 indicated that a completely distinct set of genes was differentially regulated in the double mutant compared with the single sco3-1 or phyB-9 mutants. Thus, we hypothesise that PhyB and SCO3 genetically suppress each other in plant and chloroplast development.
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Affiliation(s)
- Diep Ganguly
- ARC (Australian Research Council) Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, ACT 0200, Australia
| | - Peter Crisp
- ARC (Australian Research Council) Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, ACT 0200, Australia
| | - Klaus Harter
- Zentrum für Molekularbiologie der Pflanzen, Plant Physiology, University of Tübingen, 72076 Tübingen, Germany
| | - Barry J Pogson
- ARC (Australian Research Council) Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, ACT 0200, Australia
| | - Verónica Albrecht-Borth
- ARC (Australian Research Council) Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, ACT 0200, Australia
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Ling Q, Jarvis P. Functions of plastid protein import and the ubiquitin-proteasome system in plastid development. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:939-48. [PMID: 25762164 DOI: 10.1016/j.bbabio.2015.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 02/05/2023]
Abstract
Plastids, such as chloroplasts, are widely distributed endosymbiotic organelles in plants and algae. Apart from their well-known functions in photosynthesis, they have roles in processes as diverse as signal sensing, fruit ripening, and seed development. As most plastid proteins are produced in the cytosol, plastids have developed dedicated translocon machineries for protein import, comprising the TOC (translocon at the outer envelope membrane of chloroplasts) and TIC (translocon at the inner envelope membrane of chloroplasts) complexes. Multiple lines of evidence reveal that protein import via the TOC complex is actively regulated, based on the specific interplay between distinct receptor isoforms and diverse client proteins. In this review, we summarize recent advances in our understanding of protein import regulation, particularly in relation to control by the ubiquitin-proteasome system (UPS), and how such regulation changes plastid development. The diversity of plastid import receptors (and of corresponding preprotein substrates) has a determining role in plastid differentiation and interconversion. The controllable turnover of TOC components by the UPS influences the developmental fate of plastids, which is fundamentally linked to plant development. Understanding the mechanisms by which plastid protein import is controlled is critical to the development of breakthrough approaches to increase the yield, quality and stress tolerance of important crop plants, which are highly dependent on plastid development. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Paul Jarvis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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Demarsy E, Lakshmanan AM, Kessler F. Border control: selectivity of chloroplast protein import and regulation at the TOC-complex. FRONTIERS IN PLANT SCIENCE 2014; 5:483. [PMID: 25278954 PMCID: PMC4166117 DOI: 10.3389/fpls.2014.00483] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/01/2014] [Indexed: 05/25/2023]
Abstract
Plants have evolved complex and sophisticated molecular mechanisms to regulate their development and adapt to their surrounding environment. Particularly the development of their specific organelles, chloroplasts and other plastid-types, is finely tuned in accordance with the metabolic needs of the cell. The normal development and functioning of plastids require import of particular subsets of nuclear encoded proteins. Most preproteins contain a cleavable sequence at their N terminal (transit peptide) serving as a signal for targeting to the organelle and recognition by the translocation machinery TOC-TIC (translocon of outer membrane complex-translocon of inner membrane complex) spanning the dual membrane envelope. The plastid proteome needs constant remodeling in response to developmental and environmental factors. Therefore selective regulation of preprotein import plays a crucial role in plant development. In this review we describe the diversity of transit peptides and TOC receptor complexes, and summarize the current knowledge and potential directions for future research concerning regulation of the different Toc isoforms.
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Affiliation(s)
| | | | - Felix Kessler
- *Correspondence: Felix Kessler, Laboratory of Plant Physiology, Université de Neuchâtel, UniMail, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland e-mail:
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Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C. Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. FRONTIERS IN PLANT SCIENCE 2013; 4:423. [PMID: 24294214 PMCID: PMC3827546 DOI: 10.3389/fpls.2013.00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/05/2013] [Indexed: 05/23/2023]
Abstract
Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore, important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis, and degradation play a role in MCR.
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Affiliation(s)
- Astrid M. Draffehn
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Li Li
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Jia Ding
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KGWindeby, Germany
| | | | - Meki S. Muktar
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Birgit Walkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Christiane Gebhardt
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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29
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Chloroplast-mediated activation of plant immune signalling in Arabidopsis. Nat Commun 2012; 3:926. [PMID: 22735454 DOI: 10.1038/ncomms1926] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/28/2012] [Indexed: 12/19/2022] Open
Abstract
Chloroplasts have a critical role in plant immunity as a site for the production for salicylic acid and jasmonic acid, important mediators of plant immunity. However, the molecular link between chloroplasts and the cytoplasmic-nuclear immune system remains largely unknown. Here we show that pathogen-associated molecular pattern (PAMP) signals are quickly relayed to chloroplasts and evoke specific Ca(2+) signatures in the stroma. We further demonstrate that a chloroplast-localized protein, named calcium-sensing receptor (CAS), is involved in stromal Ca(2+) transients and responsible for both PAMP-induced basal resistance and R gene-mediated hypersensitive cell death. CAS acts upstream of salicylic acid accumulation. Transcriptome analysis demonstrates that CAS is involved in PAMP-induced expression of defence genes and suppression of chloroplast gene expression possibly through (1)O(2)-mediated retrograde signalling, allowing chloroplast-mediated transcriptional reprogramming during plant immune responses. The present study reveals a previously unknown chloroplast-mediated signalling pathway linking chloroplasts to cytoplasmic-nuclear immune responses.
