1
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Zhou L, Li K, Hunt AG. Natural variation in the plant polyadenylation complex. FRONTIERS IN PLANT SCIENCE 2024; 14:1303398. [PMID: 38317838 PMCID: PMC10839035 DOI: 10.3389/fpls.2023.1303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
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Affiliation(s)
| | | | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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2
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Xu C, Zhang Z, He J, Bai Y, Cui J, Liu L, Tang J, Tang G, Chen X, Mo B. The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:144-160. [PMID: 37415266 DOI: 10.1111/tpj.16366] [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: 04/10/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
RCF1 is a highly conserved DEAD-box RNA helicase found in yeast, plants, and mammals. Studies about the functions of RCF1 in plants are limited. Here, we uncovered the functions of RCF1 in Arabidopsis thaliana as a player in pri-miRNA processing and splicing, as well as in pre-mRNA splicing. A mutant with miRNA biogenesis defects was isolated, and the defect was traced to a recessive point mutation in RCF1 (rcf1-4). We show that RCF1 promotes D-body formation and facilitates the interaction between pri-miRNAs and HYL1. Finally, we show that intron-containing pri-miRNAs and pre-mRNAs exhibit a global splicing defect in rcf1-4. Together, this work uncovers roles for RCF1 in miRNA biogenesis and RNA splicing in Arabidopsis.
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Affiliation(s)
- Chi Xu
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guiliang Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biological Sciences and Biotechnology Research Center, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Xuemei Chen
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
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3
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Zhang L, Xiang Y, Chen S, Shi M, Jiang X, He Z, Gao S. Mechanisms of MicroRNA Biogenesis and Stability Control in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:844149. [PMID: 35350301 PMCID: PMC8957957 DOI: 10.3389/fpls.2022.844149] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20-24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.
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Affiliation(s)
- Lu Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yu Xiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shengbo Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Min Shi
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xianda Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhuoli He
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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4
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Seok HY, Kim T, Lee SY, Moon YH. Non-TZF Transcriptional Activator AtC3H12 Negatively Affects Seed Germination and Seedling Development in Arabidopsis. Int J Mol Sci 2022; 23:1572. [PMID: 35163496 PMCID: PMC8835867 DOI: 10.3390/ijms23031572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/09/2022] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
CCCH zinc finger proteins are a large protein family and are classified as either tandem CCCH zinc finger (TZF) or non-TZF proteins. The roles of TZF genes in several plants have been well determined, whereas the functions of many non-TZF genes in plants remain uncharacterized. Herein, we describe biological and molecular functions of AtC3H12, an Arabidopsis non-TZF protein containing three CCCH zinc finger motifs. AtC3H12 has orthologs in several plant species but has no paralog in Arabidopsis. AtC3H12-overexpressing transgenic plants (OXs) germinated slower than wild-type (WT) plants, whereas atc3h12 mutants germinated faster than WT plants. The fresh weight (FW) and primary root lengths of AtC3H12 OX seedlings were lighter and shorter than those of WT seedlings, respectively. In contrast, FW and primary root lengths of atc3h12 seedlings were heavier and longer than those of WT seedlings, respectively. AtC3H12 was localized in the nucleus and displayed transactivation activity in both yeast and Arabidopsis. We found that the 97-197 aa region of AtC3H12 is an important part for its transactivation activity. Detection of expression levels and analysis of Arabidopsis transgenic plants harboring a PAtC3H12::GUS construct showed that AtC3H12 expression increases as the Arabidopsis seedlings develop. Taken together, our results demonstrate that AtC3H12 negatively affects seed germination and seedling development as a nuclear transcriptional activator in Arabidopsis. To our knowledge, this is the first report to show that non-TZF proteins negatively affect plant development as nuclear transcriptional activators.
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Affiliation(s)
- Hye-Yeon Seok
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Taehyoung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
| | - Sun-Young Lee
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Yong-Hwan Moon
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
- Department of Molecular Biology, Pusan National University, Busan 46241, Korea
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5
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Li X, Chen L, Yao L, Zou J, Hao J, Wu W. Calcium-dependent protein kinase CPK32 mediates calcium signaling in regulating Arabidopsis flowering time. Natl Sci Rev 2021; 9:nwab180. [PMID: 35079411 PMCID: PMC8783668 DOI: 10.1093/nsr/nwab180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/29/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Appropriate flowering time is critical for the reproductive success of plant species. Emerging evidence indicates that calcium may play an important role in the regulation of flowering time. However, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that calcium-dependent protein kinase 32 (CPK32) regulates flowering time by affecting the alternative polyadenylation of FLOWERING CONTROL LOCUS A (FCA) and altering the transcription of FLOWERING LOCUS C (FLC), a central repressor of flowering time. The knockdown of CPK32 results in an obvious late flowering phenotype and dramatically enhanced FLC transcription. CPK32 interacts with FCA, and phosphorylates the serine592 of FCA in a Ca2+-dependent manner. Moreover, the ratio of abundance of the FCA transcripts (FCA-D and FCA-P) changes significantly in the cpk32 mutant, which subsequently affects FLC expression and consequently regulates floral transition. The present evidence demonstrates that CPK32 modulates flowering time by regulating FCA alternative polyadenylation and consequent FLC expression.
