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Wang Z, Wang P, He J, Kong L, Zhang W, Liu W, Liu X, Ma W. Genome-Wide Analysis of the HSF Gene Family Reveals Its Role in Astragalus mongholicus under Different Light Conditions. BIOLOGY 2024; 13:280. [PMID: 38666892 PMCID: PMC11048653 DOI: 10.3390/biology13040280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Astragalus mongholicus is a traditional Chinese medicine (TCM) with important medicinal value and is widely used worldwide. Heat shock (HSF) transcription factors are among the most important transcription factors in plants and are involved in the transcriptional regulation of various stress responses, including drought, salinity, oxidation, osmotic stress, and high light, thereby regulating growth and developmental processes. However, the HFS gene family has not yet been identified in A. mongholicus, and little is known regarding the role of HSF genes in A. mongholicus. This study is based on whole genome analysis of A. mongholicus, identifying a total of 22 AmHSF genes and analyzing their physicochemical properties. Divided into three subgroups based on phylogenetic and gene structural characteristics, including subgroup A (12), subgroup B (9), and subgroup C (1), they are randomly distributed in 8 out of 9 chromosomes of A. mongholicus. In addition, transcriptome data and quantitative real time polymerase chain reaction (qRT-PCR) analyses revealed that AmHSF was differentially transcribed in different tissues, suggesting that AmHSF gene functions may differ. Red and blue light treatment significantly affected the expression of 20 HSF genes in soilless cultivation of A. mongholicus seedlings. AmHSF3, AmHSF3, AmHSF11, AmHSF12, and AmHSF14 were upregulated after red light and blue light treatment, and these genes all had light-corresponding cis-elements, suggesting that AmHSF genes play an important role in the light response of A. mongholicus. Although the responses of soilless-cultivated A. mongholicus seedlings to red and blue light may not represent the mature stage, our results provide fundamental research for future elucidation of the regulatory mechanisms of HSF in the growth and development of A. mongholicus and its response to different light conditions.
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Affiliation(s)
- Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
| | - Panpan Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
| | - Jiajun He
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
| | - Lingyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
| | - Wenwei Zhang
- Experimental Teaching and Practical Training Center, Heilongjiang University of Chinese Medicine, Harbin 150040, China;
| | - Weili Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
- Experimental Teaching and Practical Training Center, Heilongjiang University of Chinese Medicine, Harbin 150040, China;
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, Jiamusi 154007, China
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (Z.W.); (P.W.); (J.H.); (L.K.); (W.L.)
- Experimental Teaching and Practical Training Center, Heilongjiang University of Chinese Medicine, Harbin 150040, China;
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Identification of a biomass unaffected pale green mutant gene in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Sci Rep 2022; 12:7731. [PMID: 35546169 PMCID: PMC9095832 DOI: 10.1038/s41598-022-11825-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/27/2022] [Indexed: 11/29/2022] Open
Abstract
Chlorophyll (Chl) is an essential component of the photosynthetic apparatus and pigments in plant greening. Leaf color is an important agronomic and commercial trait of Chinese cabbage. In this study, we identified a pale green mutant pgm created by ethyl methane sulfonate (EMS) mutagenesis in Chinese cabbage. Compared with wild-type (FT), pgm had a lower Chl content with a higher Chl a/b ratio, imperfect chloroplast structure, and lower non-photochemical quenching. However, its net photosynthetic rate and biomass showed no significant differences. Genetic analysis revealed that the pale green phenotype of pgm was controlled by a recessive nuclear gene, designated as Brpgm. We applied BSR-Seq, linkage analysis, and whole-genome resequencing to map Brpgm and predicted that the target gene was BraA10g007770.3C (BrCAO), which encodes chlorophyllide a oxygenase (CAO). Brcao sequencing results showed that the last nucleotide of its first intron changed from G to A, causing the deletion of the first nucleotide in its second CDS and termination of the protein translation. The expression of BrCAO in pgm was upregulated, and the enzyme activity of CAO in pgm was significantly decreased. These results provide an approach to explore the function of BrCAO and create a pale green variation in Chinese cabbage.
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Genome-Scale Computational Identification and Characterization of UTR Introns in Atalantia buxifolia. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accumulated evidence has shown that CDS introns (CIs) play important roles in regulating gene expression. However, research on UTR introns (UIs) is limited. In this study, UIs (including 5′UTR and 3′UTR introns (5UIs and 3UIs)) were identified from the Atalantia buxifolia genome. The length and nucleotide distribution characteristics of both 5UIs and 3UIs and the distributions of cis-acting elements and transcription factor binding sites (TFBSs) in 5UIs were investigated. Moreover, PageMan enrichment analysis was applied to show the possible roles of transcripts containing UIs (UI-Ts). In total, 1077 5UIs and 866 3UIs were identified from 897 5UI-Ts and 670 3UI-Ts, respectively. Among them, 765 (85.28%) 5UI-Ts and 527 (78.66%) 3UI-Ts contained only one UI, and 94 (6.38%) UI-Ts contained both 5UI and 3UI. The UI density was lower than that of CDS introns, but their mean and median intron sizes were ~2 times those of the CDS introns. The A. buxifolia 5UIs were rich in gene-expression-enhancement-related elements and contained many TFBSs for BBR-BPC, MIKC_MADS, AP2 and Dof TFs, indicating that 5UIs play a role in regulating or enhancing the expression of downstream genes. Enrichment analysis revealed that UI-Ts involved in ‘not assigned’ and ‘RNA’ pathways were significantly enriched. Noteworthily, 119 (85.61%) of the 3UI-Ts were genes encoding pentatricopeptide (PPR) repeat-containing proteins. These results will be helpful for the future study of the regulatory roles of UIs in A. buxifolia.
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Park HY, Lee HT, Lee JH, Kim JK. Arabidopsis U2AF65 Regulates Flowering Time and the Growth of Pollen Tubes. FRONTIERS IN PLANT SCIENCE 2019; 10:569. [PMID: 31130976 PMCID: PMC6510283 DOI: 10.3389/fpls.2019.00569] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/15/2019] [Indexed: 05/19/2023]
Abstract
During pre-mRNA splicing, U2 small nuclear ribonucleoprotein auxiliary factor 65 (U2AF65) interacts with U2AF35 and splicing factor 1 (SF1), allowing for the recognition of the 3'-splice site by the ternary complex. The functional characterization of U2AF65 homologs has not been performed in Arabidopsis thaliana yet. Here, we show that normal plant development, including floral transition, and male gametophyte development, requires two Arabidopsis U2AF65 isoforms (AtU2AF65a and AtU2AF65b). Loss-of-function mutants of these two isoforms displayed opposite flowering phenotypes: atu2af65a mutants showed late flowering, whereas atu2af65b mutants were characterized by slightly early flowering, as compared to that in the wild-type (Col-0) plants. These abnormal flowering phenotypes were well-correlated with the expression patterns of the flowering time genes such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). However, the two atu2af65 mutants did not display any morphological abnormalities or alterations in abiotic stress tests. Double mutation of the AtU2AF65a and AtU2AF65b genes resulted in non-viable seeds due to defective male gametophyte. In vitro pollen germination test revealed that mutations in both AtU2AF65a and AtU2AF65b genes significantly impaired pollen tube growth. Collectively, our findings suggest that two protein isoforms of AtU2AF65 are differentially involved in regulating flowering time and display a redundant role in pollen tube growth.