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Li H, Goodwin PH, Han Q, Huang L, Kang Z. Microscopy and proteomic analysis of the non-host resistance of Oryza sativa to the wheat leaf rust fungus, Puccinia triticina f. sp. tritici. PLANT CELL REPORTS 2012; 31:637-50. [PMID: 22038417 DOI: 10.1007/s00299-011-1181-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/28/2011] [Accepted: 10/14/2011] [Indexed: 05/26/2023]
Abstract
Rice (Oryza sativa) cv. Nipponbare expresses non-host resistance (NHR) to the wheat leaf rust fungus, Puccinia triticina f. sp. tritici (Ptt). When the leaves of cv. Nipponbare were inoculated with Ptt, approx 93% of the urediniospores germinated on the leaf surface, but only 10% of the germinated spores formed appressoria over the stomata at one day post inoculation (1 dpi). Hydrogen peroxide (H(2)O(2)) accumulated in host cells around the appressoria at 3 dpi. Approx. 3% of the appressoria produced short hyphae inside the leaf, and fluorescence was observed in tissue invaded by the hyphae by 7 dpi. At 22 dpi, 0.2% of the sites with appressoria formed branching infection hypha in mesophyll cells, but no substomatal vesicles, haustorial mother cells or haustoria were observed. Proteins were extracted from leaves 3 dpi and analyzed by two-dimensional gel electrophoresis (2-DE). A total 33 spots were reproducibly up-regulated and 9 were down-regulated by infection compared to the water inoculated control. Of these, 30 were identified by MALDI-TOF Mass Spectrometry. The identified proteins participate in defense/stress responses, energy/carbohydrate metabolism, oxidation-reduction processes, protein folding/turnover/cleavage/degradation, signal transduction and cell death regulation. The results indicates that NHR of rice to Ptt is consistent with a shift in protein and energy metabolism, increased antimicrobial activities, possibly including phytoalexin accumulation and cell wall reinforcement, increased cell repair, antioxidive and detoxification reactions, and enhanced prevention of plant cell death. Nearly half of the up-regulated identified proteins were associated with chloroplast and mitochondrial physiology suggesting important roles for these organelles during NHR.
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Affiliation(s)
- Hongbing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
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31
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Martin SF, Munagapati VS, Salvo-Chirnside E, Kerr LE, Le Bihan T. Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry. J Proteome Res 2011; 11:476-86. [PMID: 22077659 DOI: 10.1021/pr2009302] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein synthesis and degradation determine the cellular levels of proteins, and their control hence enables organisms to respond to environmental change. Experimentally, these are little known proteome parameters; however, recently, SILAC-based mass spectrometry studies have begun to quantify turnover in the proteomes of cell lines, yeast, and animals. Here, we present a proteome-scale method to quantify turnover and calculate synthesis and degradation rate constants of individual proteins in autotrophic organisms such as algae and plants. The workflow is based on the automated analysis of partial stable isotope incorporation with (15)N. We applied it in a study of the unicellular pico-alga Ostreococcus tauri and observed high relative turnover in chloroplast-encoded ATPases (0.42-0.58% h(-1)), core photosystem II proteins (0.34-0.51% h(-1)), and RbcL (0.47% h(-1)), while nuclear-encoded RbcS2 is more stable (0.23% h(-1)). Mitochondrial targeted ATPases (0.14-0.16% h(-1)), photosystem antennae (0.09-0.14% h(-1)), and histones (0.07-0.1% h(-1)) were comparatively stable. The calculation of degradation and synthesis rate constants k(deg) and k(syn) confirms RbcL as the bulk contributor to overall protein turnover. This study performed over 144 h of incorporation reveals dynamics of protein complex subunits as well as isoforms targeted to different organelles.
