1
|
Liu X, Du F, Sun L, Li J, Chen S, Li N, Chang Y, Cui J, Chen W, Yao D. Anthocyanin metabolism in Nelumbo: translational and post-translational regulation control transcription. BMC PLANT BIOLOGY 2023; 23:61. [PMID: 36710356 PMCID: PMC9885672 DOI: 10.1186/s12870-023-04068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Lotus (Nelumbo Adans.) is used as an herbal medicine and the flowers are a source of natural flavonoids. 'Da Sajin', which was firstly found in the plateau area, is a natural mutant in flower color with red streamers dyeing around white petals. RESULTS The LC-MS-MS results showed that eight anthocyanin compounds, including cyanidin 3-O-glucoside, cyanidin 3-O-galactoside, malvidin 3-O-galactoside, and malvidin 3-O-glucoside, were differentially enriched in red-pigmented tissues of the petals, whereas most of these metabolites were undetected in white tissues of the petals. Transcriptome profiling indicated that the relative high expression levels of structural genes, such as NnPAL, NnF3H, and NnANS, was inconsistent with the low anthocyanin concentration in white tissues. Members of the NnMYB and NnbHLH transcription factor families were presumed to play a role in the metabolic flux in the anthocyanin and proanthocyanidin biosynthetic pathway. The expression model of translational initiation factor, ribosomal proteins and SKP1-CUL1-F-box protein complex related genes suggested an important role for translational and post-translational network in anthocyanin biosynthesis. In addition, pathway analysis indicated that light reaction or photo destruction might be an important external cause for floral color determination in lotus. CONCLUSIONS In this study, it is supposed that the natural lotus mutant 'Da Sajin' may have originated from a red-flowered ancestor. Partial loss of anthocyanin pigments in petals may result from metabolic disorder caused by light destruction. This disorder is mainly regulated at post translation and translation level, resulting in a non-inherited phenotype. These results contribute to an improved understanding of anthocyanin metabolism in lotus, and indicate that the translational and post-translational regulatory network determines the metabolic flux of anthocyanins and proanthocyanidins under specific environmental conditions.
Collapse
Affiliation(s)
- Xiaojing Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Fengfeng Du
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Linhe Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jinfeng Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Shaozhou Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yajun Chang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jian Cui
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Wen Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China
| | - Dongrui Yao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/Jiangsu Engineering Research Center of Aquatic Plant Resources and Water Environment Remediation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| |
Collapse
|
2
|
Peniche-Pavía HA, Guzmán TJ, Magaña-Cerino JM, Gurrola-Díaz CM, Tiessen A. Maize Flavonoid Biosynthesis, Regulation, and Human Health Relevance: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165166. [PMID: 36014406 PMCID: PMC9413827 DOI: 10.3390/molecules27165166] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022]
Abstract
Maize is one of the most important crops for human and animal consumption and contains a chemical arsenal essential for survival: flavonoids. Moreover, flavonoids are well known for their beneficial effects on human health. In this review, we decided to organize the information about maize flavonoids into three sections. In the first section, we include updated information about the enzymatic pathway of maize flavonoids. We describe a total of twenty-one genes for the flavonoid pathway of maize. The first three genes participate in the general phenylpropanoid pathway. Four genes are common biosynthetic early genes for flavonoids, and fourteen are specific genes for the flavonoid subgroups, the anthocyanins, and flavone C-glycosides. The second section explains the tissue accumulation and regulation of flavonoids by environmental factors affecting the expression of the MYB-bHLH-WD40 (MBW) transcriptional complex. The study of transcription factors of the MBW complex is fundamental for understanding how the flavonoid profiles generate a palette of colors in the plant tissues. Finally, we also include an update of the biological activities of C3G, the major maize anthocyanin, including anticancer, antidiabetic, and antioxidant effects, among others. This review intends to disclose and integrate the existing knowledge regarding maize flavonoid pigmentation and its relevance in the human health sector.
