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Ido A, Iwata S, Iwata Y, Igarashi H, Hamada T, Sonobe S, Sugiura M, Yukawa Y. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription. PLANT PHYSIOLOGY 2016; 170:642-52. [PMID: 26662274 PMCID: PMC4734572 DOI: 10.1104/pp.15.01614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin).
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Affiliation(s)
- Ayaka Ido
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Shinya Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yuka Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Hisako Igarashi
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Takahiro Hamada
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Seiji Sonobe
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
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Yukawa Y, Dieci G, Alzapiedi M, Hiraga A, Hirai K, Yamamoto YY, Sugiura M. A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genes. Genomics 2010; 97:166-72. [PMID: 21147216 DOI: 10.1016/j.ygeno.2010.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/12/2010] [Accepted: 12/02/2010] [Indexed: 11/28/2022]
Abstract
The transcription start site (TSS) is useful to predict gene and to understand transcription initiation. Although vast data on mRNA TSSs are available, little is known about tRNA genes because of rapid processing. Using a tobacco in vitro transcription system under conditions of impaired 5' end processing, TSSs were determined for 64 Arabidopsis tRNA genes. This analysis revealed multiple TSSs distributed in a region from 10 to 2bp upstream of the mature tRNA coding sequence (-10 to -2). We also analyzed 31 Saccharomyces cerevisiae tRNA genes that showed a smaller number but a broader distribution (-13 to -1) of TSSs. In both cases, transcription was initiated preferentially at adenosine, and a common 'TCAACA' sequence was found spanning the TSSs. In plant, this motif caused multiple TSSs to converge at one site and enhanced transcription. The TATA-like sequence upstream of Arabidopsis tRNA genes also contributed to TSS selection.
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Affiliation(s)
- Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, 467-8501 Nagoya, Japan.
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The plant-specific TFIIB-related protein, pBrp, is a general transcription factor for RNA polymerase I. EMBO J 2009; 27:2317-27. [PMID: 18668124 DOI: 10.1038/emboj.2008.151] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 07/07/2008] [Indexed: 01/19/2023] Open
Abstract
TFIIB and BRF are general transcription factors (GTFs) for eukaryotic RNA polymerases II and III, respectively, and have important functions in transcriptional initiation. In this study, the third type of TFIIB-related protein, pBrp, found in plant lineages was characterized in the red alga Cyanidioschyzon merolae. Chromatin immunoprecipitation analysis revealed that CmpBrp specifically occupied the rDNA promoter region in vivo, and the occupancy was proportional to de novo 18S rRNA synthesis. Consistently, CmpBrp and CmTBP cooperatively bound the rDNA promoter region in vitro, and the binding site was identified at a proximal downstream region of the transcription start point. alpha-Amanitin-resistant transcription from the rDNA promoter in crude cell lysate was severely inhibited by the CmpBrp antibody and was also inhibited when DNA template with a mutated CmpBrp-CmTBP binding site was used. CmpBrp was shown to co-immunoprecipitate and co-localize with the RNA polymerase I subunit, CmRPA190, in the cell. Thus, together with comparative studies of Arabidopsis pBrp, we concluded that pBrp is a GTF for RNA polymerase I in plant cells.
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