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Affiliation(s)
- Hyo-Young Park
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Hee Tae Lee
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jeong Hwan Lee
- Division of Life Science, Chonbuk National University, Jeonju, South Korea
- *Correspondence: Jeong Hwan Lee, Jeong-Kook Kim,
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
- *Correspondence: Jeong Hwan Lee, Jeong-Kook Kim,
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He P, Wang X, Zhang X, Jiang Y, Tian W, Zhang X, Li Y, Sun Y, Xie J, Ni J, He G, Sang X. Short and narrow flag leaf1, a GATA zinc finger domain-containing protein, regulates flag leaf size in rice (Oryza sativa). BMC PLANT BIOLOGY 2018; 18:273. [PMID: 30413183 PMCID: PMC6230254 DOI: 10.1186/s12870-018-1452-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 09/27/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND The flag leaf of rice (Oryza sativa L.) is an important determinant of plant type characteristics and grain yield. Identification of flag leaf mutants of rice is crucial to elucidate the molecular mechanism of flag-leaf development, and for exploitation of rice germplasm resources. RESULTS In this study, we describe a mutant designated short and narrow flag leaf 1 (snfl1). Histological analysis showed that the length of epidermal cells and number of longitudinal veins were decreased in the flag leaf of the snfl1 mutant. Map-based cloning indicated that a member of the GATA family of transcription factors is a candidate gene for SNFL1. A single-nucleotide transition at the last base in the single intron of snfl1 led to variation in alternative splicing and early termination of translation. Complemented transgenic plants harbouring the candidate SNFL1 gene rescued the snfl1 mutant. Analysis of RT-PCR and the SNFL1 promoter by means of a GUS fusion expression assay showed that abundance of SNFL1 transcripts was higher in the culm, leaf sheath, and root. Expression of the SNFL1-GFP fusion protein in rice protoplasts showed that SNFL1 was localized in nucleus. CONCLUSIONS We conclude that SNFL1 is an important regulator of leaf development, the identification of which might have important implications for future research on GATA transcription factors.
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Affiliation(s)
- Peilong He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaowen Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaobo Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yudong Jiang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Institute of Rice and Sorghum, Sichuan Academy of Agricultural Sciences, Deyang, China
| | - Weijiang Tian
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaoqiong Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yangyang Li
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ying Sun
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jia Xie
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jile Ni
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Xianchun Sang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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Shi X, Castandet B, Germain A, Hanson MR, Bentolila S. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2833-2847. [PMID: 28549172 PMCID: PMC5853588 DOI: 10.1093/jxb/erx139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/30/2017] [Indexed: 05/02/2023]
Abstract
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors. Here we report the identification of organelle RRM protein 5 (ORRM5) as a mitochondrial editing factor with a unique mode of action. Unlike other ORRM editing factors, the absence of ORRM5 in orrm5 mutant plants results in an increase of the editing extent in 14% of the mitochondrial sites surveyed. The orrm5 mutant also exhibits a reduced splicing efficiency of the first nad5 intron and slower growth and delayed flowering time. ORRM5 contains an RNA recognition motif (RRM) and a glycine-rich domain at the C terminus. The RRM provides the editing activity of ORRM5 and is able to complement the splicing but not the morphological defects.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Correspondence:
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Kianianmomeni A, Ong CS, Rätsch G, Hallmann A. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics 2014; 15:1117. [PMID: 25516378 PMCID: PMC4378016 DOI: 10.1186/1471-2164-15-1117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/11/2014] [Indexed: 11/15/2022] Open
Abstract
Background Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction. Results Here we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5′ (17.9%) and 3′ (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types (Mol Biol Evol 31:1402-1413, 2014). To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR. Conclusions The results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1117) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany.
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Kelliher T, Walbot V. Maize germinal cell initials accommodate hypoxia and precociously express meiotic genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:639-52. [PMID: 24387628 PMCID: PMC3928636 DOI: 10.1111/tpj.12414] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/24/2013] [Accepted: 12/09/2013] [Indexed: 05/20/2023]
Abstract
In flowering plants, anthers are the site of de novo germinal cell specification, male meiosis, and pollen development. Atypically, anthers lack a meristem. Instead, both germinal and somatic cell types differentiate from floral stem cells packed into anther lobes. To better understand anther cell fate specification and to provide a resource for the reproductive biology community, we isolated cohorts of germinal and somatic initials from maize anthers within 36 h of fate acquisition, identifying 815 specific and 1714 significantly enriched germinal transcripts, plus 2439 specific and 2112 significantly enriched somatic transcripts. To clarify transcripts involved in cell differentiation, we contrasted these profiles to anther primordia prior to fate specification and to msca1 anthers arrested in the first step of fate specification and hence lacking normal cell types. The refined cell-specific profiles demonstrated that both germinal and somatic cell populations differentiate quickly and express unique transcription factor sets; a subset of transcript localizations was validated by in situ hybridization. Surprisingly, germinal initials starting 5 days of mitotic divisions were enriched significantly in >100 transcripts classified in meiotic processes that included recombination and synapsis, along with gene sets involved in RNA metabolism, redox homeostasis, and cytoplasmic ATP generation. Enrichment of meiotic-specific genes in germinal initials challenges current dogma that the mitotic to meiotic transition occurs later in development during pre-meiotic S phase. Expression of cytoplasmic energy generation genes suggests that male germinal cells accommodate hypoxia by diverting carbon away from mitochondrial respiration into alternative pathways that avoid producing reactive oxygen species (ROS).
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Affiliation(s)
- Timothy Kelliher
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
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Natural rules for Arabidopsis thaliana pre-mRNA splicing site selection. Open Life Sci 2012. [DOI: 10.2478/s11535-012-0060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe accurate prediction of plant pre-mRNA splicing sites has been studied extensively. The rules for plant pre-mRNA splicing still remain unknown. This study, based on confirmed sequence data, systematically analyzed all expressed genes on Arabidopsis thaliana chromosome IV to quantitatively explore the natural splicing rules. The results indicated that defining Arabidopsis thaliana pre-mRNA splicing sites required a combination of multiple factors including (1) relative conserved consensus sequence at splicing site; (2) individual nucleotide distribution pattern in 50 nucleotides up- and down-stream regions of splicing site; (3) quantitative analysis of individual nucleotide distribution by using the formulations concluded from this study. The combination of all these factors together can bring the accuracy of Arabidopsis thaliana splicing site recognition over 99%. The results provide additional information to the future of plant pre-mRNA splicing research.
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Mathew LG, Maloney B, Takeda N, Mason HS. Spurious polyadenylation of Norovirus Narita 104 capsid protein mRNA in transgenic plants. PLANT MOLECULAR BIOLOGY 2011; 75:263-75. [PMID: 21203799 DOI: 10.1007/s11103-010-9725-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 12/22/2010] [Indexed: 05/30/2023]
Abstract
Noroviruses are members of the family Caliciviridae, and cause a highly communicable gastroenteritis in humans. We explored the potential to develop a plant-based vaccine against Narita 104 virus, a Genogroup II Norovirus. In stably transgenic potato, we obtained very poor expression of Narita 104 virus capsid protein (NaVCP) despite the use of a strong constitutive promoter (dual enhancer 35S) driving the native coding sequence. We identified potentially detrimental sequence motifs that could mediate aberrant mRNA processing via spurious polyadenylation signals. Northern blots and RT-PCR analysis of total RNA revealed truncated transcripts that suggested premature polyadenylation. Site-directed mutagenesis to remove one potential polyadenylation near-upstream element resulted in an increased expression of NaVCP when transiently expressed in leaves of Nicotiana benthamiana. Further, cloning of the truncated cDNAs from transgenic NaVCP potato plants and transiently transfected N. benthamiana allowed us to identify at least ten different truncated transcripts resulting from premature polyadenylation of full length NaVCP transcripts. Comparative studies using real time PCR analysis from cDNA samples revealed lower accumulation of full length transcripts of NaVCP as compared to those from a gene encoding Norwalk Virus capsid protein (a related Genogroup I Norovirus) in transiently transfected plants. These findings provide evidence for impaired expression of NaVCP in transgenic plants mediated by spurious polyadenylation signals, and demonstrate the need to scrupulously search for potential polyadenylation signals in order to improve transgene expression in plants.