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Affiliation(s)
- Sarah F Martin
- Centre for Systems Biology at Edinburgh, University of Edinburgh, CH Waddington Building, The Kings Buildings, Mayfield Road, EH9 3JD, United Kingdom
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Alboresi A, Dall'Osto L, Aprile A, Carillo P, Roncaglia E, Cattivelli L, Bassi R. Reactive oxygen species and transcript analysis upon excess light treatment in wild-type Arabidopsis thaliana vs a photosensitive mutant lacking zeaxanthin and lutein. BMC PLANT BIOLOGY 2011; 11:62. [PMID: 21481232 PMCID: PMC3083342 DOI: 10.1186/1471-2229-11-62] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/11/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Reactive oxygen species (ROS) are unavoidable by-products of oxygenic photosynthesis, causing progressive oxidative damage and ultimately cell death. Despite their destructive activity they are also signalling molecules, priming the acclimatory response to stress stimuli. RESULTS To investigate this role further, we exposed wild type Arabidopsis thaliana plants and the double mutant npq1lut2 to excess light. The mutant does not produce the xanthophylls lutein and zeaxanthin, whose key roles include ROS scavenging and prevention of ROS synthesis. Biochemical analysis revealed that singlet oxygen (1O2) accumulated to higher levels in the mutant while other ROS were unaffected, allowing to define the transcriptomic signature of the acclimatory response mediated by 1O2 which is enhanced by the lack of these xanthophylls species. The group of genes differentially regulated in npq1lut2 is enriched in sequences encoding chloroplast proteins involved in cell protection against the damaging effect of ROS. Among the early fine-tuned components, are proteins involved in tetrapyrrole biosynthesis, chlorophyll catabolism, protein import, folding and turnover, synthesis and membrane insertion of photosynthetic subunits. Up to now, the flu mutant was the only biological system adopted to define the regulation of gene expression by 1O2. In this work, we propose the use of mutants accumulating 1O2 by mechanisms different from those activated in flu to better identify ROS signalling. CONCLUSIONS We propose that the lack of zeaxanthin and lutein leads to 1O2 accumulation and this represents a signalling pathway in the early stages of stress acclimation, beside the response to ADP/ATP ratio and to the redox state of both plastoquinone pool. Chloroplasts respond to 1O2 accumulation by undergoing a significant change in composition and function towards a fast acclimatory response. The physiological implications of this signalling specificity are discussed.
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Affiliation(s)
- Alessandro Alboresi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, I - 37134 Verona, Italy
| | - Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, I - 37134 Verona, Italy
| | - Alessio Aprile
- CRA Centro di Ricerca per la Genomica, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Petronia Carillo
- Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, Via Vivaldi 43, Caserta, Italy
| | - Enrica Roncaglia
- Dipartimento di Scienze Biomediche, Università di Modena e Reggio Emilia, Via Campi 287, 41100 Modena, Italy
| | - Luigi Cattivelli
- CRA Centro di Ricerca per la Genomica, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, I - 37134 Verona, Italy
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Lin M, Zhou X, Shen X, Mao C, Chen X. The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. THE PLANT CELL 2011; 23:911-22. [PMID: 21441435 PMCID: PMC3082272 DOI: 10.1105/tpc.110.082529] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 12/30/2010] [Accepted: 03/10/2011] [Indexed: 05/17/2023]
Abstract
Predicted interactions are a valuable complement to experimentally reported interactions in molecular mechanism studies, particularly for higher organisms, for which reported experimental interactions represent only a small fraction of their total interactomes. With careful engineering consideration of the lessons from previous efforts, the predicted arabidopsis interactome resource (PAIR; ) presents 149,900 potential molecular interactions, which are expected to cover approximately 24% of the entire interactome with approximately 40% precision. This study demonstrates that, although PAIR still has limited coverage, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes. These inferred interactions can nicely power several network topology-based systems biology analyses, such as gene set linkage analysis, protein function prediction, and identification of regulatory genes demonstrating insignificant expression changes. The drastically expanded molecular network in PAIR has considerably improved the capability of these analyses to integrate existing knowledge and suggest novel insights into the function and coordination of genes and gene networks.
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Affiliation(s)
- Mingzhi Lin
- State Key Laboratory of Plant Physiology and Biochemistry, Zhejiang University, Hangzhou 310058, People’s Republic of China
- Department of Bioinformatics, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xi Zhou
- Department of Bioinformatics, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xueling Shen
- Institute of Biochemistry, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xin Chen
- State Key Laboratory of Plant Physiology and Biochemistry, Zhejiang University, Hangzhou 310058, People’s Republic of China
- Department of Bioinformatics, Zhejiang University, Hangzhou 310058, People’s Republic of China
- Institute of Biochemistry, Zhejiang University, Hangzhou 310058, People’s Republic of China
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Abstract
Most proteins in chloroplasts are encoded by the nuclear genome and synthesized as precursors with N-terminal targeting signals called transit peptides. Novel machinery has evolved to specifically import these proteins from the cytosol into chloroplasts. This machinery consists of more than a dozen components located in and around the chloroplast envelope, including a pair of GTPase receptors, a beta-barrel-type channel across the outer membrane, and an AAA(+)-type motor in the stroma. How individual components assemble into functional subcomplexes and the sequential steps of the translocation process are being mapped out. An increasing number of noncanonical import pathways, including a pathway with initial transport through the endomembrane system, is being revealed. Multiple levels of control on protein transport into chloroplasts have evolved, including the development of two receptor subfamilies, one for photosynthetic proteins and one for housekeeping proteins. The functions or expression levels of some translocon components are further adjusted according to plastid type, developmental stage, and metabolic conditions.
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Affiliation(s)
- Hsou-min Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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