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Luján-Soto E, Aguirre de la Cruz PI, Juárez-González VT, Reyes JL, Sanchez MDLP, Dinkova TD. Transcriptional Regulation of zma- MIR528a by Action of Nitrate and Auxin in Maize. Int J Mol Sci 2022; 23:ijms232415718. [PMID: 36555358 PMCID: PMC9779399 DOI: 10.3390/ijms232415718] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome.
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Affiliation(s)
- Eduardo Luján-Soto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
| | - Paola I. Aguirre de la Cruz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
| | - Vasti T. Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - José L. Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Av. Universidad 2001, Cuernavaca 62210, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
- Correspondence: ; Tel.: +52-55-5622-5277
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2
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Salazar-Díaz K, Dong Y, Papdi C, Ferruzca-Rubio EM, Olea-Badillo G, Ryabova LA, Dinkova TD. TOR senses and regulates spermidine metabolism during seedling establishment and growth in maize and Arabidopsis. iScience 2021; 24:103260. [PMID: 34765910 PMCID: PMC8571727 DOI: 10.1016/j.isci.2021.103260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/27/2020] [Revised: 04/23/2021] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Spermidine (Spd) is a nitrogen sink and signaling molecule that plays pivotal roles in eukaryotic cell growth and must be finetuned to meet various energy demands. In eukaryotes, target of rapamycin (TOR) is a central nutrient sensor, especially N, and a master-regulator of growth and development. Here, we discovered that Spd stimulates the growth of maize and Arabidopsis seedlings through TOR signaling. Inhibition of Spd biosynthesis led to TOR inactivation and growth defects. Furthermore, disruption of a TOR complex partner RAPTOR1B abolished seedling growth stimulation by Spd. Strikingly, TOR activated by Spd promotes translation of key metabolic enzyme upstream open reading frame (uORF)-containing mRNAs, PAO and CuAO, by facilitating translation reinitiation and providing feedback to polyamine metabolism and TOR activation. The Spd-TOR relay protected young-age seedlings of maize from expeditious stress heat shock. Our results demonstrate Spd is an upstream effector of TOR kinase in planta and provide its potential application for crop protection. Spermidine (Spd) stimulates growth of maize and Arabidopsis by activating TOR signaling TOR stimulates translation efficiency of uORF-containing mRNAs involved in Spd catabolism TOR provides feedback to polyamine homeostasis in response to excess of Spd The Spd-TOR signaling axis protects maize seedlings from expeditious heat stress
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Affiliation(s)
- Kenia Salazar-Díaz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Yihan Dong
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Csaba Papdi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Ernesto Miguel Ferruzca-Rubio
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Grecia Olea-Badillo
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Lyubov A Ryabova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
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3
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Salazar-Díaz K, Aquino-Luna M, Hernández-Lucero E, Nieto-Rivera B, Pulido-Torres MA, Jorge-Pérez JH, Gavilanes-Ruiz M, Dinkova TD. Arabidopsis thaliana eIF4E1 and eIF(iso)4E Participate in Cold Response and Promote Translation of Some Stress-Related mRNAs. Front Plant Sci 2021; 12:698585. [PMID: 34659280 PMCID: PMC8514651 DOI: 10.3389/fpls.2021.698585] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Plant defense and adaptation to adverse environmental conditions rely on gene expression control, such as mRNA transcription, processing, stability, and translation. Sudden temperature changes are common in the era of global warming; thus, understanding plant acclimation responses at the molecular level becomes imperative. mRNA translation initiation regulation has a pivotal role in achieving the synthesis of the appropriate battery of proteins needed to cope with temperature stress. In this study, we analyzed the role of translation initiation factors belonging to the eIF4E family in Arabidopsis acclimation to cold temperatures and freezing tolerance. Using knockout (KO) and overexpressing mutants of AteIF4E1 or AteIF(iso)4E, we found that AteIF4E1 but not AteIF(iso)4E overexpressing lines displayed enhanced tolerance to freezing without previous acclimation at 4°C. However, KO mutant lines, eif(iso)4e-1 and eif4e1-KO, were more sensitive to the stress. Cold acclimation in wild-type plants was accompanied by increased levels of eIF4E1 and eIF(iso)4E transcript levels, polysomes (P) enrichment, and shifts of these factors from translationally non-active to active fractions. Transcripts, previously found as candidates for eIF(iso)4E or eIF4E1 selective translation, changed their distribution in both P and total RNA in the presence of cold. Some of these transcripts changed their polysomal distribution in the mutant and one eIF4E1 overexpressing line. According to this, we propose a role of eIF4E1 and eIF(iso)4E in cold acclimation and freezing tolerance by regulating the expression of stress-related genes.
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4
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. Plants (Basel) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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5
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Hernández-López A, Sánchez Félix D, Zuñiga Sierra Z, García Bravo I, Dinkova TD, Avila-Alejandre AX. Quantification of Reducing Sugars Based on the Qualitative Technique of Benedict. ACS Omega 2020; 5:32403-32410. [PMID: 33376877 PMCID: PMC7758970 DOI: 10.1021/acsomega.0c04467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
Determination of reducing sugars is carried out routinely in the food industry, in biological research, or pharmaceutical and biomedical quality control to estimate metabolically assimilable sugars. Widespread detection methods are complex, expensive, or highly polluting. Here, we propose the use of spectrophotometric quantification for reducing sugars (Benedictq) based on the qualitative method of Benedict. The protocol was validated, to verify its reproducibility and precision. With the proposed method (Benedictq), the reducing sugar glucose can be determined in a range of 0.167-10 mg mL-1, with an R 2 of 0.997 and accuracy (expressed as % of recovery) greater than 97%. Other reducing sugars, such as maltose, fructose, and lactose, showed similar values. The method robustness was verified for pH values greater than or equal to 4. In the case of protein presence, a correction is proposed in the range of 0-1.67 mg mL-1. Modifications implemented in the protocol reduce cost, working time, and reaction volumes with respect to the original assay without detriments in accuracy and precision. In addition, waste reduction represents an important contribution of the method.