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Affiliation(s)
- Lolita G Mathew
- Center for Infectious Diseases and Vaccinology (CIDV), The Biodesign Institute at Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287-5401, USA
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Hensel G, Himmelbach A, Chen W, Douchkov DK, Kumlehn J. Transgene expression systems in the Triticeae cereals. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:30-44. [PMID: 20739094 DOI: 10.1016/j.jplph.2010.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 07/19/2010] [Accepted: 07/21/2010] [Indexed: 05/29/2023]
Abstract
The control of transgene expression is vital both for the elucidation of gene function and for the engineering of transgenic crops. Given the dominance of the Triticeae cereals in the agricultural economy of the temperate world, the development of well-performing transgene expression systems of known functionality is of primary importance. Transgenes can be expressed either transiently or stably. Transient expression systems based on direct or virus-mediated gene transfer are particularly useful in situations where the need is to rapidly screen large numbers of genes. However, an unequivocal understanding of gene function generally requires that a transgene functions throughout the plant's life and is transmitted through the sexual cycle, since this alone allows its effect to be decoupled from the plant's response to the generally stressful gene transfer event. Temporal, spatial and quantitative control of a transgene's expression depends on its regulatory environment, which includes both its promoter and certain associated untranslated region sequences. While many transgenic approaches aim to manipulate plant phenotype via ectopic gene expression, a transgene sequence can be also configured to down-regulate the expression of its endogenous counterpart, a strategy which exploits the natural gene silencing machinery of plants. In this review, current technical opportunities for controlling transgene expression in the Triticeae species are described. Apart from protocols for transient and stable gene transfer, the choice of promoters and other untranslated regulatory elements, we also consider signal peptides, as they too govern the abundance and particularly the sub-cellular localization of transgene products.
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Affiliation(s)
- Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Gatersleben, Germany
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Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 2008; 9:159. [PMID: 18402682 PMCID: PMC2375911 DOI: 10.1186/1471-2164-9-159] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 04/10/2008] [Indexed: 11/10/2022] Open
Abstract
Background Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. Results In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. Conclusion NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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Transcriptional and post-transcriptional enhancement of gene expression by the 5' UTR intron of rice rubi3 gene in transgenic rice cells. Mol Genet Genomics 2008; 279:429-39. [PMID: 18236078 DOI: 10.1007/s00438-008-0323-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 01/13/2008] [Indexed: 01/01/2023]
Abstract
Introns play a very important role in regulating gene expression in eukaryotes. In plants, many introns enhance gene expression, and the effect of intron-mediated enhancement (IME) of gene expression is reportedly often more profound in monocots than in dicots. To further gain insight of IME in monocot plants, we quantitatively dissected the effect of the 5' UTR intron of the rice rubi3 gene at various gene expression levels in stably transformed suspension cell lines. The intron enhanced the GUS reporter gene activity in these lines by about 29-fold. Nuclear run-on experiments demonstrated a nearly twofold enhancement by the 5' UTR intron at the transcriptional level. RNA analysis by RealTime quantitative RT-PCR assays indicated the intron enhanced the steady state RNA level of the GUS reporter gene by nearly 20-fold, implying a strong role of the intron in RNA processing and/or export. The results also implicated a moderate role of the intron in enhancement at the translational level ( approximately 45%). Moreover, results from a transient assay experiment using a shortened exon 1 sequence revealed an important role of exon 1 of rubi3 in gene expression. It may also hint a divergence in IME mechanisms between plant and animal cells. These results demonstrated transcriptional enhancement by a plant intron, but suggested that post-transcriptional event(s) be the major source of IME.
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Dong H, Guo X, Pei Y, Dai C, Fang Y, Tu Q, Zhuang J, Zhao D, Zheng K, Li D. Multiple splicing types of OsRIX4, an RAD21 homolog in rice (Oryza sativa L.). CHINESE SCIENCE BULLETIN-CHINESE 2007. [DOI: 10.1007/s11434-007-0218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, Fluhr R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 39:877-85. [PMID: 15341630 DOI: 10.1111/j.1365-313x.2004.02172.x] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Alternative splicing (AS) combines different transcript splice junctions that result in transcripts with shuffled exons, alternative 5' or 3' splicing sites, retained introns and different transcript termini. In this way, multiple mRNA species and proteins can be created from a single gene expanding the potential informational content of eukaryotic genomes. Search algorithms of AS forms in a variety of Arabidopsis databases showed they contained an unusually high fraction of retained introns (above 30%), compared with 10% that was reported for humans. The preponderance of retained introns (65%) were either part of open reading frames, present in the UTR region or present as the last intron in the transcript, indicating that their occurrence would not participate in non-sense-mediated decay. Interestingly, the functional distribution of the transcripts with retained introns is skewed towards stress and external/internal stimuli-related functions. A sampling of the alternative transcripts with retained introns were confirmed by RT-PCR and were shown to co-purify with polyribosomes, indicating their nuclear export. Thus, retained introns are a prominent feature of AS in Arabidopsis and as such may play a regulatory function.
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Affiliation(s)
- Hadas Ner-Gaon
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Simpson CG, Jennings SN, Clark GP, Thow G, Brown JWS. Dual functionality of a plant U-rich intronic sequence element. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:82-91. [PMID: 14675434 DOI: 10.1046/j.1365-313x.2003.01941.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In potato invertase genes, the constitutively included, 9-nucleotide (nt)-long mini-exon requires a strong branchpoint and U-rich polypyrimidine tract for inclusion. The strength of these splicing signals was demonstrated by greatly enhanced splicing of a poorly spliced intron and by their ability to support splicing of an artificial mini-exon, following their introduction. Plant introns also require a second splicing signal, UA-rich intronic elements, for efficient intron splicing. Mutation of the branchpoint caused loss of mini-exon inclusion without loss of splicing enhancement, showing that the same U-rich sequence can function as either a polypyrimidine tract or a UA-rich intronic element. The distinction between the splicing signals depended on intron context (the presence or absence of an upstream, adjacent and functional branchpoint), and on the sequence context of the U-rich elements. Polypyrimidine tracts tolerated C residues while UA-rich intronic elements tolerated As. Thus, in plant introns, U-rich splicing elements can have dual roles as either a general plant U-rich splicing signal or a polypyrimidine tract. Finally, overexpression of two different U-rich binding proteins enhanced intron recognition significantly. These results highlight the importance of co-operation between splicing signals, the importance of other nucleotides within U-rich elements for optimal binding of competing splicing factors and effects on splicing efficiency of U-rich binding proteins.
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Affiliation(s)
- Craig G Simpson
- Gene Expression, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
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Ali GS, Golovkin M, Reddy ASN. Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:883-93. [PMID: 14675452 DOI: 10.1046/j.1365-313x.2003.01932.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Serine/arginine-rich (SR) proteins in non-plant systems are known to play important roles in both constitutive and alternative splicing of pre-messenger RNAs (pre-mRNAs). Recently, we isolated a novel SR protein (SR45), which interacts with U1 snRNP 70K protein, a key protein involved in 5' splice site recognition. SR45 is found only in plants and is unique in having two SR domains separated by an RNA recognition motif (RRM). To study the localization and dynamics of SR45, we expressed it as a fusion to green fluorescent protein (GFP) in cultured cells and transgenic Arabidopsis plants. The SR45 is localized exclusively to nuclei. In interphase nuclei, GFP-SR45 was found both in speckles and nucleoplasm. The speckles exhibited intranuclear movements and changes in morphology. Inhibition of transcription and protein phosphorylation resulted in redistribution of SR45 to bigger speckles. The change in the number and morphology of speckles caused by inhibition of transcription was blocked by an inhibitor of phosphatases. These results indicate that transcription activity of the cell and protein (de)phosphorylation regulate the intranuclear distribution of SR45.
