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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1137. [PMID: 38674546 PMCID: PMC11055055 DOI: 10.3390/plants13081137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.
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Affiliation(s)
- T. N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - D. Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. Y. Morozov
- Biological Faculty, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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2
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Gultyaev AP, Koster C, van Batenburg DC, Sistermans T, van Belle N, Vijfvinkel D, Roussis A. Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements. NAR Genom Bioinform 2023; 5:lqad091. [PMID: 37850034 PMCID: PMC10578108 DOI: 10.1093/nargab/lqad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023] Open
Abstract
Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.
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Affiliation(s)
- Alexander P Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Celine Koster
- Life Science & Technology Honours College, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
- Amsterdam University Medical Center, Department of Human Genetics, section Ophthalmogenetics, Location AMC, Meibergdreef 9, Amsterdam, The Netherlands
| | - Diederik Cames van Batenburg
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- CareRate, Unit E1.165, Stationsplein 45, 3013 AK Rotterdam, The Netherlands
| | - Tom Sistermans
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Niels van Belle
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Daan Vijfvinkel
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Andreas Roussis
- National & Kapodistrian University of Athens, Faculty of Biology, Section of Botany, Group Molecular Plant Physiology, Panepistimiopolis - Zografou - Athens, 15784, Greece
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3
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Wang X, Fan H, Wang B, Yuan F. Research progress on the roles of lncRNAs in plant development and stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1138901. [PMID: 36959944 PMCID: PMC10028117 DOI: 10.3389/fpls.2023.1138901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) are RNAs of more than 200 nucleotides in length that are not (or very rarely) translated into proteins. In eukaryotes, lncRNAs regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. lncRNAs are categorized according to their genomic position and molecular mechanism. This review summarized the characteristics and mechanisms of plant lncRNAs involved in vegetative growth, reproduction, and stress responses. Our discussion and model provide a theoretical basis for further studies of lncRNAs in plant breeding.
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Affiliation(s)
| | | | | | - Fang Yuan
- *Correspondence: Baoshan Wang, ; Fang Yuan,
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4
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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5
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Short Peptides Induce Development of Root Hair Nicotiana tabacum. PLANTS 2022; 11:plants11070852. [PMID: 35406832 PMCID: PMC9002736 DOI: 10.3390/plants11070852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022]
Abstract
Root hairs absorb soil nutrients and water, and anchor the plant in the soil. Treatment of tobacco (Nicotiana tabacum) roots with glycine (Gly) amino acid, and glycilglycine (GlyGly) and glycilaspartic acid (GlyAsp) dipeptides (10−7 M concentration) significantly increased the development of root hairs. In the root, peptide accumulation was tissue-specific, with predominant localization to the root cap, meristem, elongation zone, and absorption zone. Peptides penetrated the epidermal and cortical cell and showed greater localization to the nucleus than to the cytoplasm. Compared with the control, tobacco plants grown in the presence of Gly, GlyGly, and GlyAsp exhibited the activation of WER, CPC, bHLH54, and bHLH66 genes and suppression of GTL1 and GL2 genes during root hair lengthening. Although Gly, GlyGly, and GlyAsp have a similar structure, the mechanism of regulation of root hair growth in each case were different, and these differences are most likely due to the fact that neutral Gly and GlyGly and negatively charged GlyAsp bind to different motives of functionally important proteins. Short peptides site-specifically interact with DNA, and histones. The molecular mechanisms underlying the effect of exogenous peptides on cellular processes remain unclear. Since these compounds acted at low concentrations, gene expression regulation by short peptides is most likely of epigenetic nature.
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Nizan IEF, Kamaruddin K, Ong PW, Ramli Z, Singh R, Rose RJ, Chan PL. Overexpression of Oil Palm Early Nodulin 93 Protein Gene (EgENOD93) Enhances In Vitro Shoot Regeneration in Arabidopsis thaliana. Mol Biotechnol 2022; 64:743-757. [PMID: 35107753 DOI: 10.1007/s12033-022-00450-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022]
Abstract
EgENOD93 was first identified in a cDNA microarray study of oil palm tissue culture where it was highly expressed in leaf explants with embryogenic potential. Functional characterization via an RNA interference study of its orthologue in Medicago truncatula demonstrated a significant role of this gene in somatic embryo formation. In this study, EgENOD93 was overexpressed in the important model plant Arabidopsis thaliana to investigate the embryogenic potential of EgENOD93 transgenic Arabidopsis explants compared to explants from control plants (pMDC140 and WT). Experiments using leaf explants revealed higher numbers of regenerated shoots at day 27 in all the homozygous transgenic Arabidopsis cultures (Tg01, Tg02 and Tg03) compared to controls. The expression level of EgENOD93 in Arabidopsis cultures was quantified using reverse transcription quantitative real-time PCR (RT-qPCR). The results supported the overexpression of this gene in transgenic Arabidopsis cultures, with 6 and 10 times higher expression of EgENOD93 in callus at Day 9 and Day 20, respectively. Overall, the results support the role of EgENOD93 in the enhancement of shoot regeneration in transgenic Arabidopsis. This together with the previous results observed in oil palm and Medicago truncatula suggests that ENOD93 plays a key role in the induction of somatic embryogenesis. A similarity to early nodulation-like ontogeny is possible.
