101
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Ma K, Shi W, Xu M, Liu J, Zhang F. Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca 2+ Channel Blocker. FRONTIERS IN PLANT SCIENCE 2018; 9:244. [PMID: 29559983 PMCID: PMC5845709 DOI: 10.3389/fpls.2018.00244] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/12/2018] [Indexed: 05/12/2023]
Abstract
It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.
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Affiliation(s)
- Keshi Ma
- College of Life Sciences, Capital Normal University, Beijing, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Wenshuo Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Mengyue Xu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiaxi Liu
- College of Life Sciences, Capital Normal University, Beijing, China
- *Correspondence: Jiaxi Liu
| | - Feixiong Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
- Feixiong Zhang
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102
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Yin D, Liu X, Shi Z, Li D, Zhu L. An AT-hook protein DEPRESSED PALEA1 physically interacts with the TCP Family transcription factor RETARDED PALEA1 in rice. Biochem Biophys Res Commun 2018; 495:487-492. [DOI: 10.1016/j.bbrc.2017.11.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 11/30/2022]
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103
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Bonaldi K, Li Z, Kang SE, Breton G, Pruneda-Paz JL. Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens. Nucleic Acids Res 2017; 45:e157. [PMID: 28985361 PMCID: PMC5737895 DOI: 10.1093/nar/gkx682] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/25/2017] [Indexed: 01/08/2023] Open
Abstract
Gene-centered yeast one-hybrid (Y1H) screens provide a powerful and effective strategy to identify transcription factor (TF)-promoter interactions. While genome-wide TF ORFeome clone collections are increasingly available, screening protocols have limitations inherent to the properties of the enzymatic reaction used to identify interactions and to the procedure required to perform the assay in a high-throughput format. Here, we present the development and validation of a streamlined strategy for quantitative and fully automated gene-centered Y1H screens using a novel cell surface Gaussia luciferase reporter.
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Affiliation(s)
- Katia Bonaldi
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Zheng Li
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - S Earl Kang
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, TX 77030, USA
| | - Jose L Pruneda-Paz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
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104
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Lei N, Yu X, Li S, Zeng C, Zou L, Liao W, Peng M. Phylogeny and expression pattern analysis of TCP transcription factors in cassava seedlings exposed to cold and/or drought stress. Sci Rep 2017; 7:10016. [PMID: 28855620 PMCID: PMC5577251 DOI: 10.1038/s41598-017-09398-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022] Open
Abstract
The TCP transcription factors usually act as integrators of multiple growth regulatory and environmental stimuli. However, little is known about this gene family in the important tropical crop cassava (Manihot esculenta). In this study, 36 TCP genes were identified and renamed based on cassava whole-genome sequence and their sequence similarity with Arabidopsis TCPs. Typical TCP domains were detected in these proteins by multiple sequence alignment analysis. Evolutionary analysis indicated that MeTCPs could be divided into 8 subgroups, which was further supported by gene structure and conserved motif analyses. qRT-PCR analysis revealed tissue-specific and hormone-responsive expression patterns of MeTCP genes. Moreover, with global expression and promoter analysis, we found that MeTCPs showed similar or distinct expression patterns under cold and/or drought stress, suggesting that they might participate in distinct signaling pathways. Our study provides the first comprehensive analysis of TCP gene family in the cassava genome. The data will be useful for uncovering the potential functions of MeTCP genes, and their possible roles in mediating hormone and abiotic stress responses in cassava.
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Affiliation(s)
- Ning Lei
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Xiang Yu
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shuxia Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Changying Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wenbin Liao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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105
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Xie Q, Liu X, Zhang Y, Tang J, Yin D, Fan B, Zhu L, Han L, Song G, Li D. Identification and Characterization of microRNA319a and Its Putative Target Gene, PvPCF5, in the Bioenergy Grass Switchgrass ( Panicum virgatum). FRONTIERS IN PLANT SCIENCE 2017; 8:396. [PMID: 28424710 PMCID: PMC5371612 DOI: 10.3389/fpls.2017.00396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/08/2017] [Indexed: 05/20/2023]
Abstract
Due to its high biomass yield, low environmental impact, and widespread adaptability to poor soils and harsh conditions, switchgrass (Panicum virgatum L.), a warm-region perennial herbaceous plant, has attracted much attention in recent years. However, little is known about microRNAs (miRNAs) and their functions in this bioenergy grass. Here, we identified and characterized a miRNA gene, Pvi-MIR319a, encoding microRNA319a in switchgrass. Transgenic rice lines generated by overexpressing the Pvi-MIR319a precursor gene exhibited broader leaves and delayed flowering compared with the control. Gene expression analysis indicated at least four putative target genes were downregulated. Additionally, we cloned a putative target gene (PvPCF5) of Pvi-MIR319a from switchgrass. PvPCF5, a TCP transcription factor, is a nuclear-localized protein with transactivation activity and control the development of leaf. Our results suggest that Pvi-MIR319a and its target genes may be used as potential genetic regulators for future switchgrass genetic improvement.
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Affiliation(s)
- Qi Xie
- Institute of Turfgrass Science, College of Forestry, Beijing Forestry UniversityBeijing, China
| | - Xue Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Yinbing Zhang
- Institute of Turfgrass Science, College of Forestry, Beijing Forestry UniversityBeijing, China
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Dedong Yin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Bo Fan
- ShenZhen Guo Yi Park Developments Co. LtdShenzhen, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Liebao Han
- Institute of Turfgrass Science, College of Forestry, Beijing Forestry UniversityBeijing, China
| | - Guilong Song
- Institute of Turfgrass Science, College of Forestry, Beijing Forestry UniversityBeijing, China
- *Correspondence: Guilong Song, Dayong Li,
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- *Correspondence: Guilong Song, Dayong Li,
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106
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Mazur MJ, Spears BJ, Djajasaputra A, van der Gragt M, Vlachakis G, Beerens B, Gassmann W, van den Burg HA. Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci. FRONTIERS IN PLANT SCIENCE 2017; 8:2043. [PMID: 29250092 PMCID: PMC5714883 DOI: 10.3389/fpls.2017.02043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 05/20/2023]
Abstract
In Arabidopsis more than 400 proteins have been identified as SUMO targets, both in vivo and in vitro. Among others, transcription factors (TFs) are common targets for SUMO conjugation. Here we aimed to exhaustively screen for TFs that interact with the SUMO machinery using an arrayed yeast two-hybrid library containing more than 1,100 TFs. We identified 76 interactors that foremost interact with the SUMO conjugation enzyme SCE1 and/or the SUMO E3 ligase SIZ1. These interactors belong to various TF families, which control a wide range of processes in plant development and stress signaling. Amongst these interactors, the TCP family was overrepresented with several TCPs interacting with different proteins of the SUMO conjugation cycle. For a subset of these TCPs we confirmed that the catalytic site of SCE1 is essential for this interaction. In agreement, TCP1, TCP3, TCP8, TCP14, and TCP15 were readily SUMO modified in an E. coli sumoylation assay. Strikingly, these TCP-SCE1 interactions were found to redistribute these TCPs into nuclear foci/speckles, suggesting that these TCP foci represent sites for SUMO (conjugation) activity.
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Affiliation(s)
- Magdalena J. Mazur
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Benjamin J. Spears
- Division of Plant Sciences, C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - André Djajasaputra
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Michelle van der Gragt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Georgios Vlachakis
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Bas Beerens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Walter Gassmann
- Division of Plant Sciences, C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Harrold A. van den Burg
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