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Affiliation(s)
- Gul Shad Ali
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Golovkin M, Reddy ASN. Expression of U1 small nuclear ribonucleoprotein 70K antisense transcript using APETALA3 promoter suppresses the development of sepals and petals. PLANT PHYSIOLOGY 2003; 132:1884-91. [PMID: 12913145 PMCID: PMC181274 DOI: 10.1104/pp.103.023192] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2003] [Revised: 04/08/2003] [Accepted: 04/24/2003] [Indexed: 05/21/2023]
Abstract
U1 small nuclear ribonucleoprotein (snRNP)-70K (U1-70K), a U1 snRNP-specific protein, is involved in the early stages of spliceosome formation. In non-plant systems, it is involved in constitutive and alternative splicing. It has been shown that U1snRNP is dispensable for in vitro splicing of some animal pre-mRNAs, and inactivation of U1-70K in yeast (Saccharomyces cerevisiae) is not lethal. As in yeast and humans (Homo sapiens), plant U1-70K is coded by a single gene. In this study, we blocked the expression of Arabidopsis U1-70K in petals and stamens by expressing U1-70K antisense transcript using the AP3 (APETALA3) promoter specific to these floral organs. Flowers of transgenic Arabidopsis plants expressing U1-70K antisense transcript showed partially developed stamens and petals that are arrested at different stages of development. In some transgenic lines, flowers have rudimentary petals and stamens and are male sterile. The severity of the phenotype is correlated with the level of the antisense transcript. Molecular analysis of transgenic plants has confirmed that the observed phenotype is not due to disruption of whorl-specific homeotic genes, AP3 or PISTILLATA, responsible for petal and stamen development. The AP3 transcript was not detected in transgenic flowers with severe phenotype. Flowers of Arabidopsis plants transformed with a reporter gene driven by the same promoter showed no abnormalities. These results show that U1-70K is necessary for the development of sepals and petals and is an essential gene in plants.
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Affiliation(s)
- Maxim Golovkin
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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Clancy M, Hannah LC. Splicing of the maize Sh1 first intron is essential for enhancement of gene expression, and a T-rich motif increases expression without affecting splicing. PLANT PHYSIOLOGY 2002; 130:918-29. [PMID: 12376656 PMCID: PMC166618 DOI: 10.1104/pp.008235] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2002] [Revised: 06/09/2002] [Accepted: 06/23/2002] [Indexed: 05/19/2023]
Abstract
Certain plant and animal introns increase expression of protein-coding sequences when placed in the 5' region of the transcription unit. The mechanisms of intron-mediated enhancement have not been defined, but are generally accepted to be post- or cotranscriptional in character. One of the most effective plant introns in stimulating gene expression is the 1,028-bp first intron of the Sh1 gene that encodes maize (Zea mays) sucrose synthase. To address the mechanisms of intron-mediated enhancement, we used reporter gene fusions to identify features of the Sh1 first intron required for enhancement in cultured maize cells. A 145-bp derivative conferred approximately the same 20- to 50-fold stimulation typical for the full-length intron in this transient expression system. A 35-bp motif contained within the intron is required for maximum levels of enhancement but not for efficient transcript splicing. The important feature of this redundant 35-bp motif is T-richness rather than the specific sequence. When transcript splicing was abolished by mutations at the intron borders, enhancement was reduced to about 2-fold. The requirement of splicing for enhancement was not because of upstream translation initiation codons contained in unspliced transcripts. On the basis of our current findings, we conclude that splicing of the Sh1 intron is integral to enhancement, and we hypothesize that transcript modifications triggered by the T-rich motif and splicing may link the mRNA with the trafficking system of the cell.
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Affiliation(s)
- Maureen Clancy
- Program in Plant Molecular and Cellular Biology, Horticultural Sciences, University of Florida, P.O. Box 110690, 2211 Fifield Hall, Gainesville, FL 32611-0690, USA
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20
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Lambermon MHL, Fu Y, Wieczorek Kirk DA, Dupasquier M, Filipowicz W, Lorković ZJ. UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants. Mol Cell Biol 2002; 22:4346-57. [PMID: 12024044 PMCID: PMC133861 DOI: 10.1128/mcb.22.12.4346-4357.2002] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nicotiana plumbaginifolia UBP1 is an hnRNP-like protein associated with the poly(A)(+) RNA in the cell nucleus. Consistent with a role in pre-mRNA processing, overexpression of UBP1 in N. plumabaginifolia protoplasts enhances the splicing of suboptimal introns and increases the steady-state levels of reporter mRNAs, even intronless ones. The latter effect of UBP1 is promoter specific and appears to be due to UBP1 binding to the 3' untranslated region (3'-UTR) and protecting the mRNA from exonucleolytic degradation (M. H. L. Lambermon, G. G. Simpson, D. A. Kirk, M. Hemmings-Mieszczak, U. Klahre, and W. Filipowicz, EMBO J. 19:1638-1649, 2000). To gain more insight into UBP1 function in pre-mRNA maturation, we characterized proteins interacting with N. plumbaginifolia UBP1 and one of its Arabidopsis thaliana counterparts, AtUBP1b, by using yeast two-hybrid screens and in vitro pull-down assays. Two proteins, UBP1-associated proteins 1a and 2a (UBA1a and UBA2a, respectively), were identified in A. thaliana. They are members of two novel families of plant-specific proteins containing RNA recognition motif-type RNA-binding domains. UBA1a and UBA2a are nuclear proteins, and their recombinant forms bind RNA with a specificity for oligouridylates in vitro. As with UBP1, transient overexpression of UBA1a in protoplasts increases the steady-state levels of reporter mRNAs in a promoter-dependent manner. Similarly, overexpression of UBA2a increases the levels of reporter mRNAs, but this effect is promoter independent. Unlike UBP1, neither UBA1a nor UBA2a stimulates pre-mRNA splicing. These and other data suggest that UBP1, UBA1a, and UBA2a may act as components of a complex recognizing U-rich sequences in plant 3'-UTRs and contributing to the stabilization of mRNAs in the nucleus.
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Affiliation(s)
- Mark H L Lambermon
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
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21
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Dinges JR, Colleoni C, Myers AM, James MG. Molecular structure of three mutations at the maize sugary1 locus and their allele-specific phenotypic effects. PLANT PHYSIOLOGY 2001; 125:1406-18. [PMID: 11244120 PMCID: PMC65619 DOI: 10.1104/pp.125.3.1406] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2000] [Revised: 12/15/2000] [Accepted: 12/21/2000] [Indexed: 05/18/2023]
Abstract
Starch production in all plants examined is altered by mutations of isoamylase-type starch-debranching enzymes (DBE), although how these proteins affect glucan polymer assembly is not understood. Various allelic mutations in the maize (Zea mays) gene sugary1 (su1), which codes for an isoamylase-type DBE, condition distinct kernel phenotypes. This study characterized the recessive mutations su1-Ref, su1-R4582::Mu1, and su1-st, regarding their molecular basis, chemical phenotypes, and effects on starch metabolizing enzymes. The su1-Ref allele results in two specific amino acid substitutions without affecting the Su1 mRNA level. The su1-R4582::Mu1 mutation is a null allele that abolishes transcript accumulation. The su1-st mutation results from insertion of a novel transposon-like sequence, designated Toad, which causes alternative pre-mRNA splicing. Three su1-st mutant transcripts are produced, one that is nonfunctional and two that code for modified SU1 polypeptides. The su1-st mutation is dominant to the null allele su1-R4582::Mu1, but recessive to su1-Ref, suggestive of complex effects involving quaternary structure of the SU1 enzyme. All three su1- alleles severely reduce or eliminate isoamylase-type DBE activity, although su1-st kernels accumulate less phytoglycogen and Suc than su1-Ref or su1-R4582::Mu1 mutants. The chain length distribution of residual amylopectin is significantly altered by su1-Ref and su1-R4582::Mu1, whereas su1-st has modest effects. These results, together with su1 allele-specific effects on other starch- metabolizing enzymes detected in zymograms, suggest that total DBE catalytic activity is the not the sole determinant of Su1 function and that specific interactions between SU1 and other components of the starch biosynthetic system are required.
