51
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Guo DL, Li Q, Lv WQ, Zhang GH, Yu YH. MicroRNA profiling analysis of developing berries for 'Kyoho' and its early-ripening mutant during berry ripening. BMC PLANT BIOLOGY 2018; 18:285. [PMID: 30445920 PMCID: PMC6240241 DOI: 10.1186/s12870-018-1516-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/31/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND 'Fengzao' is an early-ripening bud mutant of 'Kyoho', which matures nearly 30 days earlier than 'Kyoho'. To gain a better understanding of the regulatory role of miRNAs in early-ripening of grape berry, high-throughput sequencing approach and quantitative RT-PCR validation were employed to identify miRNAs at the genome-wide level and profile the expression patterns of the miRNAs during berry development in 'Kyho' and 'Fengzao', respectively. RESULTS Nine independent small RNA libraries were constructed and sequenced in two varieties from key berry development stages. A total of 108 known miRNAs and 61 novel miRNAs were identified. Among that, 159 miRNAs identified in 'Fengzao' all completely expressed in 'Kyoho' and there were 10 miRNAs specifically expressed in 'Kyoho'. The expression profiles of known and novel miRNAs were quite similar between two varieties. As the major differentially expressed miRNAs, novel_144, vvi-miR3626-3p and vvi-miR3626-5p only expressed in 'Kyoho', vvi-miR399b and vvi-miR399e were down-regulated in 'Fengzao', while vvi-miR477b-3p up-regulated in 'Fengzao'. According to the expression analysis and previous reports, miR169-NF-Y subunit, miR398-CSD, miR3626-RNA helicase, miR399- phosphate transporter and miR477-GRAS transcription factor were selected as the candidates for further investigations of miRNA regulation role in the early-ripening of grape. The qRT-PCR analyses validated the contrasting expression patterns for these miRNAs and their target genes. CONCLUSIONS The miRNAome of the grape berry development of 'Kyoho', and its early-ripening bud mutant, 'Fengzao' were compared by high-throughput sequencing. The expression pattern of several key miRNAs and their target genes during grape berry development and ripening stages was examined. Our results provide valuable basis towards understanding the regulatory mechanisms of early-ripening of grape berry.
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Affiliation(s)
- Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
| | - Qiong Li
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
| | - Wen-Qing Lv
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
| | - Guo-Hai Zhang
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
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52
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Gomez MD, Barro-Trastoy D, Escoms E, Saura-Sánchez M, Sánchez I, Briones-Moreno A, Vera-Sirera F, Carrera E, Ripoll JJ, Yanofsky MF, Lopez-Diaz I, Alonso JM, Perez-Amador MA. Gibberellins negatively modulate ovule number in plants. Development 2018; 145:dev163865. [PMID: 29914969 PMCID: PMC6053663 DOI: 10.1242/dev.163865] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/04/2018] [Indexed: 01/06/2023]
Abstract
Ovule formation is a complex developmental process in plants, with a strong impact on the production of seeds. Ovule primordia initiation is controlled by a gene network, including components of the signaling pathways of auxin, brassinosteroids and cytokinins. By contrast, gibberellins (GAs) and DELLA proteins, the negative regulators of GA signaling, have never been shown to be involved in ovule initiation. Here, we provide molecular and genetic evidence that points to DELLA proteins as novel players in the determination of ovule number in Arabidopsis and in species of agronomic interest, such as tomato and rapeseed, adding a new layer of complexity to this important developmental process. DELLA activity correlates positively with ovule number, acting as a positive factor for ovule initiation. In addition, ectopic expression of a dominant DELLA in the placenta is sufficient to increase ovule number. The role of DELLA proteins in ovule number does not appear to be related to auxin transport or signaling in the ovule primordia. Possible crosstalk between DELLA proteins and the molecular and hormonal network controlling ovule initiation is also discussed.