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Affiliation(s)
- Alejandro Hernández-López
- LABIOTT
Av. Jesús Carranza Mz 6 Lt 12 Colonia Universidad. San Juan
Bautista Tuxtepec, c.p. 68336, Oaxaca, México
| | - Daniel
A. Sánchez Félix
- Instituto
de Biotecnología, Universidad del
Papaloapan-Tuxtepec, Circuito central 200, Parque Industrial, San Juan
Bautista Tuxtepec, Oaxaca 68300, México
| | - Zenaida Zuñiga Sierra
- Instituto
de Biotecnología, Universidad del
Papaloapan-Tuxtepec, Circuito central 200, Parque Industrial, San Juan
Bautista Tuxtepec, Oaxaca 68300, México
| | - Itzel García Bravo
- Instituto
de Biotecnología, Universidad del
Papaloapan-Tuxtepec, Circuito central 200, Parque Industrial, San Juan
Bautista Tuxtepec, Oaxaca 68300, México
| | - Tzvetanka D. Dinkova
- Departamento
de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 CDMX, México
| | - Alma X. Avila-Alejandre
- Instituto
de Biotecnología, Universidad del
Papaloapan-Tuxtepec, Circuito central 200, Parque Industrial, San Juan
Bautista Tuxtepec, Oaxaca 68300, México
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Díaz-Granados VH, López-López JM, Flores-Sánchez J, Olguin-Alor R, Bedoya-López A, Dinkova TD, Salazar-Díaz K, Vázquez-Santana S, Vázquez-Ramos JM, Lara-Núñez A. Glucose modulates proliferation in root apical meristems via TOR in maize during germination. Plant Physiol Biochem 2020; 155:126-135. [PMID: 32745931 DOI: 10.1016/j.plaphy.2020.07.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/11/2020] [Revised: 07/08/2020] [Accepted: 07/21/2020] [Indexed: 05/25/2023]
Abstract
The Glucose-Target of Rapamycin (Glc-TOR) pathway has been studied in different biological systems, but scarcely during early seed germination. This work examines its importance for cell proliferation, expression of cell cycle key genes, their protein levels, besides morphology and cellularization of the root apical meristem of maize (Zea mays) embryo axes during germination under the influence of two simple sugars, glucose and sucrose, and a specific inhibitor of TOR activity, AZD 8055. The two sugars promote germination similarly and to an extent, independently of TOR activity. However, the Glc-TOR pathway increases the number of cells committed to proliferation, increasing the expression of a cell cycle gene, ZmCycD4;2, a putative G1/S regulator. Also, Glc-TOR may have influence on the protein stability of another G1/S cyclin, ZmCycD3, but had no influence on ZmCDKA;1 or ZmKRP3 or their proteins. Results suggest that the Glc-TOR pathway participates in the regulation of proliferation through different mechanisms that, in the end, modify the timing of seed germination.
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Affiliation(s)
- Víctor Hugo Díaz-Granados
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Jorge Manuel López-López
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Jesús Flores-Sánchez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Roxana Olguin-Alor
- Laboratorio Nacional de Citometría de Flujo, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Andrea Bedoya-López
- Laboratorio Nacional de Citometría de Flujo, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Tzvetanka D Dinkova
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Kenia Salazar-Díaz
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Sonia Vázquez-Santana
- Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Jorge Manuel Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Aurora Lara-Núñez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
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7
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Reyna-Rosas E, Contreras-Treviño HI, León-Rodríguez R, Rocha-Zavaleta L, Dinkova TD, Padilla-Noriega L. The accumulation of rotavirus NSP3 dimers does not correlate with the extent of host cell translation inhibition. Future Virol 2020. [DOI: 10.2217/fvl-2020-0259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: We aimed to determine the functionality of rotavirus NSP3 dimers. Materials & methods: We expressed rhesus rotavirus NSP3 and determined the kinetics of host cell translation inhibition and the levels of accumulated dimerization intermediates and dimers. Results: We observed a linear kinetics of host cell translation inhibition, which correlated well with the sum of the dimerization intermediates and dimers. Treatment with 17-dimethylaminoethylamino-17-demethoxygeldanamycin reduced the accumulation of NSP3 dimers and potentiated host cell translation inhibition. Conclusion: Our results show that NSP3 dimer formation does not correlate with host cell translation inhibition and suggest that both NSP3 dimers and dimerization intermediates are functional and inhibit host cell translation.