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Affiliation(s)
- J R Dinges
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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23
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Isshiki M, Nakajima M, Satoh H, Shimamoto K. dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 23:451-460. [PMID: 10972871 DOI: 10.1046/j.1365-313x.2000.00803.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the endosperm of japonica rice, du-1 and du-2 mutations cause the reduction of amylose contents. It was previously shown that the Wx(b) allele of rice, which is predominantly distributed in japonica rice, has a mutation in the 5' splice site of intron 1 resulting in the creation of two weak 5' splice sites within exon 1. In du-1 and du-2 mutants, spliced Wx(b) transcripts were highly reduced, whereas the processing of transcripts derived from three other genes highly expressed in endosperm was not apparently influenced. Results of competitive RT-PCR analysis indicate that transcripts spliced at the two newly created 5' splice sites were equally affected in these two mutants. Genetic and molecular analyses of the effects of du-1 and du-2 on Wx(a) pre-mRNA with normal splice sites indicate that these two mutations do not affect the processing of Wx(a) pre-mRNA after splicing, suggesting that du-1 and du-2 are mutations of genes required for the efficient splicing of mutated Wx(b) pre-mRNA. Furthermore, du-1 and du-2 showed differential effects in endosperm and pollen. Although both mutations caused similar effects on the splicing of Wx(a) transcripts in endosperm, du-1 caused higher reduction of Wx(b) mRNA in pollen than in endosperm, while du-2 had a lesser effect in pollen than in endosperm. Based on these results, we propose that the du-1 and du-2 loci of rice encode tissue-specifically regulated splicing factors that are involved in alternative splicing of pre-mRNA in rice.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
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24
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Lorković ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. Pre-mRNA splicing in higher plants. TRENDS IN PLANT SCIENCE 2000; 5:160-7. [PMID: 10740297 DOI: 10.1016/s1360-1385(00)01595-8] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants.
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Affiliation(s)
- Z J Lorković
- Friedrich Miescher Institute, Basel, Switzerland
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25
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Lal SK, Hannah LC. Maize transposable element Ds is differentially spliced from primary transcripts in endosperm and suspension cells. Biochem Biophys Res Commun 1999; 261:798-801. [PMID: 10441504 DOI: 10.1006/bbrc.1999.1119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The process by which transposable elements are spliced from the host gene transcripts remains poorly understood. We previously reported that a maize transposable element Ds (dissociation) and a copy of its host site duplication are perfectly spliced from the shrunken-2 transcript in the endosperm. Here, we have monitored splicing of the Ds element and its flanking Sh2 sequence following transient expression in maize suspension cells. The pattern of Ds splicing in suspension cells differs dramatically from that in the endosperm. In contrast to splicing in the endosperm, Ds in suspension cells was completely spliced from the transcripts using multiple donor and acceptor splice sites outside the element. In addition, noncanonical splice sites were utilized in suspension cells. Our results indicate that this difference in splicing is due to the context of Ds placement in the construct and/or to tissue specific differences in splicing.
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Affiliation(s)
- S K Lal
- Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida, 32611-0690, USA
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26
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Lopato S, Kalyna M, Dorner S, Kobayashi R, Krainer AR, Barta A. atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes. Genes Dev 1999; 13:987-1001. [PMID: 10215626 PMCID: PMC316644 DOI: 10.1101/gad.13.8.987] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/1998] [Accepted: 02/18/1999] [Indexed: 11/24/2022]
Abstract
SR proteins are nuclear phosphoproteins with a characteristic Ser/Arg-rich domain and one or two RNA recognition motifs. They are highly conserved in animals and plants and play important roles in spliceosome assembly and alternative splicing regulation. We have now isolated and partially sequenced a plant protein, which crossreacts with antibodies to human SR proteins. The sequence of the corresponding cDNA and genomic clones from Arabidopsis revealed a protein, atSRp30, with strong similarity to the human SR protein SF2/ASF and to atSRp34/SR1, a previously identified SR protein, indicating that plants possess two SF2/ASF-like proteins. atSRp30 expresses alternatively spliced mRNA isoforms that are expressed differentially in various organs and during development. Overexpression of atSRp30 via a strong constitutive promoter resulted in changes in alternative splicing of several endogenous plant genes, including atSRp30 itself. Interestingly, atSRp30 overexpression resulted in a pronounced down-regulation of endogenous mRNA encoding full-length atSRp34/SR1 protein. Transgenic plants overexpressing atSRp30 showed morphological and developmental changes affecting mostly developmental phase transitions. atSRp30- and atSRp34/SR1-promoter-GUS constructs exhibited complementary expression patterns during early seedling development and root formation, with overlapping expression in floral tissues. The results of the structural and expression analyses of both genes suggest that atSRp34/SR1 acts as a general splicing factor, whereas atSRp30 functions as a specific splicing modulator.
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Affiliation(s)
- S Lopato
- Institut für Biochemie, Universität Wien, Vienna Biocenter, A-1030 Vienna, Austria
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Domon C, Lorković ZJ, Valcárcel J, Filipowicz W. Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants. J Biol Chem 1998; 273:34603-10. [PMID: 9852132 DOI: 10.1074/jbc.273.51.34603] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Requirements for intron recognition during pre-mRNA splicing in plants differ from those in vertebrates and yeast. Plant introns contain neither conserved branch points nor distinct 3' splice site-proximal polypyrimidine tracts characteristic of the yeast and vertebrate introns, respectively. However, they are strongly enriched in U residues throughout the intron, property essential for splicing. To understand the roles of different sequence elements in splicing, we are characterizing proteins involved in intron recognition in plants. In this work we show that Nicotiana plumbaginifolia, a dicotyledonous plant, contains two genes encoding different homologs of the large 50-65-kDa subunit of the polypyrimidine tract binding factor U2AF, characterized previously in animals and Schizosaccharomyces pombe. Both plant U2AF65 isoforms, referred to as NpU2AF65a and NpU2AF65b, support splicing of an adenovirus pre-mRNA in HeLa cell nuclear extracts depleted of the endogenous U2AF factor. Both proteins interact with RNA fragments containing plant introns and show affinity for poly(U) and, to a lesser extend, poly(C) and poly(G). The branch point or the 3' splice site regions do not contribute significantly to intron recognition by NpU2AF65. The existence of multiple isoforms of U2AF may be quite general in plants because two genes expressing U2AF65 have been identified in Arabidopsis, and different isoforms of the U2AF small subunit are expressed in rice.
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Affiliation(s)
- C Domon
- Friedrich Miescher-Institut, CH-4002 Basel, Switzerland
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28
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Brendel V, Kleffe J. Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Res 1998; 26:4748-57. [PMID: 9753745 PMCID: PMC147908 DOI: 10.1093/nar/26.20.4748] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prediction of splice site selection and efficiency from sequence inspection is of fundamental interest (testing the current knowledge of requisite sequence features) and practical importance (genome annotation, design of mutant or transgenic organisms). In plants, the dominant variables affecting splice site selection and efficiency include the degree of matching to the extended splice site consensus and the local gradient of U- and G+C-composition (introns being U-rich and exons G+C-rich). We present a novel method for splice site prediction, which was particularly trained for maize and Arabidopsis thaliana. The method extends our previous algorithm based on logitlinear models by considering three variables simultaneously: intrinsic splice site strength, local optimality and fit with respect to the overall splice pattern prediction. We show that the method considerably improves prediction specificity without compromising the high degree of sensitivity required in gene prediction algorithms. Applications to gene identification are illustrated for Arabidopsis and suggest that successful methods must combine scoring for splice sites, coding potential and similarity with potential homologs in non-trivial ways. A WWW version of the SplicePredictor program is available at http:/gnomic.stanford.edu/volker/SplicePredi ctor.html/
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Affiliation(s)
- V Brendel
- Department of Mathematics, Stanford University, Stanford, CA 94305, USA.