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Affiliation(s)
- Intan Ernieza Farhana Nizan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Katialisa Kamaruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Pei-Wen Ong
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.,Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, 10617, Taipei, Taiwan, ROC
| | - Zubaidah Ramli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ray J Rose
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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Ganguly P, Roy D, Das T, Kundu A, Cartieaux F, Ghosh Z, DasGupta M. The Natural Antisense Transcript DONE40 Derived from the lncRNA ENOD40 Locus Interacts with SET Domain Protein ASHR3 During Inception of Symbiosis in Arachis hypogaea. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1057-1070. [PMID: 33934615 DOI: 10.1094/mpmi-12-20-0357-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The long noncoding RNA ENOD40 is required for cortical cell division during root nodule symbiosis (RNS) of legumes, though it is not essential for actinorhizal RNS. Our objective was to understand whether ENOD40 was required for aeschynomenoid nodule formation in Arachis hypogaea. AhENOD40 express from chromosome 5 (chr5) (AhENOD40-1) and chr15 (AhENOD40-2) during symbiosis, and RNA interference of these transcripts drastically affected nodulation, indicating the importance of ENOD40 in A. hypogaea. Furthermore, we demonstrated several distinct characteristics of ENOD40. (i) Natural antisense transcript (NAT) of ENOD40 was detected from the AhENOD40-1 locus (designated as NAT-AhDONE40). (ii) Both AhENOD40-1 and AhENOD40-2 had two exons, whereas NAT-AhDONE40 was monoexonic. Reverse-transcription quantitative PCR analysis indicated both sense and antisense transcripts to be present in both cytoplasm and nucleus, and their expression increased with the progress of symbiosis. (iii) RNA pull-down from whole cell extracts of infected roots at 4 days postinfection indicated NAT-AhDONE40 to interact with the SET (Su(var)3-9, enhancer of Zeste and Trithorax) domain containing absent small homeotic disc (ASH) family protein AhASHR3 and this interaction was further validated using RNA immunoprecipitation and electrophoretic mobility shift assay. (iv) Chromatin immunoprecipitation assays indicate deposition of ASHR3-specific histone marks H3K36me3 and H3K4me3 in both of the ENOD40 loci during the progress of symbiosis. ASHR3 is known for its role in optimizing cell proliferation and reprogramming. Because both ASHR3 and ENOD40 from legumes cluster away from those in actinorhizal plants and other nonlegumes in phylogenetic distance trees, we hypothesize that the interaction of DONE40 with ASHR3 could have evolved for adapting the nodule organogenesis program for legumes.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Pritha Ganguly
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Dipan Roy
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Anindya Kundu
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Fabienne Cartieaux
- LSTM, Université de Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, 700019, India
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8
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Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. Int J Mol Sci 2020; 22:ijms22010086. [PMID: 33374835 PMCID: PMC7795044 DOI: 10.3390/ijms22010086] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.
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9
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Summanwar A, Basu U, Rahman H, Kav NNV. Non-coding RNAs as emerging targets for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110521. [PMID: 32563460 DOI: 10.1016/j.plantsci.2020.110521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 05/23/2023]
Abstract
Food security is affected by climate change, population growth, as well as abiotic and biotic stresses. Conventional and molecular marker assisted breeding and genetic engineering techniques have been employed extensively for improving resistance to biotic stress in crop plants. Advances in next-generation sequencing technologies have permitted the exploration and identification of parts of the genome that extend beyond the regions with protein coding potential. These non-coding regions of the genome are transcribed to generate many types of non-coding RNAs (ncRNAs). These ncRNAs are involved in the regulation of growth, development, and response to stresses at transcriptional and translational levels. ncRNAs, including long ncRNAs (lncRNAs), small RNAs and circular RNAs have been recognized as important regulators of gene expression in plants and have been suggested to play important roles in plant immunity and adaptation to abiotic and biotic stresses. In this article, we have reviewed the current state of knowledge with respect to lncRNAs and their mechanism(s) of action as well as their regulatory functions, specifically within the context of biotic stresses. Additionally, we have provided insights into how our increased knowledge about lncRNAs may be used to improve crop tolerance to these devastating biotic stresses.
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Affiliation(s)
- Aarohi Summanwar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
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Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
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Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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12
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Deng F, Zhang X, Wang W, Yuan R, Shen F. Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC PLANT BIOLOGY 2018; 18:23. [PMID: 29370759 PMCID: PMC5785843 DOI: 10.1186/s12870-018-1238-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation. RESULTS In this study, in order to develop a comprehensive catalogue of lncRNAs in upland cotton under salt stress, we performed whole-transcriptome strand-specific RNA sequencing for three-leaf stage cotton seedlings treated with salt stress (S_NaCl) and controls (S_CK). In total we identified 1117 unique lncRNAs in this study and 44 differentially expressed RNAs were identified as potential non-coding RNAs. For the differentially expressed lncRNAs that were identified as intergenic lncRNAs (lincRNA), we analysed the gene ontology enrichment of cis targets and found that cis target protein-coding genes were mainly enriched in stress-related categories. Real-time quantitative PCR confirmed that all selected lincRNAs responsive to salt stress. We found lnc_388 was likely as regulator of Gh_A09G1182. And lnc_883 may participate in regulating tolerance to salt stress by modulating the expression of Gh_D03G0339 MS_channel. We then predicted the target mimics for miRNA in Gossypium. six miRNAs were identified, and the result of RT-qPCR with lncRNA and miRNA suggested that lnc_973 and lnc_253 may regulate the expression of ghr-miR399 and ghr-156e as a target mimic under salt stress. CONCLUSIONS We identified 44 lincRNAs that were differentially expressed under salt stress. These lincRNAs may target protein-coding genes via cis-acting regulation. We also discovered that specifically-expressed lincRNAs under salt stress may act as endogenous target mimics for conserved miRNAs. These findings extend the current view on lincRNAs as ubiquitous regulators under stress stress.
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Affiliation(s)
- Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Rui Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
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13
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Shumayla, Sharma S, Taneja M, Tyagi S, Singh K, Upadhyay SK. Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:1019. [PMID: 28649263 PMCID: PMC5465302 DOI: 10.3389/fpls.2017.01019] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/29/2017] [Indexed: 09/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few lncRNAs were predicted as precursor (19 lncRNAs), while some as target mimics (1,047 lncRNAs) of known miRNAs involved in various regulatory functions. The results suggested numerous functions of lncRNAs in T. aestivum, and unfolded the opportunities for functional characterization of individual lncRNA in future studies.
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Affiliation(s)
- Shumayla
- Department of Botany, Panjab UniversityChandigarh, India
| | | | - Mehak Taneja
- Department of Botany, Panjab UniversityChandigarh, India
| | - Shivi Tyagi
- Department of Botany, Panjab UniversityChandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab UniversityChandigarh, India
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Sampath K, Ephrussi A. CncRNAs: RNAs with both coding and non-coding roles in development. Development 2016; 143:1234-41. [PMID: 27095489 DOI: 10.1242/dev.133298] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNAs are known to regulate diverse biological processes, either as protein-encoding molecules or as non-coding RNAs. However, a third class that comprises RNAs endowed with both protein coding and non-coding functions has recently emerged. Such bi-functional 'coding and non-coding RNAs' (cncRNAs) have been shown to play important roles in distinct developmental processes in plants and animals. Here, we discuss key examples of cncRNAs and review their roles, regulation and mechanisms of action during development.
