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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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Pouresmaeil M, Azizi-Dargahlou S. Investigation of CaMV-host co-evolution through synonymous codon pattern. J Basic Microbiol 2024; 64:e2300664. [PMID: 38436477 DOI: 10.1002/jobm.202300664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/20/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
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Affiliation(s)
- Mahin Pouresmaeil
- Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Seed and Plant Certification and Registration Institute, Ardabil Agricultural and Natural Resources Research Center, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Leonetti P, Ghasemzadeh A, Consiglio A, Gursinsky T, Behrens S, Pantaleo V. Endogenous activated small interfering RNAs in virus-infected Brassicaceae crops show a common host gene-silencing pattern affecting photosynthesis and stress response. New Phytol 2021; 229:1650-1664. [PMID: 32945560 PMCID: PMC7821159 DOI: 10.1111/nph.16932] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/04/2020] [Indexed: 05/14/2023]
Abstract
Viral infections are accompanied by a massive production of small interfering RNAs (siRNAs) of plant origin, such as virus-activated (va)siRNAs, which drive the widespread silencing of host gene expression, and whose effects in plant pathogen interactions remain unknown. By combining phenotyping and molecular analyses, we characterized vasiRNAs that are associated with typical mosaic symptoms of cauliflower mosaic virus infection in two crops, turnip (Brassica rapa) and oilseed rape (Brassica napus), and the reference plant Arabidopsis thaliana. We identified 15 loci in the three infected plant species, whose transcripts originate vasiRNAs. These loci appear to be generally affected by virus infections in Brassicaceae and encode factors that are centrally involved in photosynthesis and stress response, such as Rubisco activase (RCA), senescence-associated protein, heat shock protein HSP70, light harvesting complex, and membrane-related protein CP5. During infection, the expression of these factors is significantly downregulated, suggesting that their silencing is a central component of the plant's response to virus infections. Further findings indicate an important role for 22 nt long vasiRNAs in the plant's endogenous RNA silencing response. Our study considerably enhances knowledge about the new class of vasiRNAs that are triggered in virus-infected plants and will help to advance strategies for the engineering of gene clusters involved in the development of crop diseases.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
| | - Aysan Ghasemzadeh
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
- Department of Plant PathologyFaculty of AgricultureTarbiat Modares UniversityTehran14115‐111Iran
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Arianna Consiglio
- Department of Biomedical SciencesInstitute for Biomedical TechnologiesBari UnitCNRBari70126Italy
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Sven‐Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
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4
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Bak A, Emerson JB. Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus ( CaMV) infection. BMC Biotechnol 2019; 19:73. [PMID: 31699075 PMCID: PMC6836441 DOI: 10.1186/s12896-019-0571-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 01/05/2023] Open
Abstract
Background Most genetically modified (GM) plants contain a promoter, P35S, from the plant virus, Cauliflower mosaic virus (CaMV), and many have a terminator, TNOS, derived from the bacterium, Agrobacterium tumefaciens. Assays designed to detect GM plants often target the P35S and/or TNOS DNA sequences. However, because the P35S promoter is derived from CaMV, these detection assays can yield false-positives from non-GM plants infected by this naturally-occurring virus. Results Here we report the development of an assay designed to distinguish CaMV-infected plants from GM plants in a single multiplexed quantitative PCR (qPCR) reaction. Following initial testing and optimization via PCR and singleplex-to-multiplex qPCR on both plasmid and plant DNA, TaqMan qPCR probes with different fluorescence wavelengths were designed to target actin (a positive-control plant gene), P35S, P3 (a CaMV-specific gene), and TNOS. We tested the specificity of our quadruplex qPCR assay using different DNA extracts from organic watercress and both organic and GM canola, all with and without CaMV infection, and by using commercial and industrial samples. The limit of detection (LOD) of each target was determined to be 1% for actin, 0.001% for P35S, and 0.01% for both P3 and TNOS. Conclusions This assay was able to distinguish CaMV-infected plants from GM plants in a single multiplexed qPCR reaction for all samples tested in this study, suggesting that this protocol is broadly applicable and readily transferrable to any interested parties with a qPCR platform.