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Affiliation(s)
- Edgar Reyna-Rosas
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo I Contreras-Treviño
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leticia Rocha-Zavaleta
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Padilla-Noriega
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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López-Ruiz BA, Juárez-González VT, Gómez-Felipe A, De Folter S, Dinkova TD. tasiR-ARFs Production and Target Regulation during In Vitro Maize Plant Regeneration. Plants (Basel) 2020; 9:E849. [PMID: 32640631 PMCID: PMC7411845 DOI: 10.3390/plants9070849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
During in vitro maize plant regeneration somatic cells change their normal fate and undergo restructuring to generate pluripotent cells able to originate new plants. Auxins are essential to achieve such plasticity. Their physiological effects are mediated by auxin response factors (ARFs) that bind auxin responsive elements within gene promoters. Small trans-acting (ta)-siRNAs, originated from miR390-guided TAS3 primary transcript cleavage, target ARF3/4 class (tasiR-ARFs). Here we found that TAS3b precursor as well as derived tasiR-ARFbD5 and tasiR-ARFbD6 display significantly lower levels in non-embryogenic callus (NEC), while TAS3g, miR390 and tasiR-ARFg are more abundant in the same tissue. However, Argonaute (AGO7) and leafbladeless 1 (LBLl) required for tasiR-ARF biogenesis showed significantly higher transcript levels in EC suggesting limited tasiR-ARF biogenesis in NEC. The five maize ARFs targeted by tasiR-ARFs were also significantly enriched in EC and accompanied by higher auxin accumulation with punctuate patterns in this tissue. At hormone half-reduction and photoperiod implementation, plant regeneration initiated from EC with transient TAS3g, miR390 and tasiR-ARFg increase. Upon complete hormone depletion, TAS3b became abundant and derived tasiR-ARFs gradually increased at further regeneration stages. ZmARF transcripts targeted by tasiR-ARFs, as well as AGO7 and LBL1 showed significantly lower levels during regeneration than in EC. These results indicate a dynamic tasiR-ARF mediated regulation throughout maize in vitro plant regeneration.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
| | - Vasti Thamara Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
| | - Andrea Gómez-Felipe
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), 36821 Irapuato Gto., Mexico; (A.G.-F.); (S.D.F.)
| | - Stefan De Folter
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), 36821 Irapuato Gto., Mexico; (A.G.-F.); (S.D.F.)
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
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9
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Lledías F, Gutiérrez J, Martínez-Hernández A, García-Mendoza A, Sosa E, Hernández-Bermúdez F, Dinkova TD, Reyes S, Cassab GI, Nieto-Sotelo J. Mayahuelin, a Type I Ribosome Inactivating Protein: Characterization, Evolution, and Utilization in Phylogenetic Analyses of Agave. Front Plant Sci 2020; 11:573. [PMID: 32528490 PMCID: PMC7266874 DOI: 10.3389/fpls.2020.00573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/17/2020] [Indexed: 05/12/2023]
Abstract
Agaves resist extreme heat and drought. In A. tequilana var. azul, the central spike of the rosette -containing the shoot apical meristem and folded leaves in early stages of development- is remarkably heat tolerant. We found that the most abundant protein in this organ is a 27 kDa protein. This protein was named mayahuelin to honor Mayáhuel, the agave goddess in the Aztec pantheon. LC-MS/MS analyses identified mayahuelin as a type I RIP (Ribosome Inactivating Protein). In addition to the spike, mayahuelin was expressed in the peduncle and in seeds, whereas in mature leaves, anthers, filaments, pistils, and tepals was absent. Anti-mayahuelin antibody raised against the A. tequilana var. azul protein revealed strong signals in spike leaves of A. angustifolia, A. bracteosa, A. rhodacantha, and A. vilmoriniana, and moderate signals in A. isthmensis, A. kerchovei, A. striata ssp. falcata, and A. titanota, indicating conservation at the protein level throughout the Agave genus. As in charybdin, a type I RIP characterized in Drimia maritima, mayahuelin from A. tequilana var. azul contains a natural aa substitution (Y76D) in one out of four aa comprising the active site. The RIP gene family in A. tequilana var. azul consists of at least 12 genes and Mayahuelin is the only member encoding active site substitutions. Unlike canonical plant RIPs, expression of Mayahuelin gene in S. cerevisiae did not compromise growth. The inhibitory activity of the purified protein on a wheat germ in vitro translation system was moderate. Mayahuelin orthologs from other Agave species displayed one of six alleles at Y76: (Y/Y, D/D, S/S, Y/D, Y/S, D/S) and proved to be useful markers for phylogenetic analysis. Homozygous alleles were more frequent in wild accessions whereas heterozygous alleles were more frequent in cultivars. Mayahuelin sequences from different wild populations of A. angustifolia and A. rhodacantha allowed the identification of accessions closely related to azul, manso, sigüín, mano larga, and bermejo varieties of A. tequilana and var. espadín of A. angustifolia. Four A. rhodacantha accessions and A. angustifolia var. espadín were closer relatives of A. tequilana var. azul than A. angustifolia wild accessions or other A. tequilana varieties.
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Affiliation(s)
- Fernando Lledías
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jesús Gutiérrez
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Abisaí García-Mendoza
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric Sosa
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Felipe Hernández-Bermúdez
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sandi Reyes
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gladys I. Cassab
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jorge Nieto-Sotelo
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jorge Nieto-Sotelo,
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10
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Juárez-González VT, López-Ruiz BA, Baldrich P, Luján-Soto E, Meyers BC, Dinkova TD. The explant developmental stage profoundly impacts small RNA-mediated regulation at the dedifferentiation step of maize somatic embryogenesis. Sci Rep 2019; 9:14511. [PMID: 31601893 PMCID: PMC6786999 DOI: 10.1038/s41598-019-50962-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/23/2019] [Indexed: 01/22/2023] Open
Abstract
Maize somatic embryogenesis (SE) requires the induction of embryogenic callus and establishment of proliferation before plant regeneration. The molecular mechanisms underlying callus embryogenic potential are not well understood. Here we explored the role of small RNAs (sRNAs) and the accumulation of their target transcripts in maize SE at the dedifferentiation step using VS-535 zygotic embryos collected at distinct developmental stages and displaying contrasting in vitro embryogenic potential and morphology. MicroRNAs (miRNAs), trans-acting siRNAs (tasiRNAs), heterochromatic siRNAs (hc-siRNAs) populations and their RNA targets were analyzed by high-throughput sequencing. Abundances of specific miRNAs, tasiRNAs and targets were validated by qRT-PCR. Unique accumulation patterns were found for immature embryo at 15 Days After Pollination (DAP) and for the callus induction from this explant, as compared to 23 DAP and mature embryos. miR156, miR164, miR166, tasiARFs and the 24 nt hc-siRNAs displayed the most strikingly different patterns between explants and during dedifferentiation. According to their role in auxin responses and developmental cues, we conclude that sRNA-target regulation operating within the 15 DAP immature embryo explant provides key molecular hints as to why this stage is relevant for callus induction with successful proliferation and plant regeneration.