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Affiliation(s)
- Xidong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Limei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Li Yao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Syngenta Biotechnology China Co., Ltd., Beijing 102206, China
| | - Junjie Zou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Hao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Weihua Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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6
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Lin J, Ye C, Li QQ. QPAT-seq, a rapid and deduplicatable method for quantification of poly(A) site usages. Methods Enzymol 2021; 655:73-83. [PMID: 34183134 DOI: 10.1016/bs.mie.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Alternative polyadenylation (APA) is an essential regulatory mechanism for gene expression. The next generation sequencing provides ample opportunity to precisely delineate APA sites genome-wide. Various methods for profiling transcriptome-wide poly(A) sites were developed. By comparing available methods, the ways for adding sequencing adaptors to fit with the Illumina sequencing platform are different. These methods have identified more than 50% genes that undergo APA in eukaryotes. However, due to the unbalanced PCR during library preparation, accurate quantification of poly(A) sites is still a challenge. Here, we describe an updated poly(A) tag sequencing method that incorporates unique molecular identifier (UMI) into the adaptor for removing quantification bias induced by PCR duplicates. Hence, quantification of poly(A) site usages can be achieved by counting UMIs. This protocol, quantifying poly(A) tag sequencing (QPAT-seq), can be finished in 1 day with reduced cost, and is particularly useful for application with a large number of samples.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China; Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States.
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7
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Tan YY, Du H, Wu X, Liu YH, Jiang M, Song SY, Wu L, Shu QY. Gene editing: an instrument for practical application of gene biology to plant breeding. J Zhejiang Univ Sci B 2020; 21:460-473. [PMID: 32478492 PMCID: PMC7306633 DOI: 10.1631/jzus.b1900633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/20/2022]
Abstract
Plant breeding is well recognized as one of the most important means to meet food security challenges caused by the ever-increasing world population. During the past three decades, plant breeding has been empowered by both new knowledge on trait development and regulation (e.g., functional genomics) and new technologies (e.g., biotechnologies and phenomics). Gene editing, particularly by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) and its variants, has become a powerful technology in plant research and may become a game-changer in plant breeding. Traits are conferred by coding and non-coding genes. From this perspective, we propose different editing strategies for these two types of genes. The activity of an encoded enzyme and its quantity are regulated at transcriptional and post-transcriptional, as well as translational and post-translational, levels. Different strategies are proposed to intervene to generate gene functional variations and consequently phenotype changes. For non-coding genes, trait modification could be achieved by regulating transcription of their own or target genes via gene editing. Also included is a scheme of protoplast editing to make gene editing more applicable in plant breeding. In summary, this review provides breeders with a host of options to translate gene biology into practical breeding strategies, i.e., to use gene editing as a mechanism to commercialize gene biology in plant breeding.
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Affiliation(s)
- Yuan-yuan Tan
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
| | - Hao Du
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xia Wu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan-hua Liu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meng Jiang
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shi-yong Song
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liang Wu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing-yao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
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8
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Wang B, Chai H, Zhong Y, Shen Y, Yang W, Chen J, Xin Z, Shi H. The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1598-1613. [PMID: 31745559 PMCID: PMC7242002 DOI: 10.1093/jxb/erz523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/19/2019] [Indexed: 05/29/2023]
Abstract
Gene regulation is central for growth, development, and adaptation to environmental changes in all living organisms. Many genes are induced by environmental cues, and the expression of these inducible genes is often repressed under normal conditions. Here, we show that the SHINY2 (SHI2) gene is important for repressing salt-inducible genes and also plays a role in cold response. The shi2 mutant displayed hypersensitivity to cold, abscisic acid (ABA), and LiCl. Map-based cloning demonstrates that SHI2 encodes a DEAD- (Asp-Glu-Ala-Asp) box RNA helicase with similarity to a yeast splicing factor. Transcriptomic analysis of the shi2 mutant in response to cold revealed that the shi2 mutation decreased the number of cold-responsive genes and the magnitude of their response, and resulted in the mis-splicing of some cold-responsive genes. Under salt stress, however, the shi2 mutation increased the number of salt-responsive genes but had a negligible effect on mRNA splicing. Our results suggest that SHI2 is a component in a ready-for-transcription repressor complex important for gene repression under normal conditions, and for gene activation and transcription under stress conditions. In addition, SHI2 also serves as a splicing factor required for proper splicing of cold-responsive genes and affects 5' capping and polyadenylation site selection.
