1
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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2
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Plewka P, Thompson A, Szymanski M, Nuc P, Knop K, Rasinska A, Bialkowska A, Szweykowska-Kulinska Z, Karlowski WM, Jarmolowski A. A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis. RNA Biol 2018; 15:726-738. [PMID: 29561243 PMCID: PMC6152437 DOI: 10.1080/15476286.2018.1445404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The GUT15-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.
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Affiliation(s)
- Patrycja Plewka
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Agnieszka Thompson
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Maciej Szymanski
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Przemyslaw Nuc
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Katarzyna Knop
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Agnieszka Rasinska
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Aleksandra Bialkowska
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Zofia Szweykowska-Kulinska
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Wojciech M Karlowski
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Artur Jarmolowski
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
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3
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Li D, Shao F, Lu S. Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza. PLANTA 2015; 241:1131-43. [PMID: 25601000 DOI: 10.1007/s00425-015-2246-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/09/2015] [Indexed: 05/20/2023]
Abstract
Identification and characterization of 5,446 mlncRNAs from Salvia miltiorrhiza showed that the majority of identified mlncRNAs were stress responsive, providing a framework for elucidating mlncRNA functions in S. miltiorrhiza. mRNA-like noncoding RNAs (mlncRNAs) are transcribed by RNA polymerase II and are polyadenylated, capped and spliced. They play important roles in plant development and defense responses. However, there is no information available for mlncRNAs in Salvia miltiorrhiza Bunge, the first Chinese medicinal material entering the international market. To perform a transcriptome-wide identification of S. miltiorrhiza mlncRNAs, we assembled over 8 million RNA-seq reads from GenBank database and 5,624 ESTs from PlantGDB into 44422 unigenes. Using a computational identification pipeline, we identified 5446 S. miltiorrhiza mlncRNA candidates from the assembled unigenes. Of the 5446 mlncRNAs, 2 are primary transcripts of conserved miRNAs, and 2030 can be grouped into 470 families with at least two members in a family. Quantitative real-time PCR analysis of mlncRNAs with at least 900 nt showed that the majority were differentially expressed in roots, stems, leaves and flowers and responsive to methyl jasmonate (MeJA) treatment in S. miltiorrhiza. Analysis of published RNA-seq data showed that a total of 3,044 mlncRNAs were expressed in hairy roots of S. miltiorrhiza and the expression of 1,904 of the 3,044 mlncRNAs was altered by yeast extract and Ag(+) treatment. The results indicate that the majority of mlncRNAs are involved in plant response to stress. This study provides a framework for understanding the roles of mlncRNAs in S. miltiorrhiza.
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Affiliation(s)
- Dongqiao Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,
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4
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Wang M, Wu B, Chen C, Lu S. Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:256-70. [PMID: 25040236 DOI: 10.1111/jipb.12239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/03/2014] [Indexed: 05/11/2023]
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- Gene Expression Regulation, Plant
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Panax/genetics
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Reproducibility of Results
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
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5
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Wu B, Li Y, Yan H, Ma Y, Luo H, Yuan L, Chen S, Lu S. Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics 2012; 13:15. [PMID: 22233149 PMCID: PMC3269984 DOI: 10.1186/1471-2164-13-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022] Open
Abstract
Abstract Conclusions Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in D. purpurea.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No,151, Malianwa North Road, Haidian District, Beijing 100193, China
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6
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Desai PN, Shrivastava N, Padh H. Production of heterologous proteins in plants: strategies for optimal expression. Biotechnol Adv 2010; 28:427-35. [PMID: 20152894 DOI: 10.1016/j.biotechadv.2010.01.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 01/01/2010] [Accepted: 01/25/2010] [Indexed: 11/25/2022]
Abstract
Plants are a promising expression system for the production of heterologous proteins, especially therapeutic proteins. Currently the majority of therapeutic proteins are produced in mammalian cell lines or bacteria. In a few cases insects, yeast and fungi have been developed for production of human proteins. However, these expression systems have limitations in terms of suitability, cost, scalability, purification and post-translational modifications. Therefore, alternative expression systems are being developed in transgenic animals and transgenic plants. Transgenic plants could provide an attractive alternative in terms of low production cost and lower capital investment in infrastructure, and with appropriate post-translational modifications. The potential of plants as an expression host has not been capitalized, primarily due to lower level of expression of transgenes in plants. The present review will evaluate the rate limiting steps of plant expression systems and suggest strategies to optimize protein expression at each of the steps: gene integration, transcription, translation and protein accumulation.