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Affiliation(s)
- Aurélie Bak
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
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Schoelz JE, Leisner S. Setting Up Shop: The Formation and Function of the Viral Factories of Cauliflower mosaic virus. Front Plant Sci 2017; 8:1832. [PMID: 29163571 PMCID: PMC5670102 DOI: 10.3389/fpls.2017.01832] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/10/2017] [Indexed: 05/23/2023]
Abstract
Similar to cells, viruses often compartmentalize specific functions such as genome replication or particle assembly. Viral compartments may contain host organelle membranes or they may be mainly composed of viral proteins. These compartments are often termed: inclusion bodies (IBs), viroplasms or viral factories. The same virus may form more than one type of IB, each with different functions, as illustrated by the plant pararetrovirus, Cauliflower mosaic virus (CaMV). CaMV forms two distinct types of IBs in infected plant cells, those composed mainly of the viral proteins P2 (which are responsible for transmission of CaMV by insect vectors) and P6 (required for viral intra-and inter-cellular infection), respectively. P6 IBs are the major focus of this review. Much of our understanding of the formation and function of P6 IBs comes from the analyses of their major protein component, P6. Over time, the interactions and functions of P6 have been gradually elucidated. Coupled with new technologies, such as fluorescence microscopy with fluorophore-tagged viral proteins, these data complement earlier work and provide a clearer picture of P6 IB formation. As the activities and interactions of the viral proteins have gradually been determined, the functions of P6 IBs have become clearer. This review integrates the current state of knowledge on the formation and function of P6 IBs to produce a coherent model for the activities mediated by these sophisticated virus-manufacturing machines.
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Affiliation(s)
- James E. Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Scott Leisner
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States
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Bouton C, Geldreich A, Ryabova L, Keller M, Dimitrova M. Le virus de la mosaïque du chou-fleur ( CaMV), encore et toujours. Virologie (Montrouge) 2015; 19:119-39. [PMID: 33065908 DOI: 10.1684/vir.2015.0609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As a pararetrovirus and because of the non-canonical translation of its polycistronic pregenomic 35S RNA, Cauliflower mosaic virus (CaMV) is an original model system that has been extensively studied. Recent advances have improved our understanding of CaMV aphid transmission, cell-to-cell movement, protein expression and virus counter-defense strategy against host plant defense. Since P6/TAV is involved in many aspects of viral pathogenesis as well as in some replication steps, it is considered as the key player of CaMV infectious cycle. This paper reviews our current knowledge on CaMV multiplication and pathogenesis, with special emphasis on steps in which P6/TAV has a major role.
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Lutz L, Okenka G, Schoelz J, Leisner S. Mutations within A 35 amino acid region of P6 influence self-association, inclusion body formation, and Caulimovirus infectivity. Virology 2015; 476:26-36. [PMID: 25506670 PMCID: PMC4323857 DOI: 10.1016/j.virol.2014.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 11/19/2022]
Abstract
Cauliflower mosaic virus gene VI product (P6) is an essential protein that forms cytoplasmic, inclusion bodies (IBs). P6 contains four regions involved in self-association, termed D1-D4. D3 binds to D1, along with D4 and contains a spacer region (termed D3b) between two RNA-binding domains. Here we show D3b binds full-length P6 along with D1 and D4. Full-length P6s harboring single amino acid substitutions within D3b showed reduced binding to both D1 and D4. Full-length P6s containing D3b mutations and fused with green fluorescent protein formed inclusion-like bodies (IL-Bs) when expressed in Nicotiana benthamiana leaves. However, mutant P6s with reduced binding to D1 and D4, showed smaller IL-Bs, than wild type. Likewise, viruses containing these mutations showed a decrease in inoculated leaf viral DNA levels and reduced efficiency of systemic infection. These data suggest that mutations influencing P6 self-association alter IB formation and reduce virus infection.
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Affiliation(s)
- Lindy Lutz
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Genevieve Okenka
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - James Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Scott Leisner
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA.