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Affiliation(s)
- Bangshing Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Haoxi Chai
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yingli Zhong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yun Shen
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, USA
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
- School of Life Sciences, Central China Normal University, Wuhan, China
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9
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Zhou Y, Hu L, Jiang L, Liu S. Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in cucumber (Cucumis sativus). Genes Genomics 2018; 40:579-589. [PMID: 29892943 DOI: 10.1007/s13258-018-0659-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
YTH domain-containing RNA-binding proteins are involved in post-transcriptional regulation and play important roles in the growth and development as well as abiotic stress responses of plants. However, YTH genes have not been previously studied in cucumber (Cucumis sativus). In this study, a total of five YTH genes (CsYTH1-CsYTH5) were identified in cucumber, which could be mapped on three out of the seven cucumber chromosomes. All CsYTH proteins had highly conserved C-terminal YTH domains, and two of them (CsYTH1 and CsYTH4) harbored extra CCCH and P/Q/N-rich domains. The phylogenesis, conserved motifs and exon-intron structure of YTH genes from cucumber, Arabidopsis and rice were also analyzed. The phylogenetically closely clustered YTHs shared similar gene structures and conserved motifs. An analysis of the cis-acting regulatory elements in the upstream region of these genes resulted in the identification of many cis-elements related to stress, hormone and development. Expression analysis based on the transcriptome data showed that some CsYTHs had development- or tissue-specific expression. In addition, their expression levels were altered under various stresses such as salt, drought, cold, and abscisic acid (ABA) treatments. These findings lay the foundation for the functional analysis of CsYTHs in the future.
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Affiliation(s)
- Yong Zhou
- Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Lunwei Jiang
- Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Shiqiang Liu
- Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
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10
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Hong L, Ye C, Lin J, Fu H, Wu X, Li QQ. Alternative polyadenylation is involved in auxin-based plant growth and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:246-258. [PMID: 29155478 DOI: 10.1111/tpj.13771] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/24/2017] [Accepted: 10/31/2017] [Indexed: 05/24/2023]
Abstract
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre-mRNA post-transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5'-untranslated region (UTR), but increases in the 3'UTR. APA site usage frequencies of 42 genes were switched by auxin, suggesting that auxin affects the choice of poly(A) sites. Furthermore, poly(A) signal selection was altered after auxin treatment. For example, a mutant of poly(A) signal binding protein CPSF30 showed altered sensitivity to auxin treatment, indicating interactions between auxin and the poly(A) signal recognition machinery. We also found that auxin activity on lateral root development is likely mediated by altered expression of ARF7, ARF19 and IAA14 through poly(A) site switches. Our results shed light on the molecular mechanisms of auxin responses relative to its interactions with mRNA polyadenylation.
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Affiliation(s)
- Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
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11
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Li Z, Wang R, Gao Y, Wang C, Zhao L, Xu N, Chen KE, Qi S, Zhang M, Tsay YF, Crawford NM, Wang Y. The Arabidopsis CPSF30-L gene plays an essential role in nitrate signaling and regulates the nitrate transceptor gene NRT1.1. THE NEW PHYTOLOGIST 2017; 216:1205-1222. [PMID: 28850721 DOI: 10.1111/nph.14743] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/04/2017] [Indexed: 05/20/2023]
Abstract
Plants have evolved sophisticated mechanisms to adapt to fluctuating environmental nitrogen availability. However, more underlying genes regulating the response to nitrate have yet to be characterized. We report here the identification of a nitrate regulatory mutant whose mutation mapped to the Cleavage and Polyadenylation Specificity Factor 30 gene (CPSF30-L). In the mutant, induction of nitrate-responsive genes was inhibited independent of the ammonium conditions and was restored by expression of the wild-type 65 kDa encoded by CPSF30-L. Molecular and genetic evidence suggests that CPSF30-L works upstream of NRT1.1 and independently of NLP7 in response to nitrate. Analysis of the 3'-UTR of NRT1.1 showed that the pattern of polyadenylation sites was altered in the cpsf30 mutant. Transcriptome analysis revealed that four nitrogen-related clusters were enriched in the differentially expressed genes of the cpsf30 mutant. Nitrate uptake was decreased in the mutant along with reduced expression of the nitrate transporter/sensor gene NRT1.1, while nitrate reduction and amino acid content were enhanced in roots along with increased expression of several nitrate assimilatory genes. These findings indicate that the 65 kDa protein encoded by CPSF30-L mediates nitrate signaling in part by regulating NRT1.1 expression, thus adding an important component to the nitrate signaling network.
