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Niederau PA, Eglé P, Willig S, Parsons J, Hoernstein SNW, Decker EL, Reski R. Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella. PLANT CELL REPORTS 2024; 43:43. [PMID: 38246952 PMCID: PMC10800305 DOI: 10.1007/s00299-023-03088-5] [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: 07/13/2023] [Accepted: 11/02/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Characterization of Physcomitrella 3'UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming. The production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular, the good manufacturing practice (GMP)-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features, such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3'UTRs (untranslated regions) of which 7964 transcripts contain at least one intron. Over 91% of 3'UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3'UTRs, 14 terminator candidates were selected and characterized via transient Dual-Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3'UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than tenfold, demonstrating the stronger effect promoters play as compared to terminators. Among selected terminator attributes, the number of polyadenylation sites as well as polyadenylation signals were found to influence terminator performance the most. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.
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Affiliation(s)
| | - Pauline Eglé
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sandro Willig
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliana Parsons
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centre BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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Zhu S, Wu X, Fu H, Ye C, Chen M, Jiang Z, Ji G. Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis. Front Genet 2019; 10:647. [PMID: 31333724 PMCID: PMC6616101 DOI: 10.3389/fgene.2019.00647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional modification event to process messenger RNA (mRNA) for transcriptional termination, transport, and translation. In the present study, we characterized poly(A) signals in Xenopus tropicalis using 70,918 highly confident poly(A) sites derived from 16,511 protein-coding genes to understand their roles in the regulation of embryo development and gender difference. We examined potential factors, including the gene length, the number of introns in a gene, and the intron length, that may affect the prevalence of APA. We observed 12 prominent poly(A) signal patterns, which accounted for approximately 92% of total APA sites in Xenopus tropicalis. Among them, three patterns are specific to X. tropicalis, so they are absent in other animals such as humans or mice. We catalogued APA sites based on their genomic regions and developed a bioinformatics pipeline to identify over-represented signal patterns for each class. Then the schema of cis elements for APA sites in each genomic region was proposed. More importantly, APA usage is dramatically dynamic in embryos along five developmental stages and well-coordinated with the maternal-to-zygotic transition event. We used an entropy-based method to identify developmental stage-specific APA sites and identified significant signal patterns around specific sites and constitutive sites. We found that the APA frequency in different genomic regions varies with developmental stages and that those sites located in intron or coding sequence regions contribute most to the dynamics of gene expression during developmental stages. This study deciphers the characteristics and poly(A) signal patterns for both canonical APA sites and non-canonical APA sites across different developmental stages and gender dimorphisms in X. tropicalis, providing new insights into the dynamic regulation of distal and proximal APA.
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Affiliation(s)
- Sheng Zhu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen, China
| | - Congting Ye
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Moliang Chen
- Department of Automation, Xiamen University, Xiamen, China
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
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3
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Rosenthal SH, Diamos AG, Mason HS. An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves. PLANT MOLECULAR BIOLOGY 2018; 96:429-443. [PMID: 29429129 DOI: 10.1007/s11103-018-0708-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 02/01/2018] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE We have found interesting features of a plant gene (extensin) 3' flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3'-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.
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Affiliation(s)
- Sun Hee Rosenthal
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Andrew G Diamos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Hugh S Mason
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA.
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4
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Hohn T, Rothnie H. Plant pararetroviruses: replication and expression. Curr Opin Virol 2013; 3:621-8. [PMID: 24063990 DOI: 10.1016/j.coviro.2013.08.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/26/2013] [Accepted: 08/26/2013] [Indexed: 02/07/2023]
Abstract
True retroviruses are not known in plants; however, plant pararetroviruses (caulimoviridae) share many retroviral properties, replicating by transcription in the nucleus followed by reverse transcription in the cytoplasm. Pararetroviruses have circular DNA genomes that do not integrate into the host genome, and display several unique expression strategies. Typical of plant pararetroviral pregenomic RNA is a highly structured leader of about 600nt long that is bypassed by scanning ribosomes. Caulimoviruses and Soymoviruses have a further interesting translation mechanism: at least six of the seven open reading frames are translated via polycistronic translation mediated by a specific transactivator (TAV), which modifies the translation complex. TAV also forms large intracellular inclusion bodies, which are the site of translation and virus assembly.
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Affiliation(s)
- Thomas Hohn
- Basel University, Botanical Institute, Basel, Switzerland.