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8
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Bak A, Blanc S, Gargani D, Martinière A, Drucker M. Multiples fonctions des usines virales : l'exemple du virus de la mosaïque du chou- fleur (Cauliflower mosaic virus). Virologie (Montrouge) 2014; 18:201-10. [PMID: 33065932 DOI: 10.1684/vir.2014.0572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many viruses form inclusion bodies in infected plant and mammalian cells. Their formation often requires membrane rearrangement of various organelles, but some inclusions form in the cytoplasm independently of the endomembrane system. In the latter case, they may resemble aggresomes or stress bodies but many inclusions do not seem to be related to any cellular structures. Synthesis, composition and size of these inclusions change with virus species. The best characterized inclusions create a "viral organelle" protecting viruses from host defenses and optimizing viral replication and assembly. These inclusions are also called viral factories. Recently, more complex and original functions were described for viral factories. This is exemplified here for Cauliflower mosaic virus (CaMV) factories. Unexpectedly, besides replication, CaMV factories also participate in another crucial step of the viral cycle: vector-transmission by aphids.
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Zhu C, Fan Q, Wang W, Shen C, Meng X, Tang Y, Mei B, Xu Z, Song R. Characterization of a glutamine synthetase gene DvGS2 from Dunaliella viridis and biochemical identification of DvGS2-transgenic Arabidopsis thaliana. Gene 2014; 536:407-15. [PMID: 24334123 DOI: 10.1016/j.gene.2013.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/16/2013] [Accepted: 11/05/2013] [Indexed: 01/23/2023]
Abstract
The salt-tolerant green alga Dunaliella has remarkable capability to survive in some extreme environments such as nitrogen starvation, which makes Dunaliella be a proper model for mining novel genes on nitrogen uptake or assimilation. In this study, a glutamine synthetase (GS) gene DvGS2 with amino acid identity of 72% to other homologous GS proteins, was isolated and characterized from Dunaliella viridis. Phylogenetic comparison with other GSs revealed that DvGS2 occupied an independent phylogenetic position. Expressional analysis in D. viridis cells under nitrogen starvation confirmed that DvGS2 increased its mRNA level in 12h. Subcellular localization study and functional analysis in a GS-deficient Escherichia coli mutant proved that DvGS2 was a chloroplastic and functional GS enzyme. In order to investigate the potential application of DvGS2 in higher plants, the transgenic studies of DvGS2 in Arabidopsis thaliana were carried out. Results showed that the transgenic lines expressed the DvGS2 gene and demonstrated obviously enhanced root length (29%), fresh weight (40%-48% at two concentrations of nitrate supplies), stem length (21%), leaf size (39%) and silique number (44%) in contrast with the wild-type Arabidopsis. Furthermore, the transgenic lines had higher total nitrogen content (35%-43%), total GS activity (39%-45%) and soluble protein concentration (23%-24%) than the wild type. These results indicated that the overexpression of DvGS2 in A. thaliana resulted in higher biomass and the improvement of the host's nitrogen use efficiency.
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Affiliation(s)
- Chenguang Zhu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Qianlan Fan
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Chunlei Shen
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Xiangzong Meng
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Yuanping Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Bing Mei
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Zhengkai Xu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China.
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Jung JH, Lee S, Yun J, Lee M, Park CM. The miR172 target TOE3 represses AGAMOUS expression during Arabidopsis floral patterning. Plant Sci 2014; 215-216:29-38. [PMID: 24388512 DOI: 10.1016/j.plantsci.2013.10.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/14/2013] [Accepted: 10/19/2013] [Indexed: 05/02/2023]
Abstract
microRNA172 (miR172) regulates phase transition and floral patterning in Arabidopsis by repressing targets that encode the APETALA2 (AP2) and AP2-like transcription factors. The miR172-mediated repression of the AP2 gene restricts AGAMOUS (AG) expression. In addition, most miR172 targets, including AP2, redundantly act as floral repressors, and the overexpression of the target genes causes delayed flowering. However, how miR172 targets other than AP2 regulate both of the developmental processes remains unclear. Here, we demonstrate that miR172-mediated repression of the TARGET OF EAT 3 (TOE3) gene is critical for floral patterning in Arabidopsis. Transgenic plants that overexpress a miR172-resistant TOE3 gene (rTOE3-ox) exhibit indeterminate flowers with numerous stamens and carpelloid organs, which is consistent with previous observations in transgenic plants that overexpress a miR172-resistant AP2 gene. TOE3 binds to the second intron of the AG gene. Accordingly, AG expression is significantly reduced in rTOE3-ox plants. TOE3 also interacts with AP2 in the nucleus. Given the major role of AP2 in floral patterning, miR172 likely regulates TOE3 in floral patterning, at least in part via AP2. In addition, a miR156 target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 directly activates TOE3 expression, revealing a novel signaling interaction between miR156 and miR172 in floral patterning.