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29
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Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5' splice site of the first intron. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 15:133-8. [PMID: 9744101 DOI: 10.1046/j.1365-313x.1998.00189.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In cultivated rice two wild-type alleles, Wxa and Wxb, predominate at the waxy locus, which encodes granule-bound starch synthase. The activity of Wxa is 10-fold higher than that of Wxb at the level of both protein and mRNA. Wxb has a +1G to T mutation at the 5' splice site of the first intron. Sequence analysis of Wxb transcripts revealed that splicing occurs at the mutant AG/UU site and at two cryptic sites: the first is A/GUU, one base upstream of the original site and the second is AG/GU found approximately 100 bases upstream of the mutant splice site. We introduced single base mutations to the 5' splice sites of both Wxa and Wxb, fused with the gus reporter gene and introduced them into rice protoplasts. Analysis of GUS activities and transcripts indicated that a G to T mutation in Wxa reduced GUS activity and the level of spliced RNA. Conversely, a T to G mutation of Wxb restored GUS activity and the level of spliced RNA to that of wild-type Wxa. These results demonstrated that the low level expression of Wxb results from a single base mutation at the 5' splice site of the first intron. It is of interest that the Wxb allele of rice carrying the G to T mutation of intron 1 has been conserved in the history of rice cultivation because there is a low amylose content of the seed caused by this mutation.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Takayama, Japan
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30
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Abstract
The purpose of this review is to highlight the unique and common features of splice site selection in plants compared with the better understood yeast and vertebrate systems. A key question in plant splicing is the role of AU sequences and how and at what stage they are involved in spliceosome assembly. Clearly, intronic U- or AU-rich and exonic GC- and AG-rich elements can influence splice site selection and splicing efficiency and are likely to bind proteins. It is becoming clear that splicing of a particular intron depends on a fine balance in the "strength" of the multiple intron signals involved in splice site selection. Individual introns contain varying strengths of signals and what is critical to splicing of one intron may be of less importance to the splicing of another. Thus, small changes to signals may severely disrupt splicing or have little or no effect depending on the overall sequence context of a specific intron/exon organization.
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Affiliation(s)
- J. W. S. Brown
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom; e-mail: ;
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31
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Brendel V, Kleffe J, Carle-Urioste JC, Walbot V. Prediction of splice sites in plant pre-mRNA from sequence properties. J Mol Biol 1998; 276:85-104. [PMID: 9514728 DOI: 10.1006/jmbi.1997.1523] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heterologous introns are often inaccurately or inefficiently processed in higher plants. The precise features that distinguish the process of pre-mRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and flanking G + C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection significantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing efficiency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the flanking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is sufficient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.
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Affiliation(s)
- V Brendel
- Department of Mathematics, Stanford University, CA 94305-2125, USA
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32
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Reddy AS, Narasimhulu SB, Day IS. Structural organization of a gene encoding a novel calmodulin-binding kinesin-like protein from Arabidopsis. Gene X 1997; 204:195-200. [PMID: 9434184 DOI: 10.1016/s0378-1119(97)00546-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Kinesin-like calmodulin-binding protein (KCBP) is a recently identified microtubule motor protein that appears to be unique to plants. Here we report isolation and sequence analysis of a gene encoding Arabidopsis KCBP. KCBP gene contains 21 exons and 20 introns. All exons except exon 3 are short (94-272 nt). Exons 1-9 code for the globular tail region whereas the coiled-coil region is coded by exons 10-15. The conserved motor domain is coded by exons 16-20. Calmodulin-binding domain that is present in the C-terminal region of the protein and unique to KCBP is coded by the last exon. The size of introns ranged from 71 (intron 17) to 320 (intron 19) nucleotides. As in most plant introns, the content of AT is very high in all introns (up to 76%). Phylogenetic analysis of KCBP using motor domain sequence grouped KCBP with other known C-terminal microtubule motor proteins. However, Arabidopsis KCBP together with its homologs from potato and tobacco constitute a distinct group within the C-terminal subfamily of motors which is consistent with structural and functional features of KCBP.
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Affiliation(s)
- A S Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins 80523, USA.
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33
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Kusnadi AR, Nikolov ZL, Howard JA. Production of recombinant proteins in transgenic plants: Practical considerations. Biotechnol Bioeng 1997; 56:473-84. [DOI: 10.1002/(sici)1097-0290(19971205)56:5<473::aid-bit1>3.0.co;2-f] [Citation(s) in RCA: 244] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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34
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Abstract
Cyclins are the regulatory subunits of cyclin-dependent protein kinases. In investigations of the expression of a cyclin gene during maize endosperm development, we detected a cyclin transcript with a 63-bp deletion in the region encoding the conserved 'cyclin box' where cyclin interacts with p34cdc2, the catalytic domain of the cyclin-dependent protein kinase. Analysis of cDNA and genomic sequences, and other observations, indicated that the deletion was caused by alternative splicing of a retained intron in the normally spliced transcript. Whereas the normally spliced cyclin RNA was mitotically functional, as indicated by its ability to promote maturation of Xenopus oocytes, the alternatively spliced transcript was unable to promote maturation. In addition to maize endosperm, the alternatively spliced cyclin was detected in apical meristem, mature leaf, root tip and mature root.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Cycle/genetics
- Cloning, Molecular
- Cyclins/genetics
- Cyclins/metabolism
- Gene Expression Regulation, Plant
- Genes, Plant
- Humans
- Introns
- Molecular Sequence Data
- Oocytes/metabolism
- Plant Leaves/metabolism
- Plant Roots/metabolism
- Plant Stems/metabolism
- Polymerase Chain Reaction
- RNA Processing, Post-Transcriptional
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Xenopus/genetics
- Zea mays/genetics
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Affiliation(s)
- Y Sun
- Department of Soil, Crop and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
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35
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Haseloff J, Siemering KR, Prasher DC, Hodge S. Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc Natl Acad Sci U S A 1997; 94:2122-7. [PMID: 9122158 PMCID: PMC20051 DOI: 10.1073/pnas.94.6.2122] [Citation(s) in RCA: 901] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The green fluorescent protein (GFP) from the jellyfish Aequorea victoria is finding wide use as a genetic marker that can be directly visualized in the living cells of many heterologous organisms. We have sought to express GFP in the model plant Arabidopsis thaliana, but have found that proper expression of GFP is curtailed due to aberrant mRNA processing. An 84-nt cryptic intron is efficiently recognized and excised from transcripts of the GFP coding sequence. The cryptic intron contains sequences similar to those required for recognition of normal plant introns. We have modified the codon usage of the gfp gene to mutate the intron and to restore proper expression in Arabidopsis. GFP is mainly localized within the nucleoplasm and cytoplasm of transformed Arabidopsis cells and can give rise to high levels of fluorescence, but it proved difficult to efficiently regenerate transgenic plants from such highly fluorescent cells. However, when GFP is targeted to the endoplasmic reticulum, transformed cells regenerate routinely to give highly fluorescent plants. These modified forms of the gfp gene are useful for directly monitoring gene expression and protein localization and dynamics at high resolution, and as a simply scored genetic marker in living plants.
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Affiliation(s)
- J Haseloff
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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36
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Tremousaygue D, Bardet C, Dabos P, Regad F, Pelese F, Nazer R, Gander E, Lescure B. Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions. Genome Res 1997; 7:198-209. [PMID: 9074924 DOI: 10.1101/gr.7.3.198] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Arabidopsis thaliana, EF-1 alpha proteins are encoded by a multigene family of four members. Three of them are clustered at the same locus, which was positioned 24 cM from the top of chromosome 1. A region of DNA spanning 63 kb around these locus was sequenced and analyzed. One main characteristic of the locus is the mosaic organization of both genes and intergenic regions. Fourteen genes were identified, among which only four were already described, and other unidentified are most likely present. Functionally diverse genes are found at close intervals. Exon and intron distribution is highly variable at this locus, one gene being split into at least 20 introns. Several duplications were found within the sequenced segment both in coding and noncoding regions, including two gene families. Moreover, a sequence corresponding to the 5' noncoding region of the EF-1 alpha genes and harboring a 5' intervening sequence is duplicated and found upstream of several genes, suggesting that noncoding regions can be shuffled during evolution.
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Affiliation(s)
- D Tremousaygue
- Laboratoire de Biologie Moleculaire des relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France.
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37
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Kleffe J, Hermann K, Vahrson W, Wittig B, Brendel V. Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucleic Acids Res 1996; 24:4709-18. [PMID: 8972857 PMCID: PMC146321 DOI: 10.1093/nar/24.23.4709] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pre-mRNA splicing in plants, while generally similar to the processes in vertebrates and yeast, is thought to involve plant specific cis-acting elements. Both monocot and dicot introns are typically strongly enriched in U nucleotides, and AU- or U-rich segments are thought to be involved in intron recognition, splice site selection, and splicing efficiency. We have applied logitlinear models to find optimal combinations of splice site variables for the purpose of separating true splice sites from a large excess of potential sites. It is shown that plant splice site prediction from sequence inspection is greatly improved when compositional contrast between exons and introns is considered in addition to degree of matching to the splice site consensus (signal quality). The best model involves subclassification of splice sites according to the identity of the base immediately upstream of the GU and AG signals and gives substantial performance gains compared with conventional profile methods.