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Affiliation(s)
- Priti N Desai
- B. V. Patel Pharmaceutical Education and Research Development Centre, Ahmedabad, India
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7
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Rymarquis LA, Kastenmayer JP, Hüttenhofer AG, Green PJ. Diamonds in the rough: mRNA-like non-coding RNAs. TRENDS IN PLANT SCIENCE 2008; 13:329-34. [PMID: 18448381 DOI: 10.1016/j.tplants.2008.02.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/19/2008] [Accepted: 02/21/2008] [Indexed: 05/20/2023]
Abstract
Non-coding RNAs are increasingly being identified as crucial regulators of gene expression and other cellular functions in plants. Experimental and computational methods have revealed the existence of mRNA-like non-coding RNAs (mlncRNAs), a class of non-coding RNAs that, in plants, are associated with tissue-specific expression, development and the phosphate-starvation response. Although their mechanisms of action are largely unknown, one can speculate that mlncRNAs act through secondary structures or specific sequences that bind to proteins or metabolites, or that have catalytic activity. This review summarizes the computational methods developed to identify candidate mlncRNAs, and the current experimental evidence regarding the function of several known mlncRNAs.
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Affiliation(s)
- Linda A Rymarquis
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
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8
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Song JH, Cao JS, Yu XL, Xiang X. BcMF11, a putative pollen-specific non-coding RNA from Brassica campestris ssp. chinensis. JOURNAL OF PLANT PHYSIOLOGY 2007; 164:1097-100. [PMID: 17207554 DOI: 10.1016/j.jplph.2006.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 10/07/2006] [Accepted: 10/09/2006] [Indexed: 05/13/2023]
Abstract
A full-length cDNA, BcMF11, has been cloned from Chinese cabbage (Brassica campestris L. ssp. chinensis Makino) using rapid amplification of the cDNA ends (RACE) based on a pollen-specific cDNA fragment (DN237921). The BcMF11 cDNA has a total length of 828bp with poly (A) tail. Analysis of the sequence demonstrated that BcMF11 is a novel non-coding RNA which has no prominent open reading frame (ORF) or coding capacity. No significant similarities were observed between BcMF11 and previously published sequences in GenBank. Transcription analysis indicated that BcMF11 is a novel pollen-specific ncRNA and may be involved in the pollen development of Chinese cabbage.
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Affiliation(s)
- Jiang-Hua Song
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310029, PR China
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9
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Groenenboom MAC, Marée AFM, Hogeweg P. The RNA silencing pathway: the bits and pieces that matter. PLoS Comput Biol 2005; 1:155-65. [PMID: 16110335 PMCID: PMC1185647 DOI: 10.1371/journal.pcbi.0010021] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Accepted: 06/29/2005] [Indexed: 12/24/2022] Open
Abstract
Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing pathway operates by cleaving siRNAs from dsRNA. siRNAs can associate with RISC, leading to the degradation of the target mRNA. We propose and analyze a few small extensions to the pathway: a siRNA degrading RNase, primed amplification of aberrant RNA pieces, and cooperation between aberrant RNA to trigger amplification. These extensions allow for a consistent explanation for various types of silencing phenomena, such as virus induced silencing, transgene and transposon induced silencing, and avoidance of self-reactivity, as well as for differences found between species groups.
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Affiliation(s)
- Marian A C Groenenboom
- Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands.
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10
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Gutierrez RA, Ewing RM, Cherry JM, Green PJ. Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci U S A 2002; 99:11513-8. [PMID: 12167669 PMCID: PMC123287 DOI: 10.1073/pnas.152204099] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2002] [Indexed: 11/18/2022] Open
Abstract
mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the steady state levels to which transcripts accumulate in the cytoplasm and determine the speed with which these levels change in response to the appropriate signals. When fast responses are to be achieved, rapid decay of mRNAs is necessary. Accordingly, genes with unstable transcripts often encode proteins that play important regulatory roles. Although detailed studies have been carried out on individual genes with unstable transcripts, there is limited knowledge regarding their nature and associations from a genomic perspective, or the physiological significance of rapid mRNA turnover in intact organisms. To address these problems, we have applied cDNA microarray analysis to identify and characterize genes with unstable transcripts in Arabidopsis thaliana (AtGUTs). Our studies showed that at least 1% of the 11,521 clones represented on Arabidopsis Functional Genomics Consortium microarrays correspond to transcripts that are rapidly degraded, with estimated half-lives of less than 60 min. AtGUTs encode proteins that are predicted to participate in a broad range of cellular processes, with transcriptional functions being over-represented relative to the whole Arabidopsis genome annotation. Analysis of public microarray expression data for these genes argues that mRNA instability is of high significance during plant responses to mechanical stimulation and is associated with specific genes controlled by the circadian clock.