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Affiliation(s)
- Jae-Hoon Jung
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sangmin Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ju Yun
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Minyoung Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Republic of Korea.
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von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. Plant Sci 2014; 214:1-12. [PMID: 24268158 DOI: 10.1016/j.plantsci.2013.09.006] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
We review the evidence that upstream open reading frames (uORFs) function as RNA sequence elements for post-transcriptional control of gene expression, specifically translation. uORFs are highly abundant in the genomes of angiosperms. Their negative effect on translation is often attenuated by ribosomal translation reinitiation, a process whose molecular biochemistry is still being investigated. Certain uORFs render translation responsive to small molecules, thus offering a path for metabolic control of gene expression in evolution and synthetic biology. In some cases, uORFs form modular logic gates in signal transduction. uORFs thus provide eukaryotes with a functionality analogous to, or comparable to, riboswitches and attenuators in prokaryotes. uORFs exist in many genes regulating development and point toward translational control of development. While many uORFs appear to be poorly conserved, and the number of genes with conserved-peptide uORFs is modest, many mRNAs have a conserved pattern of uORFs. Evolutionarily, the gain and loss of uORFs may be a widespread mechanism that diversifies gene expression patterns. Last but not least, this review includes a dedicated uORF database for Arabidopsis.
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Affiliation(s)
- Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA; Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840, USA.
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12
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Cai G, Wang G, Wang L, Pan J, Liu Y, Li D. ZmMKK1, a novel group A mitogen-activated protein kinase kinase gene in maize, conferred chilling stress tolerance and was involved in pathogen defense in transgenic tobacco. Plant Sci 2014; 214:57-73. [PMID: 24268164 DOI: 10.1016/j.plantsci.2013.09.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/26/2013] [Indexed: 05/18/2023]
Abstract
As an important intracellular signaling module, the mitogen-activated protein kinase (MAPK) cascades have been previously implicated in signal transduction during plants responsing to various environmental stresses as well as pathogen attack. The mitogen-activated protein kinase kinase acts as the convergent point of MAPK cascades during a variety of stress signaling. In this study, a novel MAPKK gene, ZmMKK1, in maize (Zea mays L.) belonging to group A MAPKK was isolated and functionally characterized. ZmMKK1 was mainly localized in the cytoplasm and its constitutive kinase-active form ZmMKK1DD was localized in both cytoplasm and nucleus. QRT-PCR analysis uncovered that ZmMKK1 expression was triggered by abiotic and biotic stresses and exogenous signaling molecules. Moreover, hydrogen peroxide (H2O2) and Ca(2+) mediated 12°C-induced up-regulated expressing of ZmMKK1 at mRNA level. Ectopic expression of ZmMKK1 in tobacco (Nicotiana tabacum) conferred tolerance to chilling stress by higher antioxidant enzyme activities, more accumulation of osmoregulatory substances and more significantly up-expression of ROS-related and stress-responsive genes compared with empty vector control plants. Furthermore, ZmMKK1 played differential functions in biotrophic versus necrotrophic pathogen-induced responses. These results suggested ZmMKK1 played a crucial role in chilling stress and pathogen defense in plants.
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Affiliation(s)
- Guohua Cai
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
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13
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Sun J, Peng X, Fan W, Tang M, Liu J, Shen S. Functional analysis of BpDREB2 gene involved in salt and drought response from a woody plant Broussonetia papyrifera. Gene 2013; 535:140-9. [PMID: 24315817 DOI: 10.1016/j.gene.2013.11.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/30/2013] [Accepted: 11/20/2013] [Indexed: 10/25/2022]
Abstract
The dehydration-responsive element binding proteins (DREBs) are important transcription factors in the regulation of plant responses to abiotic stresses. In this study, BpDREB2, an AP2/DREB-type transcription factor gene, was cloned from a woody plant, Broussonetia papyrifera by RACE-PCR. Sequence analyses revealed that BpDREB2 protein has three characteristic domains, including an AP2/EREBP, a nuclear localization signal and an acidic activation domain. Yeast one-hybrid assays showed that BpDREB2 protein specifically binds to the DRE sequence and activates the expression of reporter genes in yeast. These results suggested that BpDREB2 protein could function as a transcription factor of DREB family. The expression of BpDREB2 gene was remarkably induced by dehydration and high-salt treatments, but no significant change was observed under ABA or low-temperature conditions. Importantly, transgenic expression of BpDREB2 gene in Arabidopsis significantly enhanced its tolerance to salt and freezing without causing growth retardation. Taken together, these results suggested that BpDREB2 is a novel member of the AP2/EREBP trans-acting factor family which could enhance salt stress tolerance of plants and has the potential application in the improvement of crops and economical tree species.