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Affiliation(s)
- J Kleffe
- Freie Universität Berlin, Institut für Molekularbiologie und Biochemie, Germany
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38
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Brown JW, Smith P, Simpson CG. Arabidopsis consensus intron sequences. PLANT MOLECULAR BIOLOGY 1996; 32:531-5. [PMID: 8980502 DOI: 10.1007/bf00019105] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU ... AG: rule with the exception of 1% of introns with :GC at their 5' ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3' splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3' splice site was uridine. Consensus sequences for 5' and 3' splice sites and branchpoint sequences for Arabidopsis introns are presented.
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Affiliation(s)
- J W Brown
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Dundee, Scotland, UK
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39
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Küster H, Frühling M, Pühler A, Perlick AM. The modular nodulins Nvf-28/32 of broad bean (Vicia faba L.): alternative exon combinations account for different modular structures. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:648-57. [PMID: 8917307 DOI: 10.1007/bf02173970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The broad bean late nodulins, Nvf-28/32, are composed of two types of repetitively occurring sequence modules flanked by unique N- and C-terminal modules. Six isoforms of these nodulins were characterized by a specific modular structure resulting from a different individual order of repetitive sequence modules. A detailed analysis of genomic PCR fragments revealed that the repetitive modules and the N-terminal unique module exactly corresponded to exons, whereas the C-terminal module was specified by two exons. Since those exons encoding the repetitive modules missing in specific Nvf-28/32 isoforms were consistently present within genomic sequences, a post-transcriptional generation of VfNOD28/32 transcripts specifying six Nvf-28/32 nodulins was concluded. Using tissue-print hybridizations, these transcripts were localized in the interzone II-III and the nitrogen-fixing zone III of root nodules. From this and from cDNA-cDNA hybridizations demonstrating a comparable timing of expression of VfNOD28/32 and of leghemoglobin transcripts in root nodules, a function of the modular nodulins Nvf-28/32 in late developmental stages of broad bean nodules was inferred.
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Affiliation(s)
- H Küster
- Lehrstuhl für Genetik, Universität Bielefeld, Germany
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40
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Collart FR, Osipiuk J, Trent J, Olsen GJ, Huberman E. Cloning and characterization of the gene encoding IMP dehydrogenase from Arabidopsis thaliana. Gene 1996; 174:217-20. [PMID: 8890737 DOI: 10.1016/0378-1119(96)00045-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Arabidopsis thaliana (At). The transcription unit of the At gene spans approximately 1900 bp and specifies a protein of 503 amino acids with a calculated relative molecular mass (M(r)) of 54,190. The gene is comprised of a minimum of four introns and five exons with all donor and acceptor splice sequences conforming to previously proposed consensus sequences. The deduced IMPDH amino-acid sequence from At shows a remarkable similarity to other eukaryotic IMPDH sequences, with a 48% identity to human Type II enzyme. Allowing for conservative substitutions, the enzyme is 69% similar to human Type II IMPDH. The putative active-site sequence of At IMPDH conforms to the IMP dehydrogenase/guanosine monophosphate reductase motif and contains an essential active-site cysteine residue.
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Affiliation(s)
- F R Collart
- Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, IL 60439, USA
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41
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Simpson GG, Filipowicz W. Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. PLANT MOLECULAR BIOLOGY 1996; 32:1-41. [PMID: 8980472 DOI: 10.1007/bf00039375] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The removal of introns from pre-mRNA transcripts and the concomitant ligation of exons is known as pre-mRNA splicing. It is a fundamental aspect of constitutive eukaryotic gene expression and an important level at which gene expression is regulated. The process is governed by multiple cis-acting elements of limited sequence content and particular spatial constraints, and is executed by a dynamic ribonucleoprotein complex termed the spliceosome. The mechanism and regulation of pre-mRNA splicing, and the sub-nuclear organisation of the spliceosomal machinery in higher plants is reviewed here. Heterologous introns are often not processed in higher plants indicating that, although highly conserved, the process of pre-mRNA splicing in plants exhibits significant differences that distinguish it from splicing in yeast and mammals. A fundamental distinguishing feature is the presence of and requirement for AU or U-rich intron sequence in higher-plant pre-mRNA splicing. In this review we document the properties of higher-plant introns and trans-acting spliceosomal components and discuss the means by which these elements combine to determine the accuracy and efficiency of pre-mRNA processing. We also detail examples of how introns can effect regulated gene expression by affecting the nature and abundance of mRNA in plants and list the effects of environmental stresses on splicing. Spliceosomal components exhibit a distinct pattern of organisation in higher-plant nuclei. Effective probes that reveal this pattern have only recently become available, but the domains in which spliceosomal components concentrate were identified in plant nuclei as enigmatic structures some sixty years ago. The organisation of spliceosomal components in plant nuclei is reviewed and these recent observations are unified with previous cytochemical and ultrastructural studies of plant ribonuleoprotein domains.
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Affiliation(s)
- G G Simpson
- Friedrich Miescher-Institut, Basel, Switzerland
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42
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Lopato S, Mayeda A, Krainer AR, Barta A. Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors. Proc Natl Acad Sci U S A 1996; 93:3074-9. [PMID: 8610170 PMCID: PMC39763 DOI: 10.1073/pnas.93.7.3074] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The fact that animal introns are not spliced out in plants suggests that recognition of pre-mRNA splice sites differs between the two kingdoms. In plants, little is known about proteins required for splicing, as no plant in vitro splicing system is available. Several essential splicing factors from animals, such as SF2/ASF and SC-35, belong to a family of highly conserved proteins consisting of one or two RNA binding domain(s) (RRM) and a C-terminal Ser/Arg-rich (SR or RS) domain. These animal SR proteins are required for splice site recognition and spliceosome assembly. We have screened for similar proteins in plants by using monoclonal antibodies specific for a phosphoserine epitope of the SR proteins (mAb1O4) or for SF2/ASF. These experiments demonstrate that plants do possess SR proteins, including SF2/ASF-like proteins. Similar to the animal SR proteins, this group of proteins can be isolated by two salt precipitations. However, compared to the animal SR proteins, which are highly conserved in size and number, SR proteins from Arabidopsis, carrot, and tobacco exhibit a complex pattern of intra- and interspecific variants. These plant SR proteins are able to complement inactive HeLa cell cytoplasmic S1OO extracts that are deficient in SR proteins, yielding functional splicing extracts. In addition, plant SR proteins were active in a heterologous alternative splicing assay. Thus, these plant SR proteins are authentic plant splicing factors.
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Affiliation(s)
- S Lopato
- Institute of Biochemistry, Vienna Biocenter, Austria
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43
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Gruber H, Kirzinger SH, Schmitt R. Expression of the Volvox gene encoding nitrate reductase: mutation-dependent activation of cryptic splice sites and intron-enhanced gene expression from a cDNA. PLANT MOLECULAR BIOLOGY 1996; 31:1-12. [PMID: 8704142 DOI: 10.1007/bf00020601] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Use of the nitrate reductase encoding gene (nitA) as selection marker has facilitated the successful nuclear transformation of Volvox carteri. The Volvox nitA gene contains 10 introns. A stable nitA mutation in the Volvox recipient strain 153-81 resides in a G-to-A transition of the first nucleotide in the 5' splice site of nitA intron 2. This mutation resulted in at least three non-functional splice variants, namely: (1) intron 2 was not spliced at all; (2) a cryptic 5' splice site 60 nt upstream or (3) a cryptic 5' splice site 16 nt downstream of the mutation were activated and used for splicing. When we used nitA cDNA (pVcNR13) for transformation of V. carteri 153-81, a low efficiency of about 5 x 10(-5) transformants per reproductive cell was observed. Re-integration of either intron 1 (pVcNR15) or introns 9 and 10 (pVcNR16) in the transforming cDNA increased transformation rates to 5 x 10(-4). In parallel, pVcNR15-transformed Volvox exhibited growth rates that were 100-fold increased over the pVcNR13-transformed alga. This intron-enhancement of nitA gene expression appears to be associated with post-transcriptional processing and 'channelling' of the message. These data suggest an important role of splicing for gene expression in V. carteri.