Collapse
Affiliation(s)
- Héctor A. Peniche-Pavía
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
| | - Tereso J. Guzmán
- Department of Pharmacology, Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Jesús M. Magaña-Cerino
- División Académica de Ciencias de la Salud, Centro de Investigación y Posgrado, Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez Magaña 2838-A, Col. Tamulté de las Barrancas, Villahermosa 86150, Tabasco, Mexico
| | - Carmen M. Gurrola-Díaz
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Enfermedades Crónico Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Universidad de Guadalajara, C. Sierra Mojada 950. Col. Independencia, Guadalajara 44340, Jalisco, Mexico
- Correspondence: ; Tel.: +52-33-10585200 (ext. 33930)
| | - Axel Tiessen
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
| |
Collapse
|
3
|
Antonopoulou E, Ladomery M. Targeting Splicing in Prostate Cancer. Int J Mol Sci 2018; 19:ijms19051287. [PMID: 29693622 PMCID: PMC5983716 DOI: 10.3390/ijms19051287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022] Open
Abstract
Over 95% of human genes are alternatively spliced, expressing splice isoforms that often exhibit antagonistic functions. We describe genes whose alternative splicing has been linked to prostate cancer; namely VEGFA, KLF6, BCL2L2, ERG, and AR. We discuss opportunities to develop novel therapies that target specific splice isoforms, or that target the machinery of splicing. Therapeutic approaches include the development of small molecule inhibitors of splice factor kinases, splice isoform specific siRNAs, and splice switching oligonucleotides.
Collapse
Affiliation(s)
- Effrosyni Antonopoulou
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK.
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK.
| |
Collapse
|
4
|
Complex regulation of the TaMyc1 gene expression in wheat grain synthesizing anthocyanin pigments. Mol Biol Rep 2018; 45:327-334. [PMID: 29556921 DOI: 10.1007/s11033-018-4165-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 03/11/2018] [Indexed: 01/08/2023]
Abstract
The wheat TaMyc1 gene encodes for transcriptional factor (TF) with bHLH domain. The gene is expressed in purple wheat grains and activates transcription of the anthocyanin biosynthesis structural genes. To reveal the features of TaMyc1 regulation in wheat pericarp transcription start sites (TSS) were identified by 5' RACE mean and translation efficiency was predicted by in silico methods. Three alternative transcript variants of TaMyc1 differing by 5' leader sequence only were identified in purple pericarp. The three transcripts are generated from distinct TATA boxes and thereby are differed by TSS. Two transcripts (TaMyc1a, -b) have identical initiation AUG codons that lead to the TaMYC1 regulatory protein with bHLH domain. However because of different stability of secondary structures predicted in 5' leader the two transcripts might be translated with different efficiency. The third transcript is assumed to be not effectively translated. qRT-PCR and colonies counting were applied to assess contribution each of the transcripts to total TaMyc1 gene transcription level. TaMyc1c has the lowest contribution (ca. 16%), whereas the others two transcripts contribute equally (ca. 42%) to total TaMyc1 expression level. The role of the tree mRNA isoforms transcribed in one tissue is discussed.
Collapse
|
5
|
Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB. A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:694. [PMID: 28539927 PMCID: PMC5423905 DOI: 10.3389/fpls.2017.00694] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/18/2017] [Indexed: 05/19/2023]
Abstract
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.