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Affiliation(s)
- Jingwen Sun
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China; Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing,100081, PR China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China
| | - Weihong Fan
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China
| | - Mingjuan Tang
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China
| | - Jie Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China.
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Otani M, Meguro S, Gondaira H, Hayashi M, Saito M, Han DS, Inthima P, Supaibulwatana K, Mori S, Jikumaru Y, Kamiya Y, Li T, Niki T, Nishijima T, Koshioka M, Nakano M. Overexpression of the gibberellin 2-oxidase gene from Torenia fournieri induces dwarf phenotypes in the liliaceous monocotyledon Tricyrtis sp. J Plant Physiol 2013; 170:1416-23. [PMID: 23747060 DOI: 10.1016/j.jplph.2013.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 05/09/2023]
Abstract
Gibberellins (GAs) are the plant hormones that control many aspects of plant growth and development, including stem elongation. Genes encoding enzymes related to the GA biosynthetic and metabolic pathway have been isolated and characterized in many plant species. Gibberellin 2-oxidase (GA2ox) catalyzes bioactive GAs or their immediate precursors to inactive forms; therefore, playing a direct role in determining the levels of bioactive GAs. In the present study, we produced transgenic plants of the liliaceous monocotyledon Tricyrtis sp. overexpressing the GA2ox gene from the linderniaceous dicotyledon Torenia fournieri (TfGA2ox2). All six transgenic plants exhibited dwarf phenotypes, and they could be classified into two classes according to the degree of dwarfism: three plants were moderately dwarf and three were severely dwarf. All of the transgenic plants had small or no flowers, and smaller, rounder and darker green leaves. Quantitative real-time reverse transcription-polymerase chain reaction (PCR) analysis showed that the TfGA2ox2 expression level generally correlated with the degree of dwarfism. The endogenous levels of bioactive GAs, GA1 and GA4, largely decreased in transgenic plants as shown by liquid chromatography-mass spectrometry (LC-MS) analysis, and the level also correlated with the degree of dwarfism. Exogenous treatment of transgenic plants with gibberellic acid (GA3) resulted in an increased shoot length, indicating that the GA signaling pathway might normally function in transgenic plants. Thus, morphological changes in transgenic plants may result from a decrease in the endogenous levels of bioactive GAs. Finally, a possibility of molecular breeding for plant form alteration in liliaceous ornamental plants by genetically engineering the GA metabolic pathway is discussed.
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Affiliation(s)
- Masahiro Otani
- Faculty of Agriculture, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan
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15
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Jiang S, Zhang D, Wang L, Pan J, Liu Y, Kong X, Zhou Y, Li D. A maize calcium-dependent protein kinase gene, ZmCPK4, positively regulated abscisic acid signaling and enhanced drought stress tolerance in transgenic Arabidopsis. Plant Physiol Biochem 2013; 71:112-20. [PMID: 23911729 DOI: 10.1016/j.plaphy.2013.07.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/10/2013] [Indexed: 05/21/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) play essential roles in calcium-mediated signal transductions in plant response to abiotic stress. Several members have been identified to be regulators for plants response to abscisic acid (ABA) signaling. Here, we isolated a subgroup I CDPK gene, ZmCPK4, from maize. Quantitative real time PCR (qRT-PCR) analysis revealed that the ZmCPK4 transcripts were induced by various stresses and signal molecules. Transient and stable expression of the ZmCPK4-GFP fusion proteins revealed ZmCPK4 localized to the membrane. Moreover, overexpression of ZmCPK4 in the transgenic Arabidopsis enhanced ABA sensitivity in seed germination, seedling growth and stomatal movement. The transgenic plants also enhanced drought stress tolerance. Taken together, the results suggest that ZmCPK4 might be involved in ABA-mediated regulation of stomatal closure in response to drought stress.