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Affiliation(s)
- H Gruber
- Lehrstuhl für Genetik, Universität Regensburg, Germany
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44
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Gniadkowski M, Hemmings-Mieszczak M, Klahre U, Liu HX, Filipowicz W. Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia. Nucleic Acids Res 1996; 24:619-27. [PMID: 8604302 PMCID: PMC145670 DOI: 10.1093/nar/24.4.619] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U).
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Affiliation(s)
- M Gniadkowski
- Friedrich Miescher Institute, Ch-4002 Basel, Switzerland
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45
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Diehn SH, De Rocher EJ, Green PJ. Problems that can limit the expression of foreign genes in plants: lessons to be learned from B.t. toxin genes. GENETIC ENGINEERING 1996; 18:83-99. [PMID: 8785128 DOI: 10.1007/978-1-4899-1766-9_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- S H Diehn
- MSU-DOE Plant Research Laboratory, Department of Botany and Plant Pathology, Michigan State University, East Lansing 48824-1312, USA
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46
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Savouré A, Jaoua S, Hua XJ, Ardiles W, Van Montagu M, Verbruggen N. Isolation, characterization, and chromosomal location of a gene encoding the delta 1-pyrroline-5-carboxylate synthetase in Arabidopsis thaliana. FEBS Lett 1995; 372:13-9. [PMID: 7556633 DOI: 10.1016/0014-5793(95)00935-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A full-length cDNA and the corresponding At-P5S gene encoding the first enzyme of the proline biosynthetic pathway, the delta 1-pyrroline-5-carboxylate (P5C) synthetase, were isolated in Arabidopsis thaliana. The At-P5S cDNA encodes a protein of 717 amino acids showing high identity with the P5C synthetase of Vigna aconitifolia. Strong homology is also found at the N-terminus to bacterial and yeast gamma-glutamyl kinase and at the C-terminus to bacterial gamma-glutamyl phosphate reductase. Putative ATP- and NAD(P)H-binding sites are suggested in the At-P5S protein. The transcribed region of the At-P5S gene is 4.8 kb long and contains 20 exons. Southern analysis suggests the presence of only one At-P5S gene in the A. thaliana genome mapped at the bottom of the chromosome two. Expression analysis of At-P5S in different organs reveals abundant At-P5S transcripts in mature flowering plant. Rapid induction of the At-P5S gene followed by accumulation of proline was observed in NaCl-treated seedlings suggesting that At-P5S is osmoregulated.
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Affiliation(s)
- A Savouré
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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47
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Montag K, Salamini F, Thompson RD. ZEMa, a member of a novel group of MADS box genes, is alternatively spliced in maize endosperm. Nucleic Acids Res 1995; 23:2168-77. [PMID: 7610044 PMCID: PMC307004 DOI: 10.1093/nar/23.12.2168] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The identification of a number of cis-elements which direct gene expression in maize endosperm, and the characterization of corresponding DNA binding proteins, point to the interaction of different classes of transcription factors in this tissue. To assess whether MADS box genes are also involved in maize endosperm development, cDNA and genomic MADS box clones have been isolated. The three cDNA clones ZEM1, ZEM2 and ZEM3 were cloned from a maize endosperm cDNA library using a probe based on sequences conserved in plant MADS box genes. Further transcripts were cloned by RT-PCR experiments and designated ZEM4 and ZEM5. Analysis of the corresponding genomic clones led to the identification of the ZEM2 MADS box gene family, three members of which were characterized sharing 97% sequence identity in corresponding domains. 100% sequence identities between cDNA and one of the genomic clones, conserved exon-intron boundaries and the demonstration of in vivo splicing in a maize endosperm transient expression system, show that the transcripts ZEM1-5 are derived by alternative splicing of ZEMa, one ZEM2 member. The ZEMa transcripts are present in almost all maize tissues, but specific differentially spliced forms accumulate preferentially in maturing endosperm and leaf. The function of the ZEMa gene is discussed in the light of similarities in the expression pattern with members of the human MEF2/RSRF gene family.
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Affiliation(s)
- K Montag
- Max-Planck-Institut für Züchtungsforschung, Carl-von-Linné Weg 10, Köln, Germany
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48
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Theissen G, Strater T, Fischer A, Saedler H. Structural characterization, chromosomal localization and phylogenetic evaluation of two pairs of AGAMOUS-like MADS-box genes from maize. Gene X 1995; 156:155-66. [PMID: 7758952 DOI: 10.1016/0378-1119(95)00020-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In order to gain a better understanding of the development and evolution of cereal flowers, we have cloned and sequenced two MADS-box genes from maize and the partial cDNA of a third one. One of the genomic clones was identified as ZAG2 (Zea AGAMOUS 2), while the other has a very similar structure and the potential to encode a protein which shares 94% sequence identity with the putative ZAG2 gene product. The cDNA reveals considerable similarity to ZAG1. Phylogenetic evaluation of the sequence information, as well as chromosomal localization, both suggest that we have identified two pairs of AGAMOUS-like MADS-box genes which were created during duplication of chromosomal segments or complete chromosomes.
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Affiliation(s)
- G Theissen
- Max-Planck-Institut für Züchtungsforschung, Abteilung Molekulare Pflanzengenetik, Köln, Germany
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49
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Carle-Urioste JC, Ko CH, Benito MI, Walbot V. In vivo analysis of intron processing using splicing-dependent reporter gene assays. PLANT MOLECULAR BIOLOGY 1994; 26:1785-1795. [PMID: 7858217 DOI: 10.1007/bf00019492] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The mechanisms of intron recognition and processing have been well-studied in mammals and yeast, but in plants the biochemistry of splicing is not known and the rules for intron recognition are not clearly defined. To increase understanding of intron processing in plants, we have constructed new pairs of vectors, pSuccess and pFail, to assess the efficiency of splicing in maize cells. In the pFail series we use translation of pre-mRNA to monitor the amount of unspliced RNA. We inserted an ATG codon in the Bz2 (Bronze-2) intron in frame with luciferase: this construct will express luciferase activity only when splicing fails. In the pSuccess series the spliced message is monitored by inserting an ATG upstream of the Bz2 intron in frame with luciferase: this construct will express luciferase activity only when splicing succeeds. We show here, using both the wild-type Bz2 intron and the same intron with splice site mutations, that the efficiency of splicing can be estimated by the ratio between the luciferase activities of the vector pairs. We also show that mutations in the unique U-rich motif inside the intron can modulate splicing. In addition, a GC-rich insertion in the first exon increases the efficiency of splicing, suggesting that exons also play an important role in intron recognition and/or processing.
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Affiliation(s)
- J C Carle-Urioste
- Department of Biological Sciences, Stanford University, CA 94305-5020
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Abstract
Intron recognition in Angiosperms is hypothesized to require AU-rich motifs within introns. In this report we examined the role of AU-rich motifs in pre-mRNA processing. AU-rich segments of maize introns inserted near the single intron of the maize Bronze-2(Bz2) gene result in alternative splicing. Other insertions of AU-rich sequence in the Bz2 cDNA resulted in de novo intron creation using splice junctions at the edges of the AU-rich region. Surprisingly, the five AU-rich inserts that we tested also caused polyadenylation, even though none had been selected for that function in plants. Insertions of GC-rich sequence into Bz2 did not cause either splicing or polyadenylation. We propose that AU-rich motifs are a general signal for RNA processing in maize and that in the absence of a 5' splice site, polyadenylation is the default pathway.
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Affiliation(s)
- K R Luehrsen
- Department of Biological Sciences, Stanford University, California 94305-5020
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