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Affiliation(s)
- Maria D Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Daniela Barro-Trastoy
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Ernesto Escoms
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Maite Saura-Sánchez
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires C1417DSE, Argentina
| | - Ines Sánchez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Asier Briones-Moreno
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Francisco Vera-Sirera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Martin F Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Isabel Lopez-Diaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
| | - José M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC 27607, USA
| | - Miguel A Perez-Amador
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas (CSIC), Valencia 46022, Spain
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53
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Shivaraj SM, Jain A, Singh A. Highly preserved roles of Brassica MIR172 in polyploid Brassicas: ectopic expression of variants of Brassica MIR172 accelerates floral transition. Mol Genet Genomics 2018; 293:1121-1138. [PMID: 29752548 DOI: 10.1007/s00438-018-1444-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/03/2018] [Indexed: 12/21/2022]
Abstract
Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes. Copy number analysis revealed higher retention of MIR172 loci relative to AP2 in diploid and amphi-diploid Brassica species. Dendrogram of 87 MIR172 sequences from Brassicaceae showed five major clusters corresponding to MIR172a-MIR172e which further separated into sub-genome and progenitor genome specific clades. Similar groupings were observed in the phylogeny of 11 Brassica AP2 and AP2-like genes. Over-expression of a pair of natural variants for each of MIR172b, MIR172d and MIR172e representing sub-genomes, progenitor genomes and species of Brassicas displayed floral acceleration in all transgenic lines indicating a strong selection pressure on MIR172. All gain-of-function lines, except 35S::MIR172e and 35S::MIR172e' displayed floral organ defects implying altered target spectrum of MIR172e relative to MIR172b and MIR172d. Expression of MIR172e caused marginal earliness in flowering time in B. juncea. In conclusion, this study demonstrates tightly preserved role of homeologs and natural variants of MIR172 family in mediating flowering in Brassicas and suggests their deployment for introgression of early flowering trait.
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Affiliation(s)
- S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
- Département de Phytologie-Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, QC, Canada
| | - Aditi Jain
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India.
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54
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Balanzà V, Martínez-Fernández I, Sato S, Yanofsky MF, Kaufmann K, Angenent GC, Bemer M, Ferrándiz C. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat Commun 2018. [PMID: 29422669 DOI: 10.1038/s41467-018-03065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover a genetic pathway regulating GPA in Arabidopsis that responds to age-dependent factors and acts in parallel to seed-derived signals. We show that FRUITFULL (FUL), a MADS-box gene involved in flowering and fruit development, has a key role in promoting meristem arrest, as GPA is delayed and fruit production is increased in ful mutants. FUL directly and negatively regulates APETALA2 expression in the shoot apical meristem and maintains the temporal expression of WUSCHEL which is an essential factor for meristem maintenance.
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Affiliation(s)
- Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Shusei Sato
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Martin F Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kerstin Kaufmann
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain.
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55
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Balanzà V, Martínez-Fernández I, Sato S, Yanofsky MF, Kaufmann K, Angenent GC, Bemer M, Ferrándiz C. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat Commun 2018; 9:565. [PMID: 29422669 PMCID: PMC5805735 DOI: 10.1038/s41467-018-03067-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 01/17/2018] [Indexed: 11/20/2022] Open
Abstract
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover a genetic pathway regulating GPA in Arabidopsis that responds to age-dependent factors and acts in parallel to seed-derived signals. We show that FRUITFULL (FUL), a MADS-box gene involved in flowering and fruit development, has a key role in promoting meristem arrest, as GPA is delayed and fruit production is increased in ful mutants. FUL directly and negatively regulates APETALA2 expression in the shoot apical meristem and maintains the temporal expression of WUSCHEL which is an essential factor for meristem maintenance. The lifespan of monocarpic plants is determined by coordinated arrest of shoot meristems. Here the authors show that this process is promoted by the FRUITFULL transcription factor which negatively regulates expression of the meristem maintenance factor WUSCHEL in an AP2-dependent manner.
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Affiliation(s)
- Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Shusei Sato
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Martin F Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kerstin Kaufmann
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands.,Bioscience, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain.