Collapse
Affiliation(s)
- Wenbin Mei
- Department of Biology, University of Florida, GainesvilleFL, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, AmesIA, USA
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, LincolnNE, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, AmesIA, USA
| | - Nathan M. Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint PaulMN, USA
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, AmesIA, USA
- Center for Plant Genomics, Iowa State University, AmesIA, USA
| | - William B. Barbazuk
- Department of Biology, University of Florida, GainesvilleFL, USA
- Genetics Institute, University of Florida, GainesvilleFL, USA
- *Correspondence: William B. Barbazuk,
| |
Collapse
|
6
|
Li Z, Wang J, Zhang X, Xu L. Comparative transcriptome analysis of Anthurium "Albama" and its anthocyanin-loss mutant. PLoS One 2015; 10:e0119027. [PMID: 25781998 PMCID: PMC4363789 DOI: 10.1371/journal.pone.0119027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/09/2015] [Indexed: 01/12/2023] Open
Abstract
Anthurium is one of the most important tropical ornamental plants in the world. The traded value of anthurium is second only to that of tropical orchids among the tropical flowers. The spathe is the main ornamental organ and its color variation mainly arises from anthocyanin contents. Understanding the molecular regulation of spathe color will accelerate new variety creation of anthurium. To announce gene expression differences between Anthurium andraeanum ‘Albama’ and its one unique anthocyanin-loss mutant, we collected spathes of the wild-type and the mutant from two stages in spathe development (the flower separates protrude from the sheath and the spathe is fully expanded) and extracted total RNAs for transcriptome profiling. Using short read sequencing technology (Illumina), 51,955,564, 53,822,224, 54,221,990 and 52,276,418 sequencing raw reads, respectively, for wild-type and mutant in the two stages were assembled de novo into 111,268 unique sequences (unigenes) with a mean length of 652 bp. 47,563 unigenes had significant hits to the sequences in the Nr database, and 32,768 unigenes showed significant similarity to known proteins in the Swiss-Prot database. 28,350 and 19,293 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Further, analysis of differentially expressed genes in the comparison between wild-type and mutant and between the two different developmental stages was carried out, indicating that the expression of an extensive set of genes changed as the result of mutation. Taken together, these data demonstrated that the Illumina sequencing allowed de novo transcriptome assembly and could obtain differentially expressed genes between A. andraeanum wild-type and the anthocyanin-loss mutant. The expression differences of AN2 and UFGT might cause the anthocyanin-loss mutation.
Collapse
Affiliation(s)
- Zhiying Li
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Hainan University, Haikou, Hainan Province 571700, PR China
| | - Jiabin Wang
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Xuequan Zhang
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Hainan University, Haikou, Hainan Province 571700, PR China
| | - Li Xu
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Hainan University, Haikou, Hainan Province 571700, PR China
- * E-mail:
| |
Collapse
|
7
|
Horiguchi G, Van Lijsebettens M, Candela H, Micol JL, Tsukaya H. Ribosomes and translation in plant developmental control. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:24-34. [PMID: 22682562 DOI: 10.1016/j.plantsci.2012.04.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/16/2012] [Accepted: 04/16/2012] [Indexed: 05/06/2023]
Abstract
Ribosomes play a basic housekeeping role in global translation. However, a number of ribosomal-protein-defective mutants show common and rare developmental phenotypes including growth defects, changes in leaf development, and auxin-related phenotypes. This suggests that translational regulation may be occurring during development. In addition, proteomic and bioinformatic analyses have demonstrated a high heterogeneity in ribosome composition. Although this might be a sign of unequal roles of individual ribosomal proteins, it does not explain every ribosomal-protein-defective phenotype. Moreover, comprehensive interpretations concerning the relationship between ribosomal-protein-defective phenotypes and molecular changes in ribosome status are lacking. In this review, we address these phenotypes based on three models, ribosome insufficiency, heterogeneity, and aberrancy, to consider how ribosomes play developmental roles. We propose that the three models are not mutually exclusive, and ribosomal-protein-defective phenotypes can be explained with one or more of these models. The three models with reference to genetic, biochemical, and bioinformatic knowledge will serve as a foundation for future studies of translational regulation.