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Affiliation(s)
- Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AJ, UK
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
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15
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Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0405-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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Szcześniak MW, Rosikiewicz W, Makałowska I. CANTATAdb: A Collection of Plant Long Non-Coding RNAs. PLANT & CELL PHYSIOLOGY 2016; 57:e8. [PMID: 26657895 PMCID: PMC4722178 DOI: 10.1093/pcp/pcv201] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/06/2015] [Indexed: 05/11/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is still very limited. In particular, a number of model plant species still lack comprehensive data sets of lncRNAs and their annotations, and very little is known about their biological roles. To meet these shortcomings, we created an online database of lncRNAs in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries. Expression values, coding potential, sequence alignments as well as other types of data provide annotation for the identified lncRNAs. In order to better characterize them, we investigated their potential roles in splicing modulation and deregulation of microRNA functions. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb (http://cantata.amu.edu.pl, http://yeti.amu.edu.pl/CANTATA/).
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Affiliation(s)
- Michał W Szcześniak
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Wojciech Rosikiewicz
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Izabela Makałowska
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
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17
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18
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Tanaka K, Cho SH, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZJ, Xu D, Stacey G. Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5727-38. [PMID: 26049159 PMCID: PMC4566972 DOI: 10.1093/jxb/erv260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Although lipo-chitooligosaccharides (LCOs) are important signal molecules for plant-symbiont interactions, a number of reports suggest that LCOs can directly impact plant growth and development, separate from any role in plant symbioses. In order to investigate this more closely, maize and Setaria seedlings were treated with LCO and their growth was evaluated. The data indicate that LCO treatment significantly enhanced root growth. RNA-seq transcriptomic analysis of LCO-treated maize roots identified a number of genes whose expression was significantly affected by the treatment. Among these genes, some LCO-up-regulated genes are likely involved in root growth promotion. Interestingly, some stress-related genes were down-regulated after LCO treatment, which might indicate reallocation of resources from defense responses to plant growth. The promoter activity of several LCO-up-regulated genes using a β-glucuronidase reporter system was further analysed. The results showed that the promoters were activated by LCO treatment. The data indicate that LCO can directly impact maize root growth and gene expression.
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Affiliation(s)
- Kiwamu Tanaka
- Divisions of Plant Science and Biochemistry University of Missouri, Columbia, MO 65211, USA Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Sung-Hwan Cho
- Divisions of Plant Science and Biochemistry University of Missouri, Columbia, MO 65211, USA Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Hyeyoung Lee
- Plant Transformation Core Facility,Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - An Q Pham
- Divisions of Plant Science and Biochemistry University of Missouri, Columbia, MO 65211, USA Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Josef M Batek
- Divisions of Plant Science and Biochemistry University of Missouri, Columbia, MO 65211, USA Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Shiqi Cui
- Department of Statistics, University of Missouri, Columbia, MO 65211, USA
| | - Jing Qiu
- Department of Statistics, University of Missouri, Columbia, MO 65211, USA
| | - Saad M Khan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA Informatics Institute, Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA Informatics Institute, Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility,Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA Informatics Institute, Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry University of Missouri, Columbia, MO 65211, USA Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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19
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Functions of plants long non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:155-62. [PMID: 26112461 DOI: 10.1016/j.bbagrm.2015.06.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/28/2015] [Accepted: 06/09/2015] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been emerged as important players for various biological pathways, including dosage compensation, genomic imprinting, chromatin regulation, alternative splicing and nuclear organization. A large number of lncRNAs had already been identified by different approaches in plants, while the functions of only a few of them have been investigated. This review will summarize our current understanding of a wide range of plant lncRNAs functions, and highlight their roles in the regulation of diverse pathways in plants. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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20
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Liu X, Hao L, Li D, Zhu L, Hu S. Long non-coding RNAs and their biological roles in plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:137-47. [PMID: 25936895 PMCID: PMC4563214 DOI: 10.1016/j.gpb.2015.02.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 12/31/2022]
Abstract
With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.
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Affiliation(s)
- Xue Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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21
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Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase. Nat Commun 2014; 4:2191. [PMID: 23934307 DOI: 10.1038/ncomms3191] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 06/26/2013] [Indexed: 01/07/2023] Open
Abstract
Leguminous plants establish a symbiosis with rhizobia to enable nitrogen fixation in root nodules under the control of the presumed root-to-shoot-to-root negative feedback called autoregulation of nodulation. In Lotus japonicus, autoregulation is mediated by CLE-RS genes that are specifically expressed in the root, and the receptor kinase HAR1 that functions in the shoot. However, the mature functional structures of CLE-RS gene products and the molecular nature of CLE-RS/HAR1 signalling governed by these spatially distant components remain elusive. Here we show that CLE-RS2 is a post-translationally arabinosylated glycopeptide derived from the CLE domain. Chemically synthesized CLE-RS glycopeptides cause significant suppression of nodulation and directly bind to HAR1 in an arabinose-chain and sequence-dependent manner. In addition, CLE-RS2 glycopeptide specifically produced in the root is found in xylem sap collected from the shoot. We propose that CLE-RS glycopeptides are the long sought mobile signals responsible for the initial step of autoregulation of nodulation.
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Song JH, Cao JS, Wang CG. BcMF11, a novel non-coding RNA gene from Brassica campestris, is required for pollen development and male fertility. PLANT CELL REPORTS 2013; 32:21-30. [PMID: 23064614 DOI: 10.1007/s00299-012-1337-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE : BcMF11 as a non-coding RNA gene has an essential role in pollen development, and might be useful for regulating the pollen fertility of crops by antisense RNA technology. We previously identified a 828-bp full-length cDNA of BcMF11, a novel pollen-specific non-coding mRNA-like gene from Chinese cabbage (Brassica campestris L. ssp. chinensis Makino). However, little information is known about the function of BcMF11 in pollen development. To investigate its exact biological roles in pollen development, the BcMF11 cDNA was antisense inhibited in transgenic Chinese cabbage under the control of a tapetum-specific promoter BcA9 and a constitutive promoter CaMV 35S. Antisense RNA transgenic plants displayed decreasing expression of BcMF11 and showed distinct morphological defects. Pollen germination test in vitro and in vivo of the transgenic plants suggested that inhibition of BcMF11 decreased pollen germination efficiency and delayed the pollen tubes' extension in the style. Under scanning electron microscopy, many shrunken and collapsed pollen grains were detected in the antisense BcMF11 transgenic Chinese cabbage. Further cytological observation revealed abnormal pollen development process in transgenic plants, including delayed degradation of tapetum, asynchronous separation of microspore, and aborted development of pollen grain. These results suggest that BcMF11, as a non-coding RNA, plays an essential role in pollen development and male fertility.