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56
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Rodríguez-Cazorla E, Ortuño-Miquel S, Candela H, Bailey-Steinitz LJ, Yanofsky MF, Martínez-Laborda A, Ripoll JJ, Vera A. Ovule identity mediated by pre-mRNA processing in Arabidopsis. PLoS Genet 2018; 14:e1007182. [PMID: 29329291 PMCID: PMC5785034 DOI: 10.1371/journal.pgen.1007182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/25/2018] [Accepted: 01/02/2018] [Indexed: 11/18/2022] Open
Abstract
Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity. Here, we report that the HUA-PEP activity additionally governs ovule morphogenesis. Accordingly, in severe hua-pep backgrounds ovules transform into flower organ-like structures. These homeotic transformations are most likely due to the dramatic reduction in SHP1, SHP2 and STK activity. Our molecular and genome-wide profiling strategies revealed the accumulation of prematurely terminated transcripts of D-class genes in hua-pep mutants and reduced amounts of their respective functional messengers, which points to pre-mRNA processing misregulation as the origin of the ovule developmental defects in such backgrounds. RNA processing and transcription are coordinated by the RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD). Our results show that HUA-PEP activity members can interact with the CTD regulator C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 (CPL1), supporting a co-transcriptional mode of action for the HUA-PEP activity. Our findings expand the portfolio of reproductive developmental programs in which HUA-PEP activity participates, and further substantiates the importance of RNA regulatory mechanisms (pre-mRNA co-transcriptional regulation) for correct gene expression during plant morphogenesis.
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Affiliation(s)
| | - Samanta Ortuño-Miquel
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Alicante, Spain
| | - Lindsay J. Bailey-Steinitz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Martin F. Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Antonio Martínez-Laborda
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AV); (JJR)
| | - Antonio Vera
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
- * E-mail: (AV); (JJR)
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57
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Roosjen M, Paque S, Weijers D. Auxin Response Factors: output control in auxin biology. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:179-188. [PMID: 28992135 DOI: 10.1093/jxb/erx237] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal into the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family probably contribute to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis, much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics, and structural biology has helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review, we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.
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Affiliation(s)
- Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, The Netherlands
| | - Sébastien Paque
- Laboratory of Biochemistry, Wageningen University, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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58
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Cherenkov P, Novikova D, Omelyanchuk N, Levitsky V, Grosse I, Weijers D, Mironova V. Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:329-339. [PMID: 28992117 PMCID: PMC5853796 DOI: 10.1093/jxb/erx254] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
The phytohormone auxin regulates virtually every developmental process in land plants. This regulation is mediated via de-repression of DNA-binding auxin response factors (ARFs). ARFs bind TGTC-containing auxin response cis-elements (AuxREs), but there is growing evidence that additional cis-elements occur in auxin-responsive regulatory regions. The repertoire of auxin-related cis-elements and their involvement in different modes of auxin response are not yet known. Here we analyze the enrichment of nucleotide hexamers in upstream regions of auxin-responsive genes associated with auxin up- or down-regulation, with early or late response, ARF-binding domains, and with different chromatin states. Intriguingly, hexamers potentially bound by basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) factors as well as a family of A/T-rich hexamers are more highly enriched in auxin-responsive regions than canonical TGTC-containing AuxREs. We classify and annotate the whole spectrum of enriched hexamers and discuss their patterns of enrichment related to different modes of auxin response.
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Affiliation(s)
| | - Daria Novikova
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
- Department of Agrotechnology and Food Sciences, Subdivision Biochemistry, Wageningen University and Research Center, The Netherlands
| | - Nadya Omelyanchuk
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
| | - Victor Levitsky
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
| | - Ivo Grosse
- Novosibirsk State University, Russian Federation
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Dolf Weijers
- Department of Agrotechnology and Food Sciences, Subdivision Biochemistry, Wageningen University and Research Center, The Netherlands
- Correspondence: or
| | - Victoria Mironova
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
- Correspondence: or
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59
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Sánchez-Retuerta C, Suaréz-López P, Henriques R. Under a New Light: Regulation of Light-Dependent Pathways by Non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2018; 9:962. [PMID: 30140270 PMCID: PMC6095000 DOI: 10.3389/fpls.2018.00962] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/14/2018] [Indexed: 05/18/2023]
Abstract
The biological relevance of non-protein coding RNAs in the regulation of critical plant processes has been firmly established in recent years. This has been mostly achieved with the discovery and functional characterization of small non-coding RNAs, such as small interfering RNAs and microRNAs (miRNAs). However, recent next-generation sequencing techniques have widened our view of the non-coding RNA world, which now includes long non-coding RNAs (lncRNAs). Small and lncRNAs seem to diverge in their biogenesis and mode of action, but growing evidence highlights their relevance in developmental processes and in responses to particular environmental conditions. Light can affect MIRNA gene transcription, miRNA biogenesis, and RNA-induced silencing complex (RISC) activity, thus controlling not only miRNA accumulation but also their biological function. In addition, miRNAs can mediate several light-regulated processes. In the lncRNA world, few reports are available, but they already indicate a role in the regulation of photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering. In this review, we will discuss how light controls MIRNA gene expression and the accumulation of their mature forms, with a particular emphasis on those miRNAs that respond to different light qualities and are conserved among species. We will also address the role of small non-coding RNAs, particularly miRNAs, and lncRNAs in the regulation of light-dependent pathways. We will mainly focus on the recent progress done in understanding the interconnection between these non-coding RNAs and photomorphogenesis, circadian clock function, and photoperiod-dependent flowering.