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Affiliation(s)
- Shanshan Jiang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 61 Dai Zong Street, Tai'an, 271018 Shandong, PR China
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16
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Zhang R, Zhu J, Cao HZ, An YR, Huang JJ, Chen XH, Mohammed N, Afrin S, Luo ZY. Molecular cloning and expression analysis of PDR1-like gene in ginseng subjected to salt and cold stresses or hormonal treatment. Plant Physiol Biochem 2013; 71:203-11. [PMID: 23968928 DOI: 10.1016/j.plaphy.2013.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/23/2013] [Indexed: 05/04/2023]
Abstract
The plant pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters is potentially involved in diverse biological processes. Currently, little is known about their actual physiological functions. A Panax ginseng PDR transporter gene (PgPDR1) was cloned and the cDNA has an open reading frame of 4344 bp. The deduced amino acid sequence contained the characteristic domains of PDR transporters: Walker A, Walker B, and ABC signature. Genomic DNA hybridization analysis indicated that one copy of PgPDR1 gene was present in P. ginseng. Subcellular localization showed that PgPDR1-GFP fusion protein was specifically localized in the cell membrane. Promoter region analysis revealed the presence of cis-acting elements, some of which are putatively involved in response to hormone, light and stress. To understand the functional roles of PgPDR1, we investigated the expression patterns of PgPDR1 in different tissues and under various conditions. Quantitative real-time PCR (qRT-PCR) and Western blotting analysis showed that PgPDR1 was expressed at a high level in the roots and leaves compared to seeds and stems. The expression of PgPDR1 was up-regulated by salicylic acid (SA) or chilling, down-regulated by ABA, and regulated differently at transcript and protein levels by MeJA. These results suggest that PgPDR1 might be involved in responding to environmental stresses and hormones.
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Affiliation(s)
- Ru Zhang
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha 410078, China
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17
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Lei HJ, Yuan HZ, Liu Y, Guo XW, Liao X, Liu LL, Wang Q, Li TH. Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry. Gene 2013; 531:158-67. [PMID: 24055423 DOI: 10.1016/j.gene.2013.09.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/24/2013] [Accepted: 09/09/2013] [Indexed: 01/01/2023]
Abstract
A MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates multiple flowering signals to regulate floral transition in Arabidopsis. Strawberry (Fragaria spp.) is an economically important fruit crop, but its molecular control of flowering is largely unknown. In this study, a SOC1-like gene, FaSOC1, was isolated and characterized from strawberry. The open reading frame of FaSOC1 was 648bp, encoding a protein of 215 amino acids. Sequence alignment and phylogenetic analysis showed that the FaSOC1 protein contained a highly conserved MADS domain and a SOC1 motif, and that it was a member of the SOC1-like genes of dicots. The FaSOC1 protein mainly localized in the cytoplasm of onion epidermal cells and Arabidopsis protoplasts, and showed no transcriptional activation activity in yeast cells. Under the floral induction conditions, the expression of FaSOC1 increased during the first 2weeks of short-day treatment, but declined dramatically during three to 4weeks. FaSOC1 was highly expressed in reproductive organs, including shoot apices, floral buds, flowers, stamens and sepals. Overexpression of FaSOC1 in wild-type Arabidopsis caused early flowering and upregulated the expression of flowering time genes LFY and AP1. In addition, the yeast two-hybrid and BiFC assays confirmed that FaSOC1 could interact with AGL24. In conclusion, these results suggest that FaSOC1 is a flowering promoter in strawberry.
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Affiliation(s)
- Heng-Jiu Lei
- Department of Fruit Science, College of Agriculture and Biotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
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18
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Fischer JJ, Beatty PH, Good AG, Muench DG. Manipulation of microRNA expression to improve nitrogen use efficiency. Plant Sci 2013; 210:70-81. [PMID: 23849115 DOI: 10.1016/j.plantsci.2013.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/24/2013] [Accepted: 05/16/2013] [Indexed: 05/02/2023]
Abstract
Nitrogen is the key limiting nutrient required for plant growth. The application of nitrogen-based fertilizers to crops has risen dramatically in recent years, resulting in significant yield increases. However, increased production has come at the cost of substantial negative environmental consequences. Higher crop production costs, increased consumption of food and fertilizer, and a growing global population have led to calls for a "second green revolution" using modern genetic manipulation techniques to improve the production, yield, and quality of crops. Considerable research is being directed toward the study and engineering of nitrogen use efficiency in crop plants. The end goal is to reduce the amount of nitrogen-based fertilizer used and thereby reduce production costs and environmental damage while increasing yields. In this review, we present an overview of recent advances in understanding the regulation of nitrogen metabolism by the action of microRNAs with a view toward engineering crops with increased nitrogen use efficiency.