Collapse
Affiliation(s)
- Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | | | | | | | | |
Collapse
|
8
|
Saul H, Elharrar E, Gaash R, Eliaz D, Valenci M, Akua T, Avramov M, Frankel N, Berezin I, Gottlieb D, Elazar M, David-Assael O, Tcherkas V, Mizrachi K, Shaul O. The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:1031-42. [PMID: 19754518 DOI: 10.1111/j.1365-313x.2009.04021.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Approximately 20% of plant genes possess upstream open-reading frames (uORFs). The effect of uORFs on gene expression has mainly been studied at the translational level. Very little is known about the impact of plant uORFs on transcript content through the nonsense-mediated mRNA decay (NMD) pathway, which degrades transcripts bearing premature termination codons (PTCs). Here we examine the impact of the uORF of the Arabidopsis AtMHX gene on transcript accumulation. The suggestion that this uORF exposes transcripts containing it to NMD is supported by (i) the increase in transcript levels upon eliminating the uORF from constructs containing it, (ii) experiments with a modified uORF-peptide, which excluded peptide-specific degradation mechanisms, (iii) the increase in levels of the native AtMHX transcript upon treatment with cycloheximide, which inhibits translation and blocks NMD, and (iv) the sensitivity of transcripts containing the uORF of AtMHX to the presence of introns. We also showed that introns can increase NMD efficiency not only in transcripts having relatively short 3' untranslated regions (UTRs), but also in uORF-containing transcripts. AtMHX transcript levels were almost unaltered in mutants of the NMD factors UPF3 and UPF1. Possible reasons, including the existence of a NMD-compensatory mechanism, are discussed. Interestingly, the levels of UPF3 transcript were higher in upf1 mutants, suggesting a compensatory mechanism that links weak function of the NMD machinery to increased expression of UPF3. Our findings highlight that uORFs, which are abundant in plants, can not only inhibit translation but also strongly affect transcript accumulation.
Collapse
Affiliation(s)
- Helen Saul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Combier JP, de Billy F, Gamas P, Niebel A, Rivas S. Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development. Genes Dev 2008; 22:1549-59. [PMID: 18519645 DOI: 10.1101/gad.461808] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MtHAP2-1 is a CCAAT-binding transcription factor from the model legume Medicago truncatula. We previously showed that MtHAP2-1 expression is regulated both spatially and temporally by microRNA169. Here we present a novel regulatory mechanism controlling MtHAP2-1 expression. Alternative splicing of an intron in the MtHAP2-1 5'leader sequence (LS) becomes predominant during the development of root nodules, leading to the production of a small peptide, uORF1p. Our results indicate that binding of uORF1p to MtHAP2-1 5'LS mRNA leads to reduced accumulation of the MtHAP2-1 transcript and may contribute to spatial restriction of MtHAP2-1 expression within the nodule. We propose that miR169 and uORF1p play essential, sequential, and nonredundant roles in regulating MtHAP2-1 expression. Importantly, in contrast to previously described cis-acting uORFs, uORF1p is able to act in trans to down-regulate gene expression. Our work thus contributes to a better understanding of the action of upstream ORFs (uORFs) in the regulation of gene expression.
Collapse
Affiliation(s)
- Jean Philippe Combier
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), Centre National de la Recherche Scientifique-Institut National de la Recherche Agronomique UMR 2594/441, F-31320 Castanet Tolosan, France.
| | | | | | | | | |
Collapse
|
10
|
Gao H, Gordon-Kamm WJ, Lyznik LA. ASF/SF2-like maize pre-mRNA splicing factors affect splice site utilization and their transcripts are alternatively spliced. Gene 2004; 339:25-37. [PMID: 15363843 DOI: 10.1016/j.gene.2004.06.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 05/26/2004] [Accepted: 06/17/2004] [Indexed: 10/26/2022]
Abstract
Three ASF/SF2-like alternative splicing genes from maize were identified, cloned, and analyzed. Each of these genes (zmSRp30, zmSRp31, and zmSRp32) contains two RNA binding domains, a signature sequence SWQDLKD, and a characteristic serine/ariginine-rich domain. There is a strong structural similarity to the human ASF/SF2 splicing factor and to the Arabidopsis atSRp34/p30 proteins. Similar to ASF/SF2-like genes in other organisms, the maize pre-mRNA messages are alternatively spliced. They are differentially expressed in maize tissues with relatively uniform levels of zmSRp30 and zmSRp31 messages being observed throughout the plant, while zmSRp32 messages preferentially accumulated in the meristematic regions. Overexpression of zmSRp32 in maize cells leads to the enhanced selection of weak 5' intron splice sites during the processing of pre-mRNA molecules. Overexpression of the zmSRp31 or zmSRp32 gene affects regulation of wheat dwarf virus rep gene pre-mRNA splicing, presumably by interacting with the weak 5' splice site, CCGU. Our results suggest that the described genes are functional homologues of the human ASF/SF2 alternative splicing factor and they indicate a diversity of the ASF/SF2-like alternative splicing factors in monocot plant cells.