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Affiliation(s)
- Vasti T Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Brenda A López-Ruiz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Eduardo Luján-Soto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México.
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11
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Bucio-Mendez A, Cruz-Becerra G, Valadez-Graham V, Dinkova TD, Zurita M. The Dmp8-Dmp18 bicistron messenger RNA enables unusual translation during cellular stress. J Cell Biochem 2018; 120:3887-3897. [PMID: 30270456 DOI: 10.1002/jcb.27670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/31/2018] [Accepted: 08/21/2018] [Indexed: 11/07/2022]
Abstract
Alternatives to the cap mechanism in translation are often used by viruses and cells to allow them to synthesize proteins in events of stress and viral infection. In Drosophila there are hundreds of polycistronic messenger RNA (mRNA), and various mechanisms are known to achieve this. However, proteins in a same mRNA often work in the same cellular mechanism, this is not the case for Drosophila's Swc6/p18Hamlet homolog Dmp18, part of the SWR1 chromatin remodeling complex, who is encoded in a bicistronic mRNA next to Dmp8 (Dmp8-Dmp18 transcript), a structural component of transcription factor TFIIH. The organization of these two genes as a bicistron is conserved in all arthropods, however the length of the intercistronic sequence varies from more than 90 to 2 bases, suggesting an unusual translation mechanism for the second open reading frame. We found that even though translation of Dmp18 occurs independently from that of Dmp8, it is necessary for Dmp18 to be in that conformation to allow its correct translation during cellular stress caused by damage via heat-shock and UV radiation.
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Affiliation(s)
- Alyeri Bucio-Mendez
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Grisel Cruz-Becerra
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Viviana Valadez-Graham
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Tzvetanka D Dinkova
- Department of Biochemistry and Molecular Biology, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mario Zurita
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Abstract
MicroRNAs are tiny molecules that strikingly change their expression patterns and distribution during somatic embryogenesis induction and plant regeneration. It is of great relevance to analyze simultaneously the microRNA and target mRNA fates to understand their role in promoting an adequate embryogenic response to external stimulus in the regenerating tissues. Here we describe a method to evaluate the expression patterns of miRNAs or other sRNAs and their target regulation in distinctive tissues observed during maize plant regeneration. Key features of the method include the classification of regenerating plant material with reproducibly distinctive morphological characteristics and a purification procedure that renders high-quality small and large RNA separation from the same sample for qRT-PCR analysis.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Departamento Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Vasti Thamara Juárez-González
- Departamento Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | | | - Tzvetanka D Dinkova
- Departamento Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.
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13
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Alejandri-Ramírez ND, Chávez-Hernández EC, Contreras-Guerra JL, Reyes JL, Dinkova TD. Small RNA differential expression and regulation in Tuxpeño maize embryogenic callus induction and establishment. Plant Physiol Biochem 2018; 122:78-89. [PMID: 29197696 DOI: 10.1016/j.plaphy.2017.11.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 08/09/2017] [Revised: 11/23/2017] [Accepted: 11/23/2017] [Indexed: 05/02/2023]
Abstract
Somatic embryogenesis represents an alternative developmental process used to achieve genetic transformation and to approach key questions in maize development. It is known that embryogenic callus induction and plant regeneration are accompanied by microRNA expression changes. However, small RNA (sRNA) populations have not been explored during the proliferative callus subculture establishment and their impact on maintaining the dedifferentiated status and embryogenic potential is far from being completely understood. Here we globally tested the sRNA populations in explants (immature embryos), induced and established maize embryogenic callus from the Mexican cultivar VS-535, Tuxpeño landrace. We detected readjustments in 24 nt and 21-22 nt sRNAs during the embryogenic callus (EC) establishment and maintenance. A follow up on specific microRNAs (miRNAs) indicated that miRNAs related to stress response substantially increase upon the callus proliferation establishment, correlating with a reduction in some of their target levels. On the other hand, while 24 nt-long heterochromatic small interfering RNAs (hc-siRNAs) derived from transposable retroelements transiently decreased in abundance during the EC establishment, a population of 22 nt-hc-siRNAs increased. This was accompanied by reduction in transposon expression in the established callus subcultures. We conclude that stress- and development-related miRNAs are highly expressed upon maize EC callus induction and during maintenance of the subcultures, while miRNAs involved in hormone response only transiently increase during induction. In addition, the establishment of a proliferative status in embryogenic callus is accompanied by important readjustments in hc-siRNAs mapping to long tandem repeat (LTR) retrotransposons, and their expression regulation.
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Affiliation(s)
- Naholi D Alejandri-Ramírez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Elva C Chávez-Hernández
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Jose L Contreras-Guerra
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Jose L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca Mor, Mexico
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico.
