1
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Lipońska A, Lee H, Yap MNF. Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor. Nucleic Acids Res 2024:gkae596. [PMID: 38979572 DOI: 10.1093/nar/gkae596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
The hibernation-promoting factor (Hpf) in Staphylococcus aureus binds to 70S ribosomes and induces the formation of the 100S complex (70S dimer), leading to translational avoidance and occlusion of ribosomes from RNase R-mediated degradation. Here, we show that the 3'-5' exoribonuclease YhaM plays a previously unrecognized role in modulating ribosome stability. Unlike RNase R, which directly degrades the 16S rRNA of ribosomes in S. aureus cells lacking Hpf, YhaM destabilizes ribosomes by indirectly degrading the 3'-hpf mRNA that carries an intrinsic terminator. YhaM adopts an active hexameric assembly and robustly cleaves ssRNA in a manganese-dependent manner. In vivo, YhaM appears to be a low-processive enzyme, trimming the hpf mRNA by only 1 nucleotide. Deletion of yhaM delays cell growth. These findings substantiate the physiological significance of this cryptic enzyme and the protective role of Hpf in ribosome integrity, providing a mechanistic understanding of bacterial ribosome turnover.
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Affiliation(s)
- Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core in Research Resources Center, University of Illinois at Chicago (UIC), 1100 S Ashland Ave, Chicago, IL 60607, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
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2
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Bahari A, Castillo AG, Safaie N, Bejarano ER, Luna AP, Shams-Bakhsh M. Functional Analysis of V2 Protein of Beet Curly Top Iran Virus. PLANTS (BASEL, SWITZERLAND) 2022; 11:3351. [PMID: 36501393 PMCID: PMC9736138 DOI: 10.3390/plants11233351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Geminivirus beet curly top Iran virus (BCTIV) is one of the main causal agents of the beet curly top disease in Iran and the newly established Becurtovirus genus type species. Although the biological features of known becurtoviruses are similar to those of curtoviruses, they only share a limited sequence identity, and no information is available on the function of their viral genes. In this work, we demonstrate that BCTIV V2, as the curtoviral V2, is also a local silencing suppressor in Nicotiana benthamiana and can delay the systemic silencing spreading, although it cannot block the cell-to-cell movement of the silencing signal to adjacent cells. BCTIV V2 shows the same subcellular localization as curtoviral V2, being detected in the nucleus and perinuclear region, and its ectopic expression from a PVX-derived vector also causes the induction of necrotic lesions in N. benthamiana, such as the ones produced during the HR, both at the local and systemic levels. The results from the infection of N. benthamiana with a V2 BCTIV mutant showed that V2 is required for systemic infection, but not for viral replication, in a local infection. Considering all these results, we can conclude that BCTIV V2 is a functional homologue of curtoviral V2 and plays a crucial role in viral pathogenicity and systemic movement.
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Affiliation(s)
- Atiyeh Bahari
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
| | - Araceli G. Castillo
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Naser Safaie
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
| | - Eduardo R. Bejarano
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Ana P. Luna
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
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3
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López-Márquez D, Del-Espino Á, López-Pagán N, Rodríguez-Negrete EA, Rubio-Somoza I, Ruiz-Albert J, Bejarano ER, Beuzón CR. miR825-5p targets the TIR-NBS-LRR gene MIST1 and down-regulates basal immunity against Pseudomonas syringae in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7316-7334. [PMID: 34329403 PMCID: PMC8547151 DOI: 10.1093/jxb/erab354] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/29/2021] [Indexed: 05/29/2023]
Abstract
Plants encode numerous intracellular receptors known as nucleotide-binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived effectors or their activity to activate defenses. miRNAs regulate NLR genes in many species, often triggering the production of phased siRNAs (phasiRNAs). Most such examples involve genes encoding NLRs carrying coiled-coil domains, although a few include genes encoding NLRs carrying a Toll/interleukin-1 domain (TNL). Here, we characterize the role of miR825-5p in Arabidopsis, using a combination of bioinformatics, transgenic plants with altered miRNA levels and/or reporters, small RNAs, and virulence assays. We demonstrate that miR825-5p down-regulates the TNL MIST1 by targeting for endonucleolytic cleavage the sequence coding for TIR2, a highly conserved amino acid motif, linked to a catalytic residue essential for immune function. miR825-5p acts as a negative regulator of basal resistance against Pseudomonas syringae. miR825-5p triggers the production from MIST1 of a large number of phasiRNAs that can mediate cleavage of both MIST1 and additional TNL gene transcripts, potentially acting as a regulatory hub. miR825-5p is expressed in unchallenged leaves and transcriptionally down-regulated in response to pathogen-associated molecular patterns (PAMPs). Our results show that miR825-5p, which is required for full expression of PAMP-triggered immunity, establishes a link between PAMP perception and expression of uncharacterized TNL genes.
