1
|
CSN5A Subunit of COP9 Signalosome Is Required for Resetting Transcriptional Stress Memory after Recurrent Heat Stress in Arabidopsis. Biomolecules 2021; 11:biom11050668. [PMID: 33946149 PMCID: PMC8146153 DOI: 10.3390/biom11050668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
In nature, plants are exposed to several environmental stresses that can be continuous or recurring. Continuous stress can be lethal, but stress after priming can increase the tolerance of a plant to better prepare for future stresses. Reports have suggested that transcription factors are involved in stress memory after recurrent stress; however, less is known about the factors that regulate the resetting of stress memory. Here, we uncovered a role for Constitutive Photomorphogenesis 5A (CSN5A) in the regulation of stress memory for resetting transcriptional memory genes (APX2 and HSP22) and H3K4me3 following recurrent heat stress. Furthermore, CSN5A is also required for the deposition of H3K4me3 following recurrent heat stress. Thus, CSN5A plays an important role in the regulation of histone methylation and transcriptional stress memory after recurrent heat stress.
Collapse
|
2
|
Zhang X, Ma C, Wang X, Wu M, Shao J, Huang L, Yuan L, Fu Z, Li W, Zhang X, Guo Z, Tang J. Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays). BMC PLANT BIOLOGY 2021; 21:118. [PMID: 33637040 PMCID: PMC7908659 DOI: 10.1186/s12870-021-02890-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding. RESULTS Here, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes, Zm00001d049958, Zm00001d027359, Zm00001d048502 and Zm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomato SELF PRUNING, which assists SINGLE FLOWER TRUSS in driving yield-related heterosis, indicating that Zm00001d050649 is a potential contributor to drive heterotic effect on ear length. CONCLUSION Our results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F1 hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize.
Collapse
Affiliation(s)
- Xiangge Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Chenchen Ma
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xiaoqing Wang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Mingbo Wu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Jingkuan Shao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Li Huang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Liang Yuan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 433200, China.
| |
Collapse
|
3
|
Abstract
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.
Collapse
Affiliation(s)
- Shaked Bergman
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | | |
Collapse
|
4
|
Yang H, Yang Z, Mao Z, Li Y, Hu D, Li X, Shi G, Huang F, Liu B, Kong F, Yu D. Genome-Wide DNA Methylation Analysis of Soybean Curled-Cotyledons Mutant and Functional Evaluation of a Homeodomain-Leucine Zipper (HD-Zip) I Gene GmHDZ20. FRONTIERS IN PLANT SCIENCE 2020; 11:593999. [PMID: 33505408 PMCID: PMC7830220 DOI: 10.3389/fpls.2020.593999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 05/17/2023]
Abstract
DNA methylation is a major, conserved epigenetic modification that influences many biological processes. Cotyledons are specialized tissues that provide nutrition for seedlings at the early developmental stage. To investigate the patterns of genomic DNA methylation of germinated cotyledons in soybean (Glycine max) and its effect on cotyledon development, we performed a genome-wide comparative analysis of DNA methylation between the soybean curled-cotyledons (cco) mutant, which has abnormal cotyledons, and its corresponding wild type (WT) by whole-genome bisulfite sequencing. The cco mutant was methylated at more sites but at a slightly lower level overall than the WT on the whole-genome level. A total of 46 CG-, 92 CHG-, and 9723 CHH- (H = A, C, or T) differentially methylated genes (DMGs) were identified in cotyledons. Notably, hypomethylated CHH-DMGs were enriched in the gene ontology term "sequence-specific DNA binding transcription factor activity." We selected a DMG encoding a homeodomain-leucine zipper (HD-Zip) I subgroup transcription factor (GmHDZ20) for further functional characterization. GmHDZ20 localized to the nucleus and was highly expressed in leaf and cotyledon tissues. Constitutive expression of GmHDZ20 in Arabidopsis thaliana led to serrated rosette leaves, shorter siliques, and reduced seed number per silique. A yeast two-hybrid assay revealed that GmHDZ20 physically interacted with three proteins associated with multiple aspects of plant growth. Collectively, our results provide a comprehensive study of soybean DNA methylation in normal and aberrant cotyledons, which will be useful for the identification of specific DMGs that participate in cotyledon development, and also provide a foundation for future in-depth functional study of GmHDZ20 in soybean.
Collapse
Affiliation(s)
- Hui Yang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Hui Yang,
| | - Zhongyi Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Zhuozhuo Mao
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yali Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Dezhou Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiao Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Guixia Shi
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Deyue Yu,
| |
Collapse
|
5
|
Qin N, Xu D, Li J, Deng XW. COP9 signalosome: Discovery, conservation, activity, and function. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:90-103. [PMID: 31894894 DOI: 10.1111/jipb.12903] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/26/2019] [Indexed: 05/22/2023]
Abstract
The COP9 signalosome (CSN) is a conserved protein complex, typically composed of eight subunits (designated as CSN1 to CSN8) in higher eukaryotes such as plants and animals, but of fewer subunits in some lower eukaryotes such as yeasts. The CSN complex is originally identified in plants from a genetic screen for mutants that mimic light-induced photomorphogenic development when grown in the dark. The CSN complex regulates the activity of cullin-RING ligase (CRL) families of E3 ubiquitin ligase complexes, and play critical roles in regulating gene expression, cell proliferation, and cell cycle. This review aims to summarize the discovery, composition, structure, and function of CSN in the regulation of plant development in response to external (light and temperature) and internal cues (phytohormones).
Collapse
Affiliation(s)
- Nanxun Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| |
Collapse
|
6
|
Fonseca S, Rubio V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1095. [PMID: 31608079 PMCID: PMC6761389 DOI: 10.3389/fpls.2019.01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 05/10/2023]
Abstract
CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.
Collapse
|