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Affiliation(s)
- Zehui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lufei Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, 276826, China
| | - Kuo-En Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Min Zhang
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093-0116, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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12
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Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene. Sci Rep 2017; 7:2052. [PMID: 28515442 PMCID: PMC5435732 DOI: 10.1038/s41598-017-02215-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022] Open
Abstract
Pre-mRNA alternative splicing and alternative polyadenylation have been implicated to play important roles during eukaryotic gene expression. However, much remains unknown regarding the regulatory mechanisms and the interactions of these two processes in plants. Here we focus on an Arabidopsis gene OXT6 (Oxidative Tolerant-6) that has been demonstrated to encode two proteins through alternative splicing and alternative polyadenylation. Specifically, alternative polyadenylation at Intron-2 of OXT6 produces a transcript coding for AtCPSF30, an Arabidopsis ortholog of 30 kDa subunit of the Cleavage and Polyadenylation Specificity Factor. On the other hand, alternative splicing of Intron-2 generates a longer transcript encoding a protein named AtC30Y, a polypeptide including most part of AtCPSF30 and a YT521B domain. To investigate the expression outcome of OXT6 in plants, a set of mutations were constructed to alter the splicing and polyadenylation patterns of OXT6. Analysis of transgenic plants bearing these mutations by quantitative RT-PCR revealed a competition relationship between these two processes. Moreover, when both splice sites and poly(A) signals were mutated, polyadenylation became the preferred mode of OXT6 processing. These results demonstrate the interplay between alternative splicing and alternative polyadenylation, and it is their concerted actions that define a gene’s expression outcome.
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13
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Deng X, Cao X. Roles of pre-mRNA splicing and polyadenylation in plant development. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:45-53. [PMID: 27866125 DOI: 10.1016/j.pbi.2016.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Plants possess amazing plasticity of growth and development, allowing them to adjust continuously and rapidly to changes in the environment. Over the past two decades, numerous molecular studies have illuminated the role of transcriptional regulation in plant development and environmental responses. However, emerging studies in Arabidopsis have uncovered an unexpectedly widespread role for post-transcriptional regulation in development and responses to environmental changes. In this review, we summarize recent discoveries detailing the contribution of two post-transcriptional mechanisms, pre-mRNA splicing and polyadenylation, to the regulation of plant development, with an emphasis on the control of flowering time. We also discuss future directions in the field and new technological approaches.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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14
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Fray RG, Simpson GG. The Arabidopsis epitranscriptome. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:17-21. [PMID: 26048078 DOI: 10.1016/j.pbi.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
The most prevalent internal modification of plant messenger RNAs, N(6)-methyladenosine (m(6)A), was first discovered in the 1970s, then largely forgotten. However, the impact of modifications to eukaryote mRNA, collectively known as the epitranscriptome, has recently attracted renewed attention. mRNA methylation is required for normal Arabidopsis development and the first methylation maps reveal that thousands of Arabidopsis mRNAs are methylated. Arabidopsis is likely to be a model of wide utility in understanding the biological impacts of the epitranscriptome. We review recent progress and look ahead with questions awaiting answers to reveal an entire layer of gene regulation that has until recently been overlooked.
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Affiliation(s)
- Rupert G Fray
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK.
| | - Gordon G Simpson
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Cell and Molecular Sciences, James Hutton Institute, Invergowrie DD2 5DA, Scotland, UK.
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15
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Abstract
Gene expression is controlled by diverse mechanisms before, during, and after transcription. Chromatin modification factors as well as transcriptional repressors, silencers, and enhancers all feed into how eukaryotes transcribe RNA in the nucleus. However, there is increasing evidence that post-transcriptional regulation of gene expression is as widespread as transcriptional control if not more so. Studies of specific transcripts in oocytes and embryos are at the core of our mechanistic understanding of many post-transcriptional events. Coupled with genome-wide and large-scale experimental approaches, research is bringing to light how these regulatory events function independently and in concert to regulate protein expression.
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