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5
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Catoni M, Lucioli A, Doblas-Ibáñez P, Accotto GP, Vaira AM. From immunity to susceptibility: virus resistance induced in tomato by a silenced transgene is lost as TGS overcomes PTGS. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:941-953. [PMID: 23738576 DOI: 10.1111/tpj.12253] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/20/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023]
Abstract
Tomato line 30.4 was obtained engineering the nucleocapsid (N) gene of tomato spotted wilt virus into plant genome, and immunity to tomato spotted wilt virus infection of its self-pollinated homozygous progeny was observed. Despite the presence of a high amount of transgenic transcripts, transgenic proteins have not been detected, suggesting a mechanism of resistance mediated by RNA. In the present study, we identify post-transcriptional gene silencing as the main mechanism of resistance, which is able to spread systemically through grafting, and show that the line 30.4 resistant plants produce both 24 and 21-22 nt N-gene specific siRNA classes. The transgenic locus in chromosome 4 shows complex multiple insertions of four T-DNA copies in various orientations, all with 3' end deletions in the terminator and part of the N gene. However, for three of them, polyadenylated transcripts are produced, due to flanking tomato genome sequences acting as alternative terminators. Interestingly, starting at the fifth generation after the transformation event, some individual plants show a tomato spotted wilt virus-susceptible phenotype. The change is associated with the disappearance of transgene-specific transcripts and siRNAs, and with hyper-methylation of the transgene, which proceeds gradually through the generations. Once it reaches a critical threshold, the shift from post-transcriptional gene silencing to transcriptional silencing of the transgene eliminates the previously well established virus resistance.
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Affiliation(s)
- Marco Catoni
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Strada delle Cacce 73, 10135, Turin, Italy.
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Xing A, Moon BP, Mills KM, Falco SC, Li Z. Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminators. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:772-82. [PMID: 20331530 DOI: 10.1111/j.1467-7652.2010.00504.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant genetic engineering can create transgenic crops with improved characteristics by introducing trait genes through transformation. Appropriate regulatory elements such as promoters and terminators have to be present in certain configurations for the transgenes to be properly expressed. Five terminators native to soybean genes-encoding a MYB family transcription factor (MYB2), a Kunitz trypsin inhibitor (KTI1), a plasma membrane intrinsic protein (PIP1), a translation elongation factor (EF1A2) and a metallothionein protein (MTH1) were cloned and tested for their ability to enable transgene expression, mRNA polyadenylation and transcription termination. The terminators are as good as a control terminator of the potato proteinase inhibitor II gene (PINII) in conferring proper transgene expression, leading to mRNAs with various polyadenylation sites and terminating mRNA transcripts. RNA transcription read-through was detected in all transgenic plants and was quantified by qRT-PCR to be <1% at positions approximately 1 kb downstream of the 5' ends of different terminators. The detection of read-through RNA transcripts of the corresponding endogenous genes up to approximately 1 kb beyond the polyadenylation sites suggests that limited RNA transcription read-through is a normal phenomenon of gene expression. The study also provided more choices of terminators for plant genetic engineering when constructing DNA constructs containing multiple gene expression cassettes.
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Affiliation(s)
- Aiqiu Xing
- DuPont/Pioneer Crop Genetics, Experimental Station, Wilmington, DE, USA
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Lin HH, Huang LF, Su HC, Jeng ST. Effects of the multiple polyadenylation signal AAUAAA on mRNA 3'-end formation and gene expression. PLANTA 2009; 230:699-712. [PMID: 19597839 DOI: 10.1007/s00425-009-0977-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 06/19/2009] [Indexed: 05/28/2023]
Abstract
Polyadenylation (poly(A)) of eukaryotic mRNA is a critical step for gene expression. In plants, poly(A) signals leading to the formation of polyadenosine tails after mRNAs include the far upstream elements, the AAUAAA-like signals, and the mRNA cleavage sites for poly(A). Multiple AAUAAA signals leading to alternative polyadenosine formation have been found in many genes, but the effects of each AAUAAA signal on gene expression remain to be uncovered. A DNA fragment, whose transcript contains two canonical AAUAAA signals from the 3'-untranslation region of endochitinase gene of tobacco (Nicotiana tabacum L. cv. W38), was mutated and constructed into the downstream of beta-glucuronidase (GUS) coding region. Transient expression of GUS gene from these constructs indicated that the distal AAUAAA signal from the stop codon was more important than the proximal one in stimulating gene expression. Also, the sequence rather than the distance between the stop codon and the AAUAAA signal region was critical for gene expression. Transgenic tobaccos with these constructs were also generated, and the position of the polyadenosine tail formation in this region was mapped. Results revealed that both AAUAAA signals were functional, and that polyadenosine tails of most transcripts were directed by the distal AAUAAA signal. Finally, the RNA stabilities of these variants in transgenic plants were measured. RNAs from the variants with the functional distal AAUAAA signal were more stable than those with the functional proximal one only. The possible secondary structure in this poly(A) signal region was predicted and discussed.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC
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8
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Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ. Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Res 2008; 36:3150-61. [PMID: 18411206 PMCID: PMC2396415 DOI: 10.1093/nar/gkn158] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/19/2008] [Indexed: 12/24/2022] Open
Abstract
The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3'-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5'-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites.