Collapse
Affiliation(s)
- Huirong Gao
- Pioneer Hi-Bred International (a DuPont company), Johnston, IA, USA
| | | | | |
Collapse
|
11
|
Bassett CL, Nickerson ML, Farrell RE, Harrison M. Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner. Mol Genet Genomics 2004; 271:752-60. [PMID: 15221460 DOI: 10.1007/s00438-004-1031-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Accepted: 05/21/2004] [Indexed: 10/26/2022]
Abstract
TATA boxes are the most common regulatory elements found in the promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II. Often only a single TATA element is found in a given promoter, and tissue-, stage- and/or stimulus-specific expression occurs because the TATA box is associated with other cis -acting elements that enhance or repress transcription. We used software tools for gene analysis to assist in locating potential TATA box(es) in an AT-rich region of the promoter of a gene, inrpk1, which codes for a leucine-rich receptor protein kinase in morning glory (Ipomoea nil). Through the use of RT-PCR and various combinations of forward primers bracketing most of the promoter region we were able to define the 5'-ends of transcripts in this region. The region was then targeted for analysis by RNA Ligase-Mediated-5' Rapid Amplification of cDNA Ends (RLM-5' RACE) to identify the transcript initiation site(s). Positioning of initiation sites with respect to TATA boxes identified by gene analysis tools allowed us to identify three operational TATA elements which regulate basal transcription from this gene. Two TATA boxes were responsible for all of the inrpk1 transcripts found in leaves and cotyledons, and about 25-30% of the transcripts in roots. A third TATA box was involved only in expression in roots and accounted for the remaining 50-70% of root transcripts. RNAs expressed from this element lack two potentially functional upstream AUG codons, and may be translated more efficiently than transcripts originating from the other TATA boxes.
Collapse
Affiliation(s)
- C L Bassett
- The Appalachian Fruit Research Station, USDA-ARS, 2217 Wiltshire Road, Kearneysville, WV 25430, USA.
| | | | | | | |
Collapse
|
12
|
Halterman DA, Wei F, Wise RP. Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. PLANT PHYSIOLOGY 2003; 131:558-67. [PMID: 12586880 PMCID: PMC166832 DOI: 10.1104/pp.014407] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Revised: 11/08/2002] [Accepted: 11/21/2002] [Indexed: 05/20/2023]
Abstract
In barley (Hordeum vulgare), the Mla13 powdery mildew resistance gene confers Rar1-dependent, AvrMla13-specific resistance to Blumeria graminis f. sp. hordei (Bgh). We have identified cDNA and genomic copies of Mla13 and used this coiled-coil nucleotide-binding site leucine-rich repeat protein-encoding gene as a model for the regulation of host resistance to obligate biotrophic fungi in cereals. We demonstrate quantitatively that a rapid increase in the accumulation of Mla transcripts and transcripts of the Mla-signaling genes, Rar1 and Sgt1, is triggered between 16 and 20 h post inoculation, the same time frame that haustoria of avirulent Bgh make contact with the host cell plasma membrane. An abundance of Mla13 cDNAs revealed five classes of transcript leader regions containing two alternatively spliced introns and up to three upstream open reading frames (uORFs). Alternative splicing of introns in the transcript leader region results in a different number of uORFs and variability in the size of uORF2. These results indicate that regulation of Mla transcript accumulation is not constitutive and that induction is coordinately controlled by recognition-specific factors. The sudden increase in specific transcript levels could account for the rapid defense response phenotype conferred by Mla6 and Mla13.
Collapse
Affiliation(s)
- Dennis A Halterman
- Corn Insects and Crop Genetics Research, United States Department of Agriculture-Agricultural Research Service, Iowa State University, Ames, Iowa 50011-1020, USA
| | | | | |
Collapse
|
13
|
Irani NG, Hernandez JM, Grotewold E. Chapter three Regulation of anthocyanin pigmentation. RECENT ADVANCES IN PHYTOCHEMISTRY 2003. [DOI: 10.1016/s0079-9920(03)80018-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|