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Affiliation(s)
- Jeffrey J Fischer
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4
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19
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Kim SH, Ahn YO, Ahn MJ, Jeong JC, Lee HS, Kwak SS. Cloning and characterization of an Orange gene that increases carotenoid accumulation and salt stress tolerance in transgenic sweetpotato cultures. Plant Physiol Biochem 2013; 70:445-54. [PMID: 23835362 DOI: 10.1016/j.plaphy.2013.06.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/13/2013] [Indexed: 05/19/2023]
Abstract
The Orange (Or) gene is responsible for the accumulation of carotenoids in plants. We isolated the Or gene (IbOr) from storage roots of orange-fleshed sweetpotato (Ipomoea batatas L. Lam. cv. Sinhwangmi), and analyzed its function in transgenic sweetpotato calli. The IbOr gene has an open reading frame in the 942 bp cDNA, which encodes a 313-amino acid protein containing a cysteine-rich zinc finger domain. IbOr was strongly expressed in storage roots of orange-fleshed sweetpotato cultivars; it also was expressed in leaves, stems, and roots of cultivars with alternatively colored storage roots. IbOr transcription increased in response to abiotic stress, with gene expression reaching maximum at 2 h after treatment. Two different overexpression vectors of IbOr (IbOr-Wt and IbOr-Ins, which contained seven extra amino acids) were transformed into calli of white-fleshed sweetpotato [cv. Yulmi (Ym)] using Agrobacterium. The transgenic calli were easily selected because they developed a fine orange color. The expression levels of the IbOr transgene and genes involved in carotenoid biosynthesis in IbOr-Wt and IbOr-Ins transgenic calli were similar, and both transformants displayed higher expression levels than those in Ym calli. The contents of β-carotene, lutein, and total carotenoids in IbOr-Ins transgenic lines were approximately 10, 6, and 14 times higher than those in Ym calli, respectively. The transgenic IbOr calli exhibited increased antioxidant activity and increased tolerance to salt stress. Our work shows that the IbOr gene may be useful for the biotechnological development of transgenic sweetpotato plants that accumulate increased carotenoid contents on marginal agricultural lands.
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Affiliation(s)
- Sun Ha Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Uzest M, Drucker M, Blanc S. [Transmission of a complex: not so simple. The case of Cauliflower mosaic virus]. Virologie (Montrouge) 2011; 15:192-204. [PMID: 36151659 DOI: 10.1684/vir.2011.17137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Transmission by a vector is a common feature among viruses, especially plant viruses. While animal arboviruses infect literally their vector ("biological transmission"), plant viruses are mostly transmitted "mechanically". This mode of transmission is seemingly quite simple - the virus contaminates the vector mouthparts and subsequently is mechanically inoculated into new healthy hosts. In fact, the process involves astonishingly complicated virus-vector interactions that have been the focus of many studies. Nowadays, this phenomenon is considered far from being purely "mechanical" and has been renamed "non-circulative" transmission. In addition to specific ligand/receptor-like interactions between the virus and the vector, sophisticated regulatory mechanisms occur between the host cell and the virus, which seem to be dedicated exclusively to successful virus transmission. The aim of this review is to illustrate, using Cauliflower mosaic virus as a model, the remarkable intricacy of the noncirculative mode of transmission, and possibly instigate analogous research for animal viruses.
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Affiliation(s)
- Marilyne Uzest
- UMR BGPI, INRA/CIRAD/Montpellier SupAgro, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05, France
| | - Martin Drucker
- UMR BGPI, INRA/CIRAD/Montpellier SupAgro, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05, France
| | - Stéphane Blanc
- UMR BGPI, INRA/CIRAD/Montpellier SupAgro, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05, France
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