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Affiliation(s)
| | - Paula Suaréz-López
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Rossana Henriques
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
- *Correspondence: Rossana Henriques,
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60
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Díaz-Manzano FE, Cabrera J, Ripoll JJ, del Olmo I, Andrés MF, Silva AC, Barcala M, Sánchez M, Ruíz-Ferrer V, de Almeida-Engler J, Yanofsky MF, Piñeiro M, Jarillo JA, Fenoll C, Escobar C. A role for the gene regulatory module microRNA172/TARGET OF EARLY ACTIVATION TAGGED 1/FLOWERING LOCUS T (miRNA172/TOE1/FT) in the feeding sites induced by Meloidogyne javanica in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:813-827. [PMID: 29105090 PMCID: PMC5922426 DOI: 10.1111/nph.14839] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/05/2017] [Indexed: 05/20/2023]
Abstract
Root knot nematodes (RKNs) penetrate into the root vascular cylinder, triggering morphogenetic changes to induce galls, de novo formed 'pseudo-organs' containing several giant cells (GCs). Distinctive gene repression events observed in early gall/GCs development are thought to be mediated by post-transcriptional silencing via microRNAs (miRNAs), a process that is far from being fully characterized. Arabidopsis thaliana backgrounds with altered activities based on target 35S::MIMICRY172 (MIM172), 35S::TARGET OF EARLY ACTIVATION TAGGED 1 (TOE1)-miR172-resistant (35S::TOE1R ) and mutant (flowering locus T-10 (ft-10)) lines were used for functional analysis of nematode infective and reproductive parameters. The GUS-reporter lines, MIR172A-E::GUS, treated with auxin (IAA) and an auxin-inhibitor (a-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA)), together with the MIR172C AuxRE::GUS line with two mutated auxin responsive elements (AuxREs), were assayed for nematode-dependent gene expression. Arabidopsis thaliana backgrounds with altered expression of miRNA172, TOE1 or FT showed lower susceptibility to the RKNs and smaller galls and GCs. MIR172C-D::GUS showed restricted promoter activity in galls/GCs that was regulated by auxins through auxin-responsive factors. IAA induced their activity in galls while PEO-IAA treatment and mutations in AuxRe motifs abolished it. The results showed that the regulatory module miRNA172/TOE1/FT plays an important role in correct GCs and gall development, where miRNA172 is modulated by auxins.