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Affiliation(s)
- Jiang-Hua Song
- College of Horticulture, Anhui Agricultural University, Hefei 230036, PR China
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23
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Molecular Functions of Long Non-Coding RNAs in Plants. Genes (Basel) 2012; 3:176-90. [PMID: 24704849 PMCID: PMC3899965 DOI: 10.3390/genes3010176] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
The past decade has seen dramatic changes in our understanding of the scale and complexity of eukaryotic transcriptome owing to the discovery of diverse types of short and long non-protein-coding RNAs (ncRNAs). While short ncRNA-mediated gene regulation has been extensively studied and the mechanisms well understood, the function of long ncRNAs remains largely unexplored, especially in plants. Nevertheless, functional insights generated in recent studies with mammalian systems have indicated that long ncRNAs are key regulators of a variety of biological processes. They have been shown to act as transcriptional regulators and competing endogenous RNAs (ceRNAs), to serve as molecular cargos for protein re-localization and as modular scaffolds to recruit the assembly of multiple protein complexes for chromatin modifications. Some of these functions have been found to be conserved in plants. Here, we review our current understanding of long ncRNA functions in plants and discuss the challenges in functional characterization of plant long ncRNAs.
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24
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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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25
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Yokota K, Hayashi M. Function and evolution of nodulation genes in legumes. Cell Mol Life Sci 2011; 68:1341-51. [PMID: 21380559 PMCID: PMC11114672 DOI: 10.1007/s00018-011-0651-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
Abstract
Root nodule (RN) symbiosis has a unique feature in which symbiotic bacteria fix atmospheric nitrogen. The symbiosis is established with a limited species of land plants, including legumes. How RN symbiosis evolved is still a mystery, but recent findings on legumes genes that are necessary for RN symbiosis may give us a clue.
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Affiliation(s)
- Keisuke Yokota
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan.
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26
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Charon C, Moreno AB, Bardou F, Crespi M. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. MOLECULAR PLANT 2010; 3:729-739. [PMID: 20603381 DOI: 10.1093/mp/ssq037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The complex responses of eukaryotic cells to external factors are governed by several transcriptional and post-transcriptional processes. Several of them occur in the nucleus and have been linked to the action of non-protein-coding RNAs (or npcRNAs), both long and small npcRNAs, that recently emerged as major regulators of gene expression. Regulatory npcRNAs acting in the nucleus include silencing-related RNAs, intergenic npcRNAs, natural antisense RNAs, and other aberrant RNAs resulting from the interplay between global transcription and RNA processing activities (such as Dicers and RNA-dependent polymerases). Generally, the resulting npcRNAs exert their regulatory effects through interactions with RNA-binding proteins (or RBPs) within ribonucleoprotein particles (or RNPs). A large group of RBPs are implicated in the silencing machinery through small interfering RNAs (siRNAs) and their localization suggests that several act in the nucleus to trigger epigenetic and chromatin changes at a whole-genome scale. Other nuclear RBPs interact with npcRNAs and change their localization. In the fission yeast, the RNA-binding Mei2p protein, playing pivotal roles in meiosis, interact with a meiotic npcRNA involved in its nuclear re-localization. Related processes have been identified in plants and the ENOD40 npcRNA was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in RNA-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. In this review, we discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environment and, consequently, control plant developmental plasticity.
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Affiliation(s)
- Celine Charon
- University Paris-Sud, Institut de Biologie des Plantes, UMR8618, Orsay Cedex, F-91405, France
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27
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Bi YM, Kant S, Clarke J, Gidda S, Ming F, Xu J, Rochon A, Shelp BJ, Hao L, Zhao R, Mullen RT, Zhu T, Rothstein SJ. Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. PLANT, CELL & ENVIRONMENT 2009; 32:1749-60. [PMID: 19682292 DOI: 10.1111/j.1365-3040.2009.02032.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Development of genetic varieties with improved nitrogen-use efficiency (NUE) is essential for sustainable agriculture. In this study, we developed a growth system for rice wherein N was the growth-limiting factor, and identified N-responsive genes by a whole genome transcriptional profiling approach. Some genes were selected to test their functionality in NUE by a transgenic approach. One such example with positive effects on NUE is an early nodulin gene OsENOD93-1. This OsENOD93-1 gene responded significantly to both N induction and N reduction. Transgenic rice plants over-expressing the OsENOD93-1 gene had increased shoot dry biomass and seed yield. This OsENOD93-1 gene was expressed at high levels in roots of wild-type (WT) plants, and its protein product was localized in mitochondria. Transgenic plants accumulated higher concentrations of total amino acids and total N in roots. A higher concentration of amino acids in xylem sap was detected in transgenic plants, especially under N stress. In situ hybridization revealed that OsENOD93-1 is expressed in vascular bundles, as well as in epidermis and endodermis. This work demonstrates that transcriptional profiling, coupled with a transgenic validation approach, is an effective strategy for gene discovery. The knowledge gained from this study could be applied to other important crops.