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Affiliation(s)
- Diego López-Márquez
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Nieves López-Pagán
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Edgar A Rodríguez-Negrete
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), Carrer Vall Moronta Edifici CRAG, 08193, Barcelona, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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4
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. MOLECULAR PLANT 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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5
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Xie D, Chen M, Niu J, Wang L, Li Y, Fang X, Li P, Qi Y. Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis. Nat Cell Biol 2021; 23:32-39. [PMID: 33288888 DOI: 10.1038/s41556-020-00606-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/26/2020] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) production entails the step-wise processing of primary miRNAs (pri-miRNAs) into precursor miRNAs (pre-miRNAs) and miRNA/* duplexes by Dicing complexes containing DCL1, HYL1 and SE, which are localized in nuclear dicing bodies (D-bodies)1,2. Here, we show that D-bodies are phase-separated condensates. SE forms droplets and drives DCL1, HYL1 and pri/pre-miRNAs into the droplets in vitro, and mutation of SE abrogates the formation of D-bodies in vivo, which indicates that D-bodies arise through SE-mediated phase separation. Disruption of SE phase separation greatly reduces its activity in promoting miRNA processing both in vitro and in vivo. We further show that pre-miRNAs are processed into miRNA/* duplexes in the droplets and, after processing, miRNA/* duplexes are bound by HYL1 and released from the droplets. Our findings provide evidence that efficient miRNA processing depends on the SE-phase-separation-mediated formation of D-bodies and suggest a paradigm that the products made in phase-separated condensates can be shipped out for subsequent processes.
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Affiliation(s)
- Dongqi Xie
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jinrong Niu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Liang Wang
- Tsinghua-Peking Center for Life Sciences, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pilong Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, China. .,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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6
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Miguel VN, Manavella PA, Chan RL, Capella MA. The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development. PLANT & CELL PHYSIOLOGY 2020; 61:659-670. [PMID: 31868910 DOI: 10.1093/pcp/pcz233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The presence of small tooth-like indentations, or serrations, characterizes leaf margins of Arabidopsis thaliana plants. The NAC family member CUP-SHAPED COTYLEDON 2 (CUC2), which undergoes post-transcriptional gene silencing by three micro-RNA genes (MIR164A, B and C), controls the extension of leaf serration. Here, we analyzed the role of AtHB1, a transcription factor (TF) belonging to the homeodomain-leucine zipper subfamily I, in shaping leaf margins. Using mutants with an impaired silencing pathway as background, we obtained transgenic plants expressing AtHB1 over 100 times compared to controls. These plants presented an atypical developmental phenotype characterized by leaves with deep serration. Transcript measurements revealed that CUC2 expression was induced in plants overexpressing AtHB1 and repressed in athb1 mutants, indicating a positive regulation exerted by this TF. Moreover, molecular analyses of AtHB1 overexpressing and mutant plants revealed that AtHB1 represses MIR164 transcription. We found that overexpression of MIR164B was able to reverse the serration phenotype of plants overexpressing AtHB1. Finally, chromatin immunoprecipitation assays revealed that AtHB1 was able to bind in vivo the promoter regions of all three MIR164 encoding loci. Altogether, our results indicate that AtHB1 directly represses MIR164 expression to enhance leaf serration by increasing CUC2 levels.