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14
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Lázaro-Mixteco PE, Dinkova TD. Identification of Proteins from Cap-Binding Complexes by Mass Spectrometry During Maize (Zea mays L.) Germination. J MEX CHEM SOC 2017. [DOI: 10.29356/jmcs.v56i1.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This work describes the identification of components in the Cap-binding complexes in non-germinated and 24-h-imbibed seeds using mass spectrometry. This approach revealed new components particularly present in the non-germinated seed. Among these, two heat shock proteins, HSP101 and HSP70, were detected as well as several proteins involved in carbohydrate metabolism. Between the new components of maize Cap-binding complexes, several proteins contain a motif that identifies them as potential direct interactors with eIF4E or eIF(iso)4E.Together with the major abundance of eIF(iso)4E at this developmental stage, our findings indicate clear differences between the translation initiation complexes that are available for protein synthesis right upon water imibition and those that are present once germination has been completed.
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15
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Contreras-Treviño HI, Reyna-Rosas E, León-Rodríguez R, Ruiz-Ordaz BH, Dinkova TD, Cevallos AM, Padilla-Noriega L. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation. PLoS One 2017; 12:e0181871. [PMID: 28738064 PMCID: PMC5524322 DOI: 10.1371/journal.pone.0181871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Species A rotavirus non-structural protein 3 (NSP3) is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A) binding protein (PABP) from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3’-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD). We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E), whereas one mutation had the opposite effects (Y192A). Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.
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Affiliation(s)
- Hugo I. Contreras-Treviño
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edgar Reyna-Rosas
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca H. Ruiz-Ordaz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana M. Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Padilla-Noriega
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail:
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16
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Chávez-Calvillo G, Contreras-Paredes CA, Mora-Macias J, Noa-Carrazana JC, Serrano-Rubio AA, Dinkova TD, Carrillo-Tripp M, Silva-Rosales L. Antagonism or synergism between papaya ringspot virus and papaya mosaic virus in Carica papaya is determined by their order of infection. Virology 2016; 489:179-91. [PMID: 26765969 DOI: 10.1016/j.virol.2015.11.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 09/07/2015] [Revised: 09/30/2015] [Accepted: 11/25/2015] [Indexed: 11/29/2022]
Abstract
Antagonism between unrelated plant viruses has not been thoroughly described. Our studies show that two unrelated viruses, papaya ringspot virus (PRSV) and papaya mosaic virus (PapMV) produce different symptomatic outcomes during mixed infection depending on the inoculation order. Synergism occurs in plants infected first with PRSV or in plants infected simultaneously with PRSV and PapMV, and antagonism occurs in plants infected first with PapMV and later inoculated with PRSV. During antagonism, elevated pathogenesis-related (PR-1) gene expression and increased reactive oxygen species production indicated the establishment of a host defense resulting in the reduction in PRSV titers. Polyribosomal fractioning showed that PRSV affects translation of cellular eEF1α, PR-1, β-tubulin, and PapMV RNAs in planta, suggesting that its infection could be related to an imbalance in the translation machinery. Our data suggest that primary PapMV infection activates a defense response against PRSV and establishes a protective relationship with the papaya host.
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Affiliation(s)
| | | | - Javier Mora-Macias
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato Guanajuato, Mexico
| | - Juan C Noa-Carrazana
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Angélica A Serrano-Rubio
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato Guanajuato, Mexico
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México DF
| | - Mauricio Carrillo-Tripp
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato Guanajuato, Mexico
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Chávez-Hernández EC, Alejandri-Ramírez ND, Juárez-González VT, Dinkova TD. Maize miRNA and target regulation in response to hormone depletion and light exposure during somatic embryogenesis. Front Plant Sci 2015; 6:555. [PMID: 26257760 PMCID: PMC4510349 DOI: 10.3389/fpls.2015.00555] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/07/2015] [Indexed: 05/06/2023]
Abstract
Maize somatic embryogenesis (SE) is induced from the immature zygotic embryo in darkness and under the appropriate hormones' levels. Small RNA expression is reprogrammed and certain miRNAs become particularly enriched during induction while others, characteristic to the zygotic embryo, decrease. To explore the impact of different environmental cues on miRNA regulation in maize SE, we tested specific miRNA abundance and their target gene expression in response to photoperiod and hormone depletion for two different maize cultivars (VS-535 and H-565). The expression levels of miR156, miR159, miR164, miR168, miR397, miR398, miR408, miR528, and some predicted targets (SBP23, GA-MYB, CUC2, AGO1c, LAC2, SOD9, GR1, SOD1A, PLC) were examined upon staged hormone depletion in the presence of light photoperiod or darkness. Almost all examined miRNA, except miR159, increased upon hormone depletion, regardless photoperiod absence/presence. miR528, miR408, and miR398 changed the most. On the other hand, expression of miRNA target genes was strongly regulated by the photoperiod exposure. Stress-related miRNA targets showed greater differences between cultivars than development-related targets. miRNA/target inverse relationship was more frequently observed in darkness than light. Interestingly, miR528, but not miR159, miR168 or miR398, was located on polyribosome fractions suggesting a role for this miRNA at the level of translation. Overall our results demonstrate that hormone depletion exerts a great influence on specific miRNA expression during plant regeneration independently of light. However, their targets are additionally influenced by the presence of photoperiod. The reproducibility or differences observed for particular miRNA-target regulation between two different highly embryogenic genotypes provide clues for conserved miRNA roles within the SE process.