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Affiliation(s)
- Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
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28
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Hanyu M, Fujimoto H, Tejima K, Saeki K. Functional differences of two distinct catalases in Mesorhizobium loti MAFF303099 under free-living and symbiotic conditions. J Bacteriol 2009; 191:1463-71. [PMID: 19074374 PMCID: PMC2648221 DOI: 10.1128/jb.01583-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Accepted: 12/04/2008] [Indexed: 11/20/2022] Open
Abstract
Protection against reactive oxygen species (ROS) is important for legume-nodulating rhizobia during the establishment and maintenance of symbiosis, as well as under free-living conditions, because legume hosts might assail incoming microbes with ROS and because nitrogenase is extremely sensitive to ROS. We generated mutants of two potential catalase genes in Mesorhizobium loti MAFF303099 to investigate their physiological significance. Biochemical results indicated that genes with the locus tags mlr2101 and mlr6940 encoded a monofunctional catalase and a bifunctional catalase-peroxidase, respectively, that were named katE and katG. Under free-living conditions, the katG mutant demonstrated an extended generation time and elevated sensitivity to exogenous H(2)O(2), whereas the katE mutant exhibited no generation time extension and only a slight increase in sensitivity to exogenous H(2)O(2). However, the katE mutant showed a marked decrease in its survival rate during the stationary phase. With regard to symbiotic capacities with Lotus japonicus, the katG mutant was indistinguishable from the wild type; nevertheless, the mutants with disrupted katE formed nodules with decreased nitrogen fixation capacities (about 50 to 60%) compared to those formed by the wild type. These mutant phenotypes agreed with the expression profiles showing that transcription of katG, but not katE, was high during the exponential growth phase and that transcription levels of katE versus sigA were elevated during stationary phase and were approximately fourfold higher in bacteroids than mid-exponential-phase cells. Our results revealed functional separation of the two catalases, as well as the importance of KatE under conditions of strong growth limitation.
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Affiliation(s)
- Masaki Hanyu
- Department of Biological Sciences, Nara Women's University, Japan
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29
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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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30
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Hashimoto Y, Kondo T, Kageyama Y. Lilliputians get into the limelight: novel class of small peptide genes in morphogenesis. Dev Growth Differ 2008; 50 Suppl 1:S269-76. [PMID: 18459982 DOI: 10.1111/j.1440-169x.2008.00994.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Generally, bioactive small peptides are derived from precursors with signal sequences at their N-terminal ends, which undergo modification and proteolysis through a secretory pathway. By contrast, small peptides encoded in short open reading frames (sORF) lack signaling sequences and therefore are released into the cytoplasm, which may result in their having functions distinct from those of secreted peptides. Several small peptides encoded by sORF are involved in the morphogenesis of multicellular organisms. POLARIS, ROTUNDIFOLIA4, and Enod40 are plant peptides that are involved, respectively, in root formation, leaf shape control, and cortical cell division during nodule formation. Brick1/HSPC300 is an evolutionarily conserved component of the actin reorganization complex. polished rice/tarsal-less and mille-pattes encode related small peptides that are required for epithelial morphogenesis in Drosophila and segmentation in Tribolium. There are only a few known examples of small peptides encoded by sORF, and their molecular functions are still largely obscure. Nevertheless, an increasing number of sORF genes is being identified, and further research should reveal their roles in novel molecular mechanisms underlying developmental events.
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Affiliation(s)
- Yoshiko Hashimoto
- Laboratory of Developmental Genetics, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Myodaiji-Higashiyama, Okazaki 444-8787, Japan
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31
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Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:631-45. [PMID: 18393623 DOI: 10.1094/mpmi-21-5-0631] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation, timepoints that coincide with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by quantitative reverse transcriptase-polymerase chain reaction, and their expression patterns mimicked the microarray results, confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status.
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Affiliation(s)
- Laurent Brechenmacher
- National Center for Soybean Biotechnology, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO 65211, USA
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32
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Abstract
Extracellular plant peptides perform a large variety of functions, including signalling and defence. Intracellular peptides often have physiological functions or may merely be the products of general proteolysis. Plant peptides have been identified and, in part, functionally characterized through biochemical and genetic studies, which are lengthy and in some cases impractical. Peptidomics is a branch of proteomics that has been developed over the last 5 years, and has been used mainly to study neuropeptides in animals and the degradome of proteases. Peptidomics is a fast, efficient methodology that can detect minute and transient amounts of peptides and identify their post-translational modifications. This review describes known plant peptides and introduces the use of peptidomics for the detection of novel plant peptides.
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Affiliation(s)
- Naser Farrokhi
- National Institute of Genetic Engineering and Biotechnology, Pajoohesh Blvd., Tehran-Karaj Highway, 17th Km., Tehran, Iran.
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Fukuda H, Hirakawa Y, Sawa S. Peptide signaling in vascular development. CURRENT OPINION IN PLANT BIOLOGY 2007; 10:477-82. [PMID: 17904408 DOI: 10.1016/j.pbi.2007.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 08/21/2007] [Accepted: 08/28/2007] [Indexed: 05/07/2023]
Abstract
In plants and animals, putative small peptide ligands have been suggested to play crucial roles in development as signal molecules of cell-cell communication. Recent studies of CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE) genes and their products have revealed that distinctive dodeca-CLE peptide ligands function in various developmental processes. In particular, the finding and characterization of TDIF, a dodeca-CLE peptide suppressing tracheary element differentiation, indicates regulation of vascular organization by cell-cell communication through CLE peptides. In addition, other extracellular peptides such as phytosulfokine, proteins such as xylogen, and phytohormones all participate in the ordered formation of vascular tissues.
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Affiliation(s)
- Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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34
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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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35
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Gultyaev AP, Roussis A. Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants. Nucleic Acids Res 2007; 35:3144-52. [PMID: 17452360 PMCID: PMC1888808 DOI: 10.1093/nar/gkm173] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/05/2007] [Accepted: 03/06/2007] [Indexed: 11/22/2022] Open
Abstract
enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.
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Affiliation(s)
- Alexander P. Gultyaev
- Leiden Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands and Agricultural University of Athens, Department of Agricultural Biology and Biotechnology, Iera Odos 75, 118 55 Votanikos, Athens, Greece
| | - Andreas Roussis
- Leiden Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands and Agricultural University of Athens, Department of Agricultural Biology and Biotechnology, Iera Odos 75, 118 55 Votanikos, Athens, Greece
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36
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Kereszt A, Li D, Indrasumunar A, Nguyen CDT, Nontachaiyapoom S, Kinkema M, Gresshoff PM. Agrobacterium rhizogenes-mediated transformation of soybean to study root biology. Nat Protoc 2007; 2:948-52. [PMID: 17446894 DOI: 10.1038/nprot.2007.141] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This protocol is used to induce transgenic roots on soybean to study the function of genes required in biological processes of the root. Young seedlings with unfolded cotyledons are infected at the cotyledonary node and/or hypocotyl with Agrobacterium rhizogenes carrying the gene construct to be tested and the infection sites are kept in an environment of high humidity. When the emerged hairy roots can support the plants, the main roots are removed and the transgenic roots can be tested. Using this method, almost 100% of the infected plants form hairy roots within 1 month from the start of the experiments.