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Affiliation(s)
- Virginia N Miguel
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Matï As Capella
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
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7
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Ré DA, Cambiagno DA, Arce AL, Tomassi AH, Giustozzi M, Casati P, Ariel FD, Manavella PA. CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants. MOLECULAR PLANT 2020; 13:72-87. [PMID: 31606467 DOI: 10.1016/j.molp.2019.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marisol Giustozzi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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8
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Garcia L, Mansilla N, Ocampos N, Pagani MA, Welchen E, Gonzalez DH. The mitochondrial copper chaperone COX19 influences copper and iron homeostasis in arabidopsis. PLANT MOLECULAR BIOLOGY 2019; 99:621-638. [PMID: 30778722 DOI: 10.1007/s11103-019-00840-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/09/2019] [Indexed: 05/24/2023]
Abstract
The mitochondrial metallochaperone COX19 influences iron and copper responses highlighting a role of mitochondria in modulating metal homeostasis in Arabidopsis. The mitochondrial copper chaperone COX19 participates in the biogenesis of cytochrome c oxidase (COX) in yeast and humans. In this work, we studied the function of COX19 in Arabidopsis thaliana, using plants with either decreased or increased COX19 levels. A fusion of COX19 to the red fluorescent protein localized to mitochondria in vivo, suggesting that Arabidopsis COX19 is a mitochondrial protein. Silencing of COX19 using an artificial miRNA did not cause changes in COX activity levels or respiration in plants grown under standard conditions. These amiCOX19 plants, however, showed decreased expression of the low-copper responsive miRNA gene MIR398b and an induction of the miR398 target CSD1 relative to wild-type plants. Plants with increased COX19 levels, instead, showed induction of MIR398b and other low-copper responsive genes. In addition, global transcriptional changes in rosettes of amiCOX19 plants resembled those observed under iron deficiency. Phenotypic analysis indicated that the roots of amiCOX19 plants show altered growth responses to copper excess and iron deficiency. COX activity levels and COX-dependent respiration were lower in amiCOX19 plants than in wild-type plants under iron deficiency conditions, suggesting that COX19 function is particularly important for COX assembly under iron deficiency. The results indicate that the mitochondrial copper chaperone COX19 has a role in regulating copper and iron homeostasis and responses in plants.
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Affiliation(s)
- Lucila Garcia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral, Colectora Ruta Nac. Nº 168 km 0, Paraje el Pozo s/n, 3000, Santa Fe, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Ocampo y Esmeralda s/n, 2000, Rosario, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral, Colectora Ruta Nac. Nº 168 km 0, Paraje el Pozo s/n, 3000, Santa Fe, Argentina
| | - Natacha Ocampos
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral, Colectora Ruta Nac. Nº 168 km 0, Paraje el Pozo s/n, 3000, Santa Fe, Argentina
| | - María A Pagani
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 570, 2000, Rosario, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral, Colectora Ruta Nac. Nº 168 km 0, Paraje el Pozo s/n, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral, Colectora Ruta Nac. Nº 168 km 0, Paraje el Pozo s/n, 3000, Santa Fe, Argentina.
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9
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Gemmill D, D'souza S, Meier-Stephenson V, Patel TR. Current approaches for RNA-labelling to identify RNA-binding proteins. Biochem Cell Biol 2019; 98:31-41. [PMID: 30931575 DOI: 10.1139/bcb-2019-0041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA is involved in all domains of life, playing critical roles in a host of gene expression processes, host-defense mechanisms, cell proliferation, and diseases. A critical component in many of these events is the ability for RNA to interact with proteins. Over the past few decades, our understanding of such RNA-protein interactions and their importance has driven the search and development of new techniques for the identification of RNA-binding proteins. In determining which proteins bind to the RNA of interest, it is often useful to use the approach where the RNA molecule is the "bait" and allow it to capture proteins from a lysate or other relevant solution. Here, we review a collection of methods for modifying RNA to capture RNA-binding proteins. These include small-molecule modification, the addition of aptamers, DNA-anchoring, and nucleotide substitution. With each, we provide examples of their application, as well as highlight their advantages and potential challenges.