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Affiliation(s)
- Fernando E. Díaz-Manzano
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Javier Cabrera
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116 USA
| | - Iván del Olmo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Mari Fe Andrés
- Instituto de Ciencias Agrarias (ICA, CSIC), Protección Vegetal, Calle de Serrano 115, 28006 Madrid, Spain
| | - Ana Cláudia Silva
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Marta Barcala
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - María Sánchez
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Virginia Ruíz-Ferrer
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Janice de Almeida-Engler
- Institut National de la Recherche Agronomique (INRA) - University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900 Sophia Antipolis, France
| | - Martin F. Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116 USA
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Jose Antonio Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Carmen Fenoll
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Carolina Escobar
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
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Chen C, Zeng Z, Liu Z, Xia R. Small RNAs, emerging regulators critical for the development of horticultural traits. HORTICULTURE RESEARCH 2018; 5:63. [PMID: 30245834 PMCID: PMC6139297 DOI: 10.1038/s41438-018-0072-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/23/2018] [Accepted: 07/01/2018] [Indexed: 05/14/2023]
Abstract
Small RNAs (sRNAs) have been recently recognized as key genetic and epigenetic regulators in various organisms, ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding RNAs. In plants, major regulatory sRNAs are classified as respective microRNA (miRNA) and small interfering RNA (siRNA) species, with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional one. Many of these characterized sRNAs are involved in regulation of diverse biological programs, processes, and pathways in response to developmental cues, environmental signals/stresses, pathogen infection, and pest attacks. Recently, sRNAs-mediated regulations have also been extensively investigated in horticultural plants, with many novel mechanisms unveiled, which display far more mechanistic complexity and unique regulatory features compared to those studied in model species. Here, we review the recent progress of sRNA research in horticultural plants, with emphasis on mechanistic aspects as well as their relevance to trait regulation. Given that major and pioneered sRNA research has been carried out in the model and other plants, we also discuss ongoing sRNA research on these plants. Because miRNAs and phased siRNAs (phasiRNAs) are the most studied sRNA regulators, this review focuses on their biogenesis, conservation, function, and targeted genes and traits as well as the mechanistic relation between them, aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops.
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Affiliation(s)
- Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Zongrang Liu
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430 USA
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
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62
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Bürger M, Willige BC, Chory J. A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors. Nat Commun 2017; 8:2201. [PMID: 29259199 PMCID: PMC5736716 DOI: 10.1038/s41467-017-02347-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023] Open
Abstract
Several Pseudomonas and Xanthomonas species are plant pathogens that infect the model organism Arabidopsis thaliana and important crops such as Brassica. Resistant plants contain the infection by rapid cell death of the infected area through the hypersensitive response (HR). A family of highly related α/β hydrolases is involved in diverse processes in all domains of life. Functional details of their catalytic machinery, however, remained unclear. We report the crystal structures of α/β hydrolases representing two different clades of the family, including the protein SOBER1, which suppresses AvrBsT-incited HR in Arabidopsis. Our results reveal a unique hydrophobic anchor mechanism that defines a previously unknown family of protein deacetylases. Furthermore, this study identifies a lid-loop as general feature for substrate turnover in acyl-protein thioesterases and the described family of deacetylases. Furthermore, we found that SOBER1's biological function is not restricted to Arabidopsis thaliana and not limited to suppress HR induced by AvrBsT.
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Affiliation(s)
- Marco Bürger
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Björn C Willige
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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63
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Shi M, Hu X, Wei Y, Hou X, Yuan X, Liu J, Liu Y. Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches. Int J Mol Sci 2017; 18:E2599. [PMID: 29236054 PMCID: PMC5751202 DOI: 10.3390/ijms18122599] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023] Open
Abstract
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA). Our analyses identified 24 evolutionarily conserved miRNA genes as well as 16 predicted genes. Experimental verification showed that the expression levels of miR398 and miR408b were significantly upregulated after NAA treatment, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were significantly downregulated. Degradome sequencing coupled with miRNA target prediction analyses detected 119 significant cleavage sites on several mRNA targets, including SQUAMOSA promoter binding protein-like (SPL), ARF, (NAM, ATAF1/2 and CUC2) NAC, Arabidopsis thaliana homeobox protein (ATHB), the homeodomain-leucine zipper transcription factor revoluta(REV), (teosinte-like1, cycloidea and proliferating cell factor1) TCP and auxin signaling F-box protein (AFB) family genes. Our systematic profiling of miRNAs and the degradome in peach fruit suggests the existence of a post-transcriptional regulation network of miRNAs that target auxin pathway genes in fruit development.
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Affiliation(s)
- Mengya Shi
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
- National Agro-Tech Extension and Service Center, Beijing 100125, China.
| | - Xiao Hu
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
| | - Yu Wei
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xu Hou
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China.
| | - Xue Yuan
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China.
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yueping