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Affiliation(s)
- Attila Kereszt
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, St Lucia, Queensland 4072, Australia
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37
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Kumagai H, Kinoshita E, Ridge RW, Kouchi H. RNAi Knock-Down of ENOD40 s Leads to Significant Suppression of Nodule Formation in Lotus japonicus. ACTA ACUST UNITED AC 2006; 47:1102-11. [PMID: 16816411 DOI: 10.1093/pcp/pcj081] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
ENOD40 is one of the most intriguing early nodulin genes that is known to be induced very early in response to interaction of legume plants with symbiotic Rhizobium bacteria, but its function in the nodulation process is still not known. Lotus japonicus has two ENOD40 genes: LjENOD40-1 is abundantly induced in very early stages of bacterial infection or Nod factor application, whereas LjENOD40-2 is abundantly expressed only in mature nodules. We generated transgenic lines of L. japonicus with an RNAi (RNA interference) construct that expresses hairpin double-stranded RNA for LjENOD40-1 to induce sequence-specific RNA silencing. In the transgenic plants, expression of both LjENOD40-1 and -2 was significantly reduced, and no accumulation of ENOD40 transcripts was detected upon Mesorhizobium loti inoculation. The transgenic plants exhibited very poor nodulation (only 0-2 nodules per plant) and could not grow well without additional nitrogen supply. Analysis of segregation in the T(2) progeny indicated that the suppression of nodulation is perfectly linked with the presence of the transgene. Microscopic observation of the infection process using lacZ-labeled M. loti, together with expression analysis of infection-related nodulin genes, demonstrated that ENOD40 knock-down did not inhibit the initiation of the bacterial infection process. In contrast, nodule primordium initiation and subsequent nodule development were significantly suppressed in the transgenic plants. These results clearly indicate that ENOD40 is required for nodule initiation and subsequent organogenesis, but is not involved in early infection events.
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Affiliation(s)
- Hirotaka Kumagai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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38
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Germain H, Chevalier E, Matton DP. Plant bioactive peptides: an expanding class of signaling molecules. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b05-162] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Until recently, our knowledge of intercellular signaling in plants was limited to the so-called five classical plant hormones: auxin, cytokinin, gibberellin, ethylene, and abscissic acid. Other chemical compounds like sterols and lipids have also been recognized as signaling molecules in plants, but it was only recently discovered that peptides in plants, as in animal cells, play crucial roles in various aspects of growth and development, biotic and abiotic stress responses, and self/non-self recognition in sporophytic self-incompatibility. These peptides are often part of a very large gene family whose members show diverse, sometime overlapping spatial and temporal expression patterns, allowing them to regulate different aspects of plant growth and development. Only a handful of peptides have been linked to a bona fide receptor, thereby activating a cascade of events. Since these peptides have been thoroughly reviewed in the past few years, this review will focus on the small putative plant signaling peptides, some often disregarded in the plant peptide literature, which have been shown through biochemical or genetic studies to play important roles in plants.
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Affiliation(s)
- Hugo Germain
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101, rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Eric Chevalier
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101, rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Daniel P. Matton
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101, rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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39
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Abstract
In recent years, numerous biochemical and genetic studies have demonstrated that peptide signaling plays a greater than anticipated role in various aspects of plant growth and development. A substantial proportion of these peptides are secretory and act as local signals mediating cell-to-cell communication. Specific receptors for several peptides were identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. These findings illustrate the importance of peptide signaling in the regulation of plant growth, functions that were previously ascribed to the combined action of small lipophilic compounds referred to as "traditional plant hormones." Here, we outline recent advances in the current understanding of biologically active peptides in plants, currently regarded as a new class of plant hormones.
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Affiliation(s)
- Yoshikatsu Matsubayashi
- Graduate School of Bio-Agricultural Sciences, Nagoya University Chikusa, Nagoya 464-8601 Japan.
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40
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Skorpil P, Broughton WJ. Molecular interactions between Rhizobium and legumes. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2006; 41:143-64. [PMID: 16623393 DOI: 10.1007/3-540-28221-1_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Peter Skorpil
- Laboratoire de Biologie Moléculaire des Plantes Supérieures (LBMPS), Sciences III, Université de Genève, 1212 Genève 4, Switzerland
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41
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Takeda N, Okamoto S, Hayashi M, Murooka Y. Expression of LjENOD40 genes in response to symbiotic and non-symbiotic signals: LjENOD40-1 and LjENOD40-2 are differentially regulated in Lotus japonicus. PLANT & CELL PHYSIOLOGY 2005; 46:1291-8. [PMID: 15937327 DOI: 10.1093/pcp/pci138] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nitrogen fixation in nodules provides leguminous plants with an ability to grow in nitrogen-starved soil. Infection of the host plants by microsymbionts triggers various physiological and morphological changes during nodule formation. In Lotus japonicus, expression of early nodulin (ENOD) genes is triggered by perception of bacterial signal molecules, nodulation factors (Nod factors). We examined the expression patterns of ENOD40 genes during the nodule formation process. Two ENOD40 genes of L. japonicus were specifically expressed in the nodule formation process, but they showed different expression patterns upon infection. Each ENOD40 gene demonstrates an individual specificity and regulation with regard to rhizobial infection.