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Affiliation(s)
| | | | | | - Tzvetanka D. Dinkova
- *Correspondence: Tzvetanka D. Dinkova, Departamento de Bioquímica, Facultad de Química, Conjunto E, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
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18
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Villa-Hernández JM, Dinkova TD, Aguilar-Caballero R, Rivera-Cabrera F, Sánchez de Jiménez E, Pérez-Flores LJ. Regulation of ribosome biogenesis in maize embryonic axes during germination. Biochimie 2013; 95:1871-9. [PMID: 23806421 DOI: 10.1016/j.biochi.2013.06.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/14/2013] [Indexed: 11/28/2022]
Abstract
Ribosome biogenesis is a pre-requisite for cell growth and proliferation; it is however, a highly regulated process that consumes a great quantity of energy. It requires the coordinated production of rRNA, ribosomal proteins and non-ribosomal factors which participate in the processing and mobilization of the new ribosomes. Ribosome biogenesis has been studied in yeast and animals; however, there is little information about this process in plants. The objective of the present work was to study ribosome biogenesis in maize seeds during germination, a stage characterized for its fast growth, and the effect of insulin in this process. Insulin has been reported to accelerate germination and to induce seedling growth. It was observed that among the first events reactivated just after 3 h of imbibition are the rDNA transcription and the pre-rRNA processing and that insulin stimulates both of them (40-230%). The transcript of nucleolin, a protein which regulates rDNA transcription and pre-rRNA processing, is among the messages stored in quiescent dry seeds and it is mobilized into the polysomal fraction during the first hours of imbibition (6 h). In contrast, de novo ribosomal protein synthesis was low during the first hours of imbibition (3 and 6 h) increasing by 60 times in later stages (24 h). Insulin increased this synthesis (75%) at 24 h of imbibition; however, not all ribosomal proteins were similarly regulated. In this regard, an increase in RPS6 and RPL7 protein levels was observed, whereas RPL3 protein levels did not change even though its transcription was induced. Results show that ribosome biogenesis in the first stages of imbibition is carried out with newly synthesized rRNA and ribosomal proteins translated from stored mRNA.
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Affiliation(s)
- J M Villa-Hernández
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana, Av. San Rafael Atlixco 186, Col. Vicentina, CP 09340 D. F. México, Mexico
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19
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Contreras-Paredes CA, Silva-Rosales L, Daròs JA, Alejandri-Ramírez ND, Dinkova TD. The absence of eukaryotic initiation factor eIF(iso)4E affects the systemic spread of a Tobacco etch virus isolate in Arabidopsis thaliana. Mol Plant Microbe Interact 2013; 26:461-70. [PMID: 23252462 DOI: 10.1094/mpmi-09-12-0225-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Translation initiation factor eIF4E exerts an important role during infection of viral species in the family Potyviridae. Particularly, a eIF(iso)4E family member is required for Arabidopsis thaliana susceptibility to Turnip mosaic virus, Lettuce mosaic virus, and Tobacco etch virus (TEV). In addition, a resistance mechanism named restriction of TEV movement (RTM) in A. thaliana controls the systemic spread of TEV in Col-0 ecotype. Here, we describe that TEV-TAMPS, a Mexican isolate, overcomes the RTM resistance mechanism reported for TEV-7DA infection of the Col-0 ecotype but depends on eIF(iso)4E for its systemic spread. To understand at which level eIF(iso)4E participates in A. thaliana TEV-TAMPS infection, the viral RNA replication and translation were measured. The absence or overexpression of eIF(iso)4E did not affect viral translation, and replication was still observed in the absence of eIF(iso)4E. However, the TEV-TAMPS systemic spread was completely abolished in the null mutant. The viral protein genome-linked (VPg) precursor NIa was found in coimmunoprecipitated complexes with both, eIF(iso)4E and eIF4E. However, the viral coat protein (CP) was only present in the eIF(iso)4E complexes. Since both the VPg and the CP proteins are needed for systemic spread, we propose a role of A. thaliana eIF(iso)4E in the movement of TEV-TAMPS within this host.
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Lázaro-Mixteco PE, Nieto-Sotelo J, Swatek KN, Houston NL, Mendoza-Hernández G, Thelen JJ, Dinkova TD. The absence of heat shock protein HSP101 affects the proteome of mature and germinating maize embryos. J Proteome Res 2012; 11:3246-58. [PMID: 22545728 DOI: 10.1021/pr3000046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Maize heat shock protein HSP101 accumulates during embryo maturation and desiccation and persists at high levels during the first 24 h following kernel imbibition in the absence of heat stress. This protein has a known function in disaggregation of high molecular weight complexes and has been proposed to be a translational regulator of specific mRNAs. Here, a global proteomic approach was used to identify changes in the maize proteome due to the absence of HSP101 in embryos from mature-dry or 24 h-imbibed kernels. A total of 26 protein spots from the mature dry embryo exhibited statistically significant expression changes in the L10 inbred hsp101 mutant (hsp101-m5::Mu1/hsp101-m5::Mu1) line as compared to the corresponding wild type (Hsp101/Hsp101). Additional six spots reproducibly showed qualitative changes between the mutant and wild-type mature and germinating embryos. Several chaperones, translation-related proteins, actin, and enzymes participating in cytokinin metabolism were identified in these spots by tandem mass-spectrometry (MS). The proteomic changes partially explain the altered root growth and architecture observed in young hsp101 mutant seedlings. In addition, specific protein de novo synthesis was altered in the 24 h-imbibed mutant embryos indicating that maize HSP101 functions as both chaperone and translational regulator during germination. Supporting this, HSP101 was found as part of Cap-binding and translation initiation complexes during early kernel imbibition. Overall, these findings expose the relevance of maize HSP101 for protein synthesis and balance mechanisms during germination.