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Affiliation(s)
- Rodrigo A Gutierrez
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824-1312, USA
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11
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MacIntosh GC, Wilkerson C, Green PJ. Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. PLANT PHYSIOLOGY 2001; 127:765-776. [PMID: 11706161 DOI: 10.1104/pp.010501] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sequencing of the Arabidopsis genome has led to the identification of thousands of new putative genes based on the predicted proteins they encode. Genes encoding tRNAs, ribosomal RNAs, and small nucleolar RNAs have also been annotated; however, a potentially important class of genes has largely escaped previous annotation efforts. These genes correspond to RNAs that lack significant open reading frames and encode RNA as their final product. Accumulating evidence indicates that such "non-coding RNAs" (ncRNAs) can play critical roles in a wide range of cellular processes, including chromosomal silencing, transcriptional regulation, developmental control, and responses to stress. Approximately 15 putative Arabidopsis ncRNAs have been reported in the literature or have been annotated. Although several have homologs in other plant species, all appear to be plant specific, with the exception of signal recognition particle RNA. Conversely, none of the ncRNAs reported from yeast or animal systems have homologs in Arabidopsis or other plants. To identify additional genes that are likely to encode ncRNAs, we used computational tools to filter protein-coding genes from genes corresponding to 20,000 expressed sequence tag clones. Using this strategy, we identified 19 clones with characteristics of ncRNAs, nine putative peptide-coding RNAs with open reading frames smaller than 100 amino acids, and 11 that could not be differentiated between the two categories. Again, none of these clones had homologs outside the plant kingdom, suggesting that most Arabidopsis ncRNAs are likely plant specific. These data indicate that ncRNAs represent a significant and underdeveloped aspect of Arabidopsis genomics that deserves further study.
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MESH Headings
- Algorithms
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/physiology
- Cloning, Molecular
- Cytokinins/physiology
- Databases, Nucleic Acid
- Expressed Sequence Tags
- Gene Expression Regulation, Plant
- Gene Silencing
- Internet
- Molecular Sequence Data
- Open Reading Frames
- Phosphates/physiology
- RNA, Plant/analysis
- RNA, Plant/genetics
- RNA, Plant/physiology
- RNA, Untranslated/genetics
- RNA, Untranslated/physiology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Sequence Analysis, Protein
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- G C MacIntosh
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
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12
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Gil P, Dewey E, Friml J, Zhao Y, Snowden KC, Putterill J, Palme K, Estelle M, Chory J. BIG: a calossin-like protein required for polar auxin transport in Arabidopsis. Genes Dev 2001; 15:1985-97. [PMID: 11485992 PMCID: PMC312751 DOI: 10.1101/gad.905201] [Citation(s) in RCA: 205] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Polar auxin transport is crucial for the regulation of auxin action and required for some light-regulated responses during plant development. We have found that two mutants of Arabidopsis-doc1, which displays altered expression of light-regulated genes, and tir3, known for its reduced auxin transport-have similar defects and define mutations in a single gene that we have renamed BIG. BIG is very similar to the Drosophila gene Calossin/Pushover, a member of a gene family also present in Caenorhabditis elegans and human genomes. The protein encoded by BIG is extraordinary in size, 560 kD, and contains several putative Zn-finger domains. Expression-profiling experiments indicate that altered expression of multiple light-regulated genes in doc1 mutants can be suppressed by elevated levels of auxin caused by overexpression of an auxin biosynthetic gene, suggesting that normal auxin distribution is required to maintain low-level expression of these genes in the dark. Double mutants of tir3 with the auxin mutants pin1, pid, and axr1 display severe defects in auxin-dependent growth of the inflorescence. Chemical inhibitors of auxin transport change the intracellular localization of the auxin efflux carrier PIN1 in doc1/tir3 mutants, supporting the idea that BIG is required for normal auxin efflux.