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Affiliation(s)
- Naoya Takeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
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42
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Grønlund M, Roussis A, Flemetakis E, Quaedvlieg NEM, Schlaman HRM, Umehara Y, Katinakis P, Stougaard J, Spaink HP. Analysis of promoter activity of the early nodulin Enod40 in Lotus japonicus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:414-27. [PMID: 15915640 DOI: 10.1094/mpmi-18-0414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Our comparative studies on the promoter (pr) activity of Enod40 in the model legume Lotus japonicus in stably transformed GusA reporter lines and in hairy roots of L. japonicus demonstrate a stringent regulation of the Enod40 promoter in the root cortex and root hairs in response to Nod factors. Interestingly, the L. japonicus Enod40-2 promoter fragment also shows symbiotic activity in the reverse orientation. Deletion analyses of the Glycine max (Gm) Enod40 promoter revealed the presence of a minimal region -185 bp upstream of the transcription start. Stable transgenic L. japonicus reporter lines were used in bioassays to test the effect of different compounds on early symbiotic signaling. The responses of prGmEnod40 reporter lines were compared with the responses of L. japonicus (Lj) reporter lines based on the LjNin promoter. Both reporter lines show very early activity postinoculation in root hairs of the responsive zone of the root and later in the dividing cells of nodule primordia. The LjNin promoter was found to be more responsive than the GmEnod40 promoter to Nod factors and related compounds. The use of prGmEnod40 reporter lines to analyze the effect of nodulin genes on the GmEnod40 promoter activity indicates that LJNIN has a positive effect on the regulation of the Enod40 promoter, whereas the latter is not influenced by ectopic overexpression of its own gene product. In addition to pointing to a difference in the regulation of the two nodulin genes Enod40 and Nin during early time points of symbiosis, the bioassays revealed a difference in the response to the synthetic cytokinin 6-benzylaminopurine (BAP) between alfalfa and clover and L. japonicus. In alfalfa and clover, Enod40 expression was induced upon BAP treatment, whereas this seems not to be the case in L. japonicus; these results correlate with effects at the cellular level because BAP can induce pseudonodules in alfalfa and clover but not in L. japonicus. In conclusion, we demonstrate the applicability of the described L. japonicus reporter lines in analyses of the specificity of compounds related to nodulation as well as for the dissection of the interplay between different nodulin genes.
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Affiliation(s)
- Mette Grønlund
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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43
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Röhrig H, John M, Schmidt J. Modification of soybean sucrose synthase by S-thiolation with ENOD40 peptide A. Biochem Biophys Res Commun 2004; 325:864-70. [PMID: 15541370 DOI: 10.1016/j.bbrc.2004.10.100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Indexed: 11/23/2022]
Abstract
The gene ENOD40 is expressed at an early stage of root nodule organogenesis and has been postulated to play a central regulatory role in the Rhizobium-legume interaction. In vitro translation of soybean ENOD40 mRNA showed that the gene encodes two peptides of 12 and 24aa residues (peptides A and B) that bind to sucrose synthase. Here we show that the small Cys-containing peptide A binds to sucrose synthase by disulfide bond formation, which may represent a novel form of posttranslational modification of this important metabolic enzyme. Assays using nanomolar concentrations of peptide A revealed that the monomeric reduced form of this peptide binds to purified sucrose synthase. Using a cysteinyl capture strategy combined with MALDI-TOF MS analysis we identified the Cys residue C264 of soybean sucrose synthase as the binding site of peptide A. Modification of sucrose synthase with ENOD40 peptide A activates sucrose cleavage activity whereas the synthesis activity of the enzyme is unaffected. The results are discussed in relation to the role of sucrose synthase in the control of sucrose utilization in nitrogen-fixing nodules.
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Affiliation(s)
- Horst Röhrig
- Max-Planck-Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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44
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Koch K. Sucrose metabolism: regulatory mechanisms and pivotal roles in sugar sensing and plant development. CURRENT OPINION IN PLANT BIOLOGY 2004; 7:235-46. [PMID: 15134743 DOI: 10.1016/j.pbi.2004.03.014] [Citation(s) in RCA: 704] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sucrose cleavage is vital to multicellular plants, not only for the allocation of crucial carbon resources but also for the initiation of hexose-based sugar signals in importing structures. Only the invertase and reversible sucrose synthase reactions catalyze known paths of sucrose breakdown in vivo. The regulation of these reactions and its consequences has therefore become a central issue in plant carbon metabolism. Primary mechanisms for this regulation involve the capacity of invertases to alter sugar signals by producing glucose rather than UDPglucose, and thus also two-fold more hexoses than are produced by sucrose synthase. In addition, vacuolar sites of cleavage by invertases could allow temporal control via compartmentalization. In addition, members of the gene families encoding either invertases or sucrose synthases respond at transcriptional and posttranscriptional levels to diverse environmental signals, including endogenous changes that reflect their own action (e.g. hexoses and hexose-responsive hormone systems such as abscisic acid [ABA] signaling). At the enzyme level, sucrose synthases can be regulated by rapid changes in sub-cellular localization, phosphorylation, and carefully modulated protein turnover. In addition to transcriptional control, invertase action can also be regulated at the enzyme level by highly localized inhibitor proteins and by a system that has the potential to initiate and terminate invertase activity in vacuoles. The extent, path, and site of sucrose metabolism are thus highly responsive to both internal and external environmental signals and can, in turn, dramatically alter development and stress acclimation.
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Affiliation(s)
- Karen Koch
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA.
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45
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Wang Y, Yu G, Shen S, Zhu J. Promoter of soybean early nodulin geneenod2B is induced by rhizobial Nod factors in transgenic rice. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf02900316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Dey M, Complainville A, Charon C, Torrizo L, Kondorosi A, Crespi M, Datta S. Phytohormonal responses in enod40-overexpressing plants of Medicago truncatula and rice. PHYSIOLOGIA PLANTARUM 2004; 120:132-139. [PMID: 15032885 DOI: 10.1111/j.0031-9317.2004.0208.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phytohormones are well-known regulators of the symbiotic Rhizobium-legume association in the plant host. The enod40 nodulin gene is associated with the earliest phases of the nodule organogenesis programme in the legume host and modifying its expression resulted in perturbations of nodule development in Medicago truncatula. Therefore in our pursuit to mimic the initial signal transduction steps of legume nodulation in the alien physiological set-up of a rice plant, we have expressed the Mtenod40 gene in rice. Molecular data confirm the stable integration, inheritance and transcription of the foreign gene in this non-legume. We have compared the phytohormonal responses of Mtenod40-overexpressing and control plants in a homologous legume background (M. truncatula) and in the non-legume rice. An enod40-mediated root growth response, induced by inhibition of ethylene biosynthesis, was observed in both plants. On the other hand, a significant differential effect of cytokinins was observed only in rice plants. This suggests that ethylene inhibits enod40 action both in legumes and non-legumes and reinforces that some of the early signal transduction steps of the nodule developmental programme may function in rice.