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Affiliation(s)
- Pedro E Lázaro-Mixteco
- Departamento de Bioquímica, Facultad de Química, ‡Jardín Botánico, Instituto de Biología, and #Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México , 04510, México, D.F., Mexico
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21
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Abstract
The translational initiation factor eIF4E binds to the m(7)G-containing cap of mRNA and participates in recruitment of mRNA to ribosomes for protein synthesis. eIF4E also functions in nucleocytoplasmic transport of mRNA, sequestration of mRNA in a nontranslatable state, and stabilization of mRNA against decay in the cytosol. Multiple eIF4E family members have been identified in a wide range of organisms that includes plants, flies, mammals, frogs, birds, nematodes, fish, and various protists. This chapter reviews methods that have been applied to learn the biochemical properties and physiological functions that differentiate eIF4E family members within a given organism. Much has been learned to date about approaches to discover new eIF4E family members, their in vitro properties (cap binding, stimulation of cell-free translation systems), tissue and developmental expression patterns, protein-binding partners, and their effects on the translation or repression of specific subsets of mRNA. Despite these advances, new eIF4E family members continue to be found and new physiological roles discovered.
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Affiliation(s)
- Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
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Abstract
C. elegans represents a favorable system to study the extraordinarily complicated process of eukaryotic protein synthesis, which involves over 100 RNAs and over 200 polypeptides just for the core machinery. Initial research in protein synthesis relied on fractionated mammalian and plant systems, but in the mid-1970s, the powerful genetics of Saccharomyces cerevisiae began to yield new insights for translation in all eukaryotes. C. elegans has many features of higher eukaryotes that are not shared by yeast. This allows protein synthesis researchers to combine biochemistry, cell biology, developmental biology, genetics, and genomics to study regulation of gene expression at the translational level. Most components of the core translational machinery have been identified in C. elegans, including rRNAs, 5S RNA, tRNAs, ribosomal proteins, and aminoacyl tRNA synthetases. C. elegans has amino acid sequence homologs for 56 of the known initiation, elongation, and release factor polypeptides, but few of these have been isolated, functionally identified, or studied at the biochemical level. Similarly, C. elegans has homologs for 22 components of the major signal transduction pathways implicated in control of protein synthesis. The translational efficiency of individual mRNAs relies on cis-regulatory elements that include either a 7-methylguanosine- or 2,2,7-trimethylguanosine-containing cap, the 5'-terminal spliced leader, sequence elements in the 3'-untranslated regions, and the 3'-terminal poly(A) tract. Several key developmental pathways in C. elegans are predominantly governed by translational mechanisms. Some evidence has been presented that well described regulatory mechanisms in other organisms, including covalent modification of translation factors, sequestration of translation factors, and mRNA-specific changes in poly(A) length, also occur in C. elegans. The most interesting unexplored questions may involve changes in the translation of individual mRNAs during development, in response to physiological changes, or after genetic manipulations. Given the highly developed state of C. elegans genomics, it can be expected that future application of computational tools, including data visualization, will help detect new instances of translational control.
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Affiliation(s)
- Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA.
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Abstract
Maize embryonic axes contain stored mRNAs, some of which are able to undergo cap-independent translation initiation during germination. The Hsp101 mRNA, encoding a heat shock protein, is essential for thermo-tolerance induction and is present among the stored transcripts. This research aimed to investigate whether the Hsp101 transcript is IRES-driven regulated upon heat stress. Hsp101 transcribed either in vitro or in vivo was efficiently translated via a cap-independent mechanism. This was observed either in an animal in vitro translation system containing proteolytically cleaved eukaryotic initiation factor eIF4G or in a plant system lacking both eIF4E and eIFiso4E initiation factors. Deletion of the 5' untranslated region (UTR) from the Hsp101 mRNA abolished its cap-independent translation indicating that this nucleotide sequence is required to confer cap-independent initiation. Bicistronic constructs containing the Hsp101 mRNA 5'UTR in sense and anti-sense directions between two reporter genes were translated in both cap-independent systems. A similar bicistronic construct containing a viral internal ribosome entry site (IRES) element between the reporter genes was used as control. Internal translation of the second reporter gene was observed when the Hsp101 5'UTR was in the sense but not in the anti-sense orientation in the bicistronic construct. Taken together, these data suggest that the 5'UTR of maize Hsp101, a plant cellular mRNA, functions as an IRES-like element accounting for its cap-independent translation during heat stress.
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Affiliation(s)
- Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, México DF
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Trutschl M, Dinkova TD, Rhoads RE. Application of machine learning and visualization of heterogeneous datasets to uncover relationships between translation and developmental stage expression of C. elegans mRNAs. Physiol Genomics 2005; 21:264-73. [PMID: 15701728 DOI: 10.1152/physiolgenomics.00307.2004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The relationships between genes in neighboring clusters in a self-organizing map (SOM) and properties attributed to them are sometimes difficult to discern, especially when heterogeneous datasets are used. We report a novel approach to identify correlations between heterogeneous datasets. One dataset, derived from microarray analysis of polysomal distribution, contained changes in the translational efficiency of Caenorhabditis elegans mRNAs resulting from loss of specific eIF4E isoform. The other dataset contained expression patterns of mRNAs across all developmental stages. Two algorithms were applied to these datasets: a classical scatter plot and an SOM. The outputs were linked using a two-dimensional color scale. This revealed that an mRNA's eIF4E-dependent translational efficiency is strongly dependent on its expression during development. This correlation was not detectable with a traditional one-dimensional color scale.