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Affiliation(s)
- P Gil
- Plant Biology Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037 USA
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13
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Ylstra B, McCormick S. Analysis of mRNA stabilities during pollen development and in BY2 cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:101-108. [PMID: 10571869 DOI: 10.1046/j.1365-313x.1999.00580.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
RNA stability is important in post-transcriptional gene expression. However, its role during plant male gametophyte development has not been studied in detail, probably because of technical difficulties and because earlier work suggested that, in general, mRNAs expressed during late pollen development would be stable. We determined mRNA stabilities of 12 pollen-expressed genes. We measured pollen mRNA decay during in planta development and in vitro maturation after transcriptional inhibition with ActinomycinD (ActD). Because five of these genes were also expressed in somatic cells we also measured RNA decay in BY2 cells after transcriptional inhibition with ActD. Ten of the mRNAs were highly stable during pollen development (t1/2 > 30 h), including all seven pollen-specific mRNAs. However, two mRNAs showed a logarithmic decrease as pollen development proceeded, both in planta and in vitro. In fact, for one of these two, GUT8-2b, the mRNA level decreased significantly within 3 h. Our results show that many pollen-expressed mRNAs are indeed long-lived but that at least some mRNAs undergo decay during pollen maturation. Thus, there is no overall cytoplasmic condition in pollen that stabilizes mRNAs and specific mRNA turnover mechanisms must exist. We detected reciprocal mRNA stabilities with two genes that are expressed in both BY2 cells and pollen. GUT15 mRNA, known to be unstable (t1/2 < 3 h) in BY2 cells, was highly stable in pollen. In contrast, GRP2 mRNA decayed in pollen but was highly stable in BY2 cells. Therefore, we conclude that mRNA stability can be tissue-specific.
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14
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Affiliation(s)
- L Richter
- Boyce Thompson Institute for Plant Research Inc., Ithaca, NY 14850, USA
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15
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Franssen HJ. Plants embrace a stepchild: the discovery of peptide growth regulators. CURRENT OPINION IN PLANT BIOLOGY 1998; 1:384-387. [PMID: 10066615 DOI: 10.1016/s1369-5266(98)80260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Over the past decade, peptides have been added to the collection of signalling molecules in plants. As the impact of peptide hormones in non-plants is enormous, a comparison of plant and non-plant peptide signal molecules at this stage deserves our attention-not only to reveal common and unique features, but also to point to new avenues of future research on plant hormones.
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Affiliation(s)
- H J Franssen
- Department of Molecular Biology, Agricultural University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands.
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16
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De Rocher EJ, Vargo-Gogola TC, Diehn SH, Green PJ. Direct evidence for rapid degradation of Bacillus thuringiensis toxin mRNA as a cause of poor expression in plants. PLANT PHYSIOLOGY 1998; 117:1445-61. [PMID: 9701600 PMCID: PMC34908 DOI: 10.1104/pp.117.4.1445] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/1997] [Accepted: 05/09/1998] [Indexed: 05/20/2023]
Abstract
It is well established that the expression of Bacillus thuringiensis (B.t.) toxin genes in higher plants is severely limited at the mRNA level, but the cause remains controversial. Elucidating whether mRNA accumulation is limited transcriptionally or posttranscriptionally could contribute to effective gene design as well as provide insights about endogenous plant gene-expression mechanisms. To resolve this controversy, we compared the expression of an A/U-rich wild-type cryIA(c) gene and a G/C-rich synthetic cryIA(c) B.t.-toxin gene under the control of identical 5' and 3' flanking sequences. Transcriptional activities of the genes were equal as determined by nuclear run-on transcription assays. In contrast, mRNA half-life measurements demonstrated directly that the wild-type transcript was markedly less stable than that encoded by the synthetic gene. Sequences that limit mRNA accumulation were located at more than one site within the coding region, and some appeared to be recognized in Arabidopsis but not in tobacco (Nicotiana tabacum). These results support previous observations that some A/U-rich sequences can contribute to mRNA instability in plants. Our studies further indicate that some of these sequences may be differentially recognized in tobacco cells and Arabidopsis.
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Affiliation(s)
- E J De Rocher
- Michigan State University-Department of Energy Plant Research Laboratory, East Lansing, 48824, USA
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17
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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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18
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Abstract
The degradation rates of different mRNAs in higher plants can vary over a broad range and are regulated by a variety of endogenous and exogenous stimuli. During the past several years, efforts to better understand the control of mRNA stability in plants have increased considerably and this has led to improved methodologies and important mechanistic insights. In this review, we highlight some of the most interesting examples of plant transcripts that are controlled at the level of mRNA decay and discuss what has been learned from their study. Experiments that implicate or demonstrate the involvement of particular cis- and trans-acting factors in mRNA decay pathways are a major focus, as are those experiments that have led to mechanistic models. Emphasis is also placed on studies that address the relationship between translation and mRNA stability. Our current knowledge indicates that some of the determinants and pathways for mRNA decay may differ in plants compared to other eukaryotes, whereas others appear to be similar. This knowledge, coupled with the availability of biochemical, molecular and genetic approaches to elucidate plant mRNA decay mechanisms, should continue to lead to findings of novel and general significance.
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Affiliation(s)
- M L Abler
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824-1312, USA
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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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