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Affiliation(s)
- Yingjia Shen
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Guoli Ji
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Brian J. Haas
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Xiaohui Wu
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Jianti Zheng
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Greg J. Reese
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
| | - Qingshun Quinn Li
- Department of Botany, Miami University, Oxford, OH 45056, USA, Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, The Genome Research Institute, Rockville, MD 20850 and IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA
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Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J, Zhao J, Su Z, Lv Y, Wang G. Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 48:710-27. [PMID: 17076806 DOI: 10.1111/j.1365-313x.2006.02905.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Full-length cDNAs are very important for genome annotation and functional analysis of genes. The number of full-length cDNAs from maize (Zea mays L.) remains limited. Here we report the construction of a full-length enriched cDNA library from osmotically stressed maize seedlings by using the modified CAP trapper method. From this library, 2073 full-length cDNAs were collected and further analyzed by sequencing from both the 5'- and 3'-ends. A total of 1728 (83.4%) sequences did not match known maize mRNA and full-length cDNA sequences in the GenBank database and represent new full-length genes. After alignment of the 2073 full-length cDNAs with 448 maize BAC sequences, it was found that 84 full-length cDNAs could be mapped to the BACs. Of these, 43 genes (51.2%) have been correctly annotated from the BAC clones, 37 genes (44.0%) have been annotated with a different exon-intron structure from our cDNA, and four genes (4.76%) had no annotations in the TIGR database. Expression analysis of 2073 full-length maize cDNAs using a cDNA macroarray led to the identification of 79 genes upregulated by stress treatments and 329 downregulated genes. Of the 79 stress-inducible genes, 30 genes contain ABRE, DRE, MYB, MYC core sequences or other abiotic-responsive cis-acting elements in their promoters. These results suggest that these cis-acting elements and the corresponding transcription factors take part in plant responses to osmotic stress either cooperatively or independently. Additionally, the data suggest that an ethylene signaling pathway may be involved in the maize response to drought stress.
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Affiliation(s)
- Jinping Jia
- State Key Laboratory of Agrobiotechnology and National Center for Maize Improvement, China Agricultural University, Beijing, China
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10
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Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. PLANT PHYSIOLOGY 2005; 138:1457-68. [PMID: 15965016 PMCID: PMC1176417 DOI: 10.1104/pp.105.060541] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3'-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3'-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3'-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3'-ends for gene annotation.
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Affiliation(s)
- Johnny C Loke
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
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He X, Fütterer J, Hohn T. Contribution of downstream promoter elements to transcriptional regulation of the rice tungro bacilliform virus promoter. Nucleic Acids Res 2002; 30:497-506. [PMID: 11788712 PMCID: PMC99825 DOI: 10.1093/nar/30.2.497] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Downstream sequences influence activity of the rice tungro bacilliform virus (RTBV) promoter in protoplasts derived from cultured rice cells. We previously identified a DNA element located between positions +50 and +90 relative to the transcription start site to which rice nuclear proteins bind. In this study, using DNA UV crosslinking assays, we show that two rice nuclear proteins bind specifically to this DNA element. We demonstrate that the DNA element enhances RTBV promoter activity in a copy number-dependent manner when transferred to a position upstream of the promoter. In addition, using electrophoretic mobility shift assays, we show that at least two novel nuclear proteins from rice cell suspension cultures bind to a subregion (from +50 to +59) of the DNA element and that a protein from rice root, but not shoot, nuclear extracts interacts with a perfect palindromic sequence motif located within the sequence +45 to +59. Furthermore, a position-dependent GAGA motif, present in three copies within downstream promoter sequences from +1 to +50, is involved in the regulation of RTBV promoter activity.
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Affiliation(s)
- Xiaoyuan He
- Friedrich Miescher Institute, PO Box 2543, CH-4002 Basel, Switzerland
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