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Affiliation(s)
- Marjan Trutschl
- Department of Computer Science, Louisiana State University, Louisiana, USA
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Dinkova TD, Keiper BD, Korneeva NL, Aamodt EJ, Rhoads RE. Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform. Mol Cell Biol 2005; 25:100-13. [PMID: 15601834 PMCID: PMC538781 DOI: 10.1128/mcb.25.1.100-113.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 08/19/2004] [Accepted: 09/20/2004] [Indexed: 11/20/2022] Open
Abstract
The mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) participates in protein synthesis initiation, translational repression of specific mRNAs, and nucleocytoplasmic shuttling. Multiple isoforms of eIF4E are expressed in a variety of organisms, but their specific roles are poorly understood. We investigated one Caenorhabditis elegans isoform, IFE-4, which has homologues in plants and mammals. IFE-4::green fluorescent protein (GFP) was expressed in pharyngeal and tail neurons, body wall muscle, spermatheca, and vulva. Knockout of ife-4 by RNA interference (RNAi) or a null mutation produced a pleiotropic phenotype that included egg-laying defects. Sedimentation analysis demonstrated that IFE-4, but not IFE-1, was present in 48S initiation complexes, indicating that it participates in protein synthesis initiation. mRNAs affected by ife-4 knockout were determined by DNA microarray analysis of polysomal distribution. Polysome shifts, in the absence of total mRNA changes, were observed for only 33 of the 18,967 C. elegans mRNAs tested, of which a disproportionate number were related to egg laying and were expressed in neurons and/or muscle. Translational regulation was confirmed by reduced levels of DAF-12, EGL-15, and KIN-29. The functions of these proteins can explain some phenotypes observed in ife-4 knockout mutants. These results indicate that translation of a limited subset of mRNAs is dependent on a specific isoform of eIF4E.
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Affiliation(s)
- Tzvetanka D Dinkova
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932, USA
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Beltrán-Peña E, Aguilar R, Ortíz-López A, Dinkova TD, De Jiménez ES. Auxin stimulates S6 ribosomal protein phosphorylation in maize thereby affecting protein synthesis regulation. Physiol Plant 2002; 115:291-297. [PMID: 12060248 DOI: 10.1034/j.1399-3054.2002.1150216.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Auxin is known to stimulate protein synthesis in many plant tissues, but the mechanisms involved in this process are unknown. The present research inquires whether auxin might regulate selective translation of mRNAs by inducing S6 ribosomal protein phosphorylation on the 40S ribosomal subunit in maize (Zea mays L.). Maize embryonic axes auxin-stimulated by natural (IAA) or synthetic (Dicamba or 1-NAA) auxins, selectively increased ribosomal protein synthesis. This effect was not reproduced by auxin inactive analogue 2-NAA. Enhanced S6 ribosomal protein phosphorylation on the 40S ribosomal subunit was also observed after auxin stimulation, as measured by [32P] incorporation into this protein. This increment did not occur when stimulation was performed with the inactive auxin analogue. Further, increased recruitment into polysomes of two 5'TOP-like mRNAs, encoding for the initiation translation factor eIF-iso4E and the S6 ribosomal protein, was also found after auxin stimulation of maize axes. A positive correlation was established between the levels of S6 ribosomal protein phosphorylation and the S6 ribosomal protein transcript recruitment into polysomes by means of okadaic acid or heat shock application to maize axes. These data indicate that auxin stimulates S6 ribosomal protein phosphorylation on maize ribosomes, concomitant to the recruitment of specific mRNAs (5'TOP-like mRNAs) into polysomes for translation. It is proposed that by this mechanism auxin regulate the synthesis of specific proteins in maize tissues.
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Affiliation(s)
- Elda Beltrán-Peña
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, D. F. 045 0, Mexico
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Dinkova TD, Aguilar R, Sánchez de Jiménez E. Expression of maize eukaryotic initiation factor (eIF) iso4E is regulated at the translational level. Biochem J 2000; 351 Pt 3:825-31. [PMID: 11042140 PMCID: PMC1221425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mechanisms for regulation of gene expression at the translational level have been reported at specific developmental stages in eukaryotes. Control of eukaryotic initiation factor (eIF) 4E availability by insulin/growth factors constitutes a main point of translational regulation. The aim of the present research was to understand the regulatory mechanism(s) behind the differential expression of two main 4E factors present in maize embryonic axes during germination. De novo synthesis of eIFiso4E initiates earlier and is faster than that of eIF4E in maize axes. Insulin addition to maize axes stimulated de novo synthesis of the eIFiso4E protein, but not that of eIF4E. Specific recruitment of the eIFiso4E transcript into polysomes was observed in these axes after insulin stimulation. Inhibitors of the insulin signal-transduction pathway, wortmannin and rapamycin, reversed the insulin effect. In vitro translation of maize poly(A)(+) RNAs by S6 ribosomal protein (rp)-phosphorylated ribosomes demonstrated a strong increase in eIFiso4E synthesis, as compared with its translation by S6 rp-non-phosphorylated ribosomes. Other mRNAs from the poly(A)(+) RNA set, including the eIF4E mRNA, did not show differential translation with regard to the S6-phosphorylated status of the ribosomes. The overall results indicate that eIFiso4E, but not eIF4E, cell content is regulated by de novo synthesis in maize axes during germination, most probably by specific mRNA recruitment into polysomes via a signal-transduction pathway involving S6 rp phosphorylation.
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Affiliation(s)
- T D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), 04510 México, D.F
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