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Affiliation(s)
- Darren Gemmill
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Simmone D'souza
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Vanessa Meier-Stephenson
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.,Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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10
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Ré DA, Lang PLM, Yones C, Arce AL, Stegmayer G, Milone D, Manavella PA. Alternative use of miRNA-biogenesis co-factors in plants at low temperatures. Development 2019; 146:dev172932. [PMID: 30760482 DOI: 10.1242/dev.172932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/04/2019] [Indexed: 01/31/2023]
Abstract
Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plant development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs. As plants lack a stable internal temperature to which enzymatic reactions could be optimized during evolution, reactions such as miRNA processing have to be adjusted to fluctuating environmental temperatures. Here, we report that with decreasing ambient temperature, the plant miRNA biogenesis machinery becomes more robust, producing miRNAs even in the absence of the key DCL1 co-factors HYL1 and SE. This reduces the morphological and reproductive defects of se and hyl1 mutants, restoring seed production. Using small RNA-sequencing and bioinformatics analyses, we have identified specific miRNAs that become HYL1/SE independent for their production in response to temperature decrease. We found that the secondary structure of primary miRNAs is key for this temperature recovery. This finding may have evolutionary implications as a potential adaptation-driving mechanism to a changing climate.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Patricia L M Lang
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Diego Milone
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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11
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Cambiagno DA, Nota F, Zavallo D, Rius S, Casati P, Asurmendi S, Alvarez ME. Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1178-1190. [PMID: 30238536 DOI: 10.1111/tpj.14098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/24/2018] [Accepted: 09/03/2018] [Indexed: 05/04/2023]
Abstract
Pattern recognition receptors (PRR) and nucleotide-binding leucine-rich repeat proteins (NLR) are major components of the plant immune system responsible for pathogen detection. To date, the transcriptional regulation of PRR/NLR genes is poorly understood. Some PRR/NLR genes are affected by epigenetic changes of neighboring transposable elements (TEs) (cis regulation). We analyzed whether these genes can also respond to changes in the epigenetic marks of distal pericentromeric TEs (trans regulation). We found that Arabidopsis tissues infected with Pseudomonas syringae pv. tomato (Pst) initially induced the expression of pericentromeric TEs, and then repressed it by RNA-directed DNA methylation (RdDM). The latter response was accompanied by the accumulation of small RNAs (sRNAs) mapping to the TEs. Curiously these sRNAs also mapped to distal PRR/NLR genes, which were controlled by RdDM but remained induced in the infected tissues. Then, we used non-infected mom1 (Morpheus' molecule 1) mutants that expressed pericentromeric TEs to test if they lose repression of PRR/NLR genes. mom1 plants activated several PRR/NLR genes that were unlinked to MOM1-targeted TEs, and showed enhanced resistance to Pst. Remarkably, the increased defenses of mom1 were abolished when MOM1/RdDM-mediated pericentromeric TEs silencing was re-established. Therefore, common sRNAs could control PRR/NLR genes and distal pericentromeric TEs and preferentially silence TEs when they are activated.
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Affiliation(s)
- Damián A Cambiagno
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Sebastián Rius
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Buenos Aires, Argentina
| | - María E Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
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Achkar NP, Cho SK, Poulsen C, Arce AL, Re DA, Giudicatti AJ, Karayekov E, Ryu MY, Choi SW, Harholt J, Casal JJ, Yang SW, Manavella PA. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018; 46:236-247.e6. [PMID: 30016624 DOI: 10.1016/j.devcel.2018.06.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
Abstract
Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait. Here we show that plants alter microRNA (miRNA) biogenesis in response to light transition. When plants suffer an unusual extended period of light deprivation, the miRNA biogenesis factor HYPONASTIC LEAVES 1 (HYL1) is degraded but an inactive pool of phosphorylated protein remains stable inside the nucleus. Degradation of HYL1 leads to the release of gene silencing, triggering a proper response to dark and shade. Upon light restoration, a quick dephosphorylation of HYL1 leads to the reactivation of miRNA biogenesis and a switch toward a developmental program that maximizes the light uptake. Our findings define a unique and fast regulatory mechanism controlling the plant silencing machinery during plant light response.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | | | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Elizabeth Karayekov
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Suk Won Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jesper Harholt
- Carlsberg Research Laboratory, Copenhagen V 1799, Denmark
| | - Jorge J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina; Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires 1405, Argentina
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina.
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