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Affiliation(s)
- Moul Dey
- Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines Institut des Sciences du Vegetal, CNRS, 1 Avenue de la Terrasse, F91198 Gif sur Yvette, France Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY-14853, USA
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47
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Compaan B, Ruttink T, Albrecht C, Meeley R, Bisseling T, Franssen H. Identification and characterization of a Zea mays line carrying a transposon-tagged ENOD40. ACTA ACUST UNITED AC 2003; 1629:84-91. [PMID: 14522083 DOI: 10.1016/j.bbaexp.2003.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In Zea mays, two ENOD40 homologous were identified that show only 30% of sequence homology to each other. We identified line e40-mum1 carrying a Mu transposon inserted in ZmENOD40-1, the maize gene that has the highest homology to leguminous ENOD40. The insertion causes a dramatic reduction of the ZmENOD40-1 transcript level. Irrespective of this, homozygous e40-mum1 plants are still able to interact with mycorrhizal fungi. Furthermore, no phenotypic aberrations correlated to the presence of e40-mum1 have been identified and therefore it is suggested that Z. mays ENOD40 genes are functionally redundant despite their strikingly low homology.
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Affiliation(s)
- Bert Compaan
- Laboratory of Molecular Biology, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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48
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Santi C, von Groll U, Ribeiro A, Chiurazzi M, Auguy F, Bogusz D, Franche C, Pawlowski K. Comparison of nodule induction in legume and actinorhizal symbioses: the induction of actinorhizal nodules does not involve ENOD40. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:808-816. [PMID: 12971604 DOI: 10.1094/mpmi.2003.16.9.808] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two types of root nodule symbioses are known for higher plants, legume and actinorhizal symbioses. In legume symbioses, bacterial signal factors induce the expression of ENOD40 genes. We isolated an ENOD40 promoter from an actinorhizal plant, Casuarina glauca, and compared its expression pattern in a legume (Lotus japonicus) and an actinorhizal plant (Allocasuarina verticillata) with that of an ENOD40 promoter from the legume soybean (GmENOD40-2). In the actinorhizal Allocasuarina sp., CgENOD40-GUS and GmENOD40-2-GUS showed similar expression patterns in both vegetative and symbiotic development, and neither promoter was active during nodule induction. The nonsymbiotic expression pattern of CgENOD40-GUS in the legume genus Lotus resembled the nonsymbiotic expression patterns of legume ENOD40 genes; however, in contrast to GmENOD40-2-GUS, CgENOD40-GUS was not active during nodule induction. The fact that only legume, not actinorhizal, ENOD40 genes are induced during legume nodule induction can be linked to the phloem unloading mechanisms established in the zones of nodule induction in the roots of both types of host plants.
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Affiliation(s)
- Carole Santi
- Equipe Rhizogenèse, UMR 1098, Institut de Recherche pour le Développement, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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49
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Girard G, Roussis A, Gultyaev AP, Pleij CWA, Spaink HP. Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean. Nucleic Acids Res 2003; 31:5003-15. [PMID: 12930950 PMCID: PMC212817 DOI: 10.1093/nar/gkg721] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2003] [Revised: 06/30/2003] [Accepted: 07/17/2003] [Indexed: 11/13/2022] Open
Abstract
The plant gene enod40 is highly conserved among legumes and also present in various non-legume species. It is presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation. Two small peptides encoded by enod40 mRNA as well as its secondary structure have been shown to be key elements in the signalling processes underlying nodule organogenesis. Here results concerning the secondary structure of mRNA of enod40 in soybean are presented. This study combined a theoretical approach, involving structure prediction and comparison, as well as structure probing. Our study indicates five conserved domains in enod40 mRNA among numerous leguminous species. Structure comparison suggests that some domains are also conserved in non-leguminous species and that an additional domain exists that was found only in leguminous species developing indeterminate nodules. Enzymatic and chemical probing data support the structure for three of the domains, and partially for the remaining two. The rest of the molecule appears to be less structured. Some of the domains include motifs, such as U-containing internal loops and bulges, which seem to be conserved. Therefore, they might be involved in the regulatory role of enod40 RNA.
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Affiliation(s)
- Geneviève Girard
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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50
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Hardin SC, Tang GQ, Scholz A, Holtgraewe D, Winter H, Huber SC. Phosphorylation of sucrose synthase at serine 170: occurrence and possible role as a signal for proteolysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:588-603. [PMID: 12940952 DOI: 10.1046/j.1365-313x.2003.01831.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Sequence analysis identified serine 170 (S170) of the maize (Zea mays L.) SUS1 sucrose synthase (SUS) protein as a possible, second phosphorylation site. Maize leaves contained two calcium-dependent protein kinase activities and a calcium-independent kinase activity with characteristics of an sucrose non-fermenting 1 (SNF1)-related protein kinase. Phosphorylation of the novel S170 and the known serine 15 (S15) site by these protein kinases was determined in peptide substrates and detected in SUS1 protein substrates utilizing sequence- and phosphorylation-specific antibodies. We demonstrate phosphorylation of S170 in vitro and in vivo. The calcium-dependent protein kinases phosphorylated both S170 and S15, whereas SNF1-related protein kinase activity was restricted to S15. Calcium-dependent protein-kinase-mediated S170 and S15 phosphorylation kinetics were determined in wild-type and mutant SUS1 substrates. These analyses revealed that kinase specificity for S170 was threefold lower than that for S15, and that phosphorylation of S170 was stimulated by prior phosphorylation at the S15 site. The SUS-binding peptides encoded by early nodulin 40 (ENOD40) specifically antagonized S170 phosphorylation in vitro. A model wherein S170 phosphorylation functions as part of a mechanism targeting SUS for proteasome-mediated degradation is supported by the observations that SUS proteolytic fragments: (i) were detected and possessed relatively high phosphorylated-S170 (pS170) stoichiometry; (ii) were spatially coincident with proteasome activity within developing leaves; and (iii) co-sedimented with proteasome activity. In addition, full-length pS170-SUS protein was less stable than S170-SUS in cultured leaf segments and was stabilized by proteasome inhibition. Post-translational control of SUS protein level through pS170-promoted proteolysis may explain the specific and significant decrease in SUS abundance that accompanies the sink-to-source transition in developing maize leaves.
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Affiliation(s)
- Shane C Hardin
- United States Department of Agriculture-Agricultural Research Service, Raleigh, NC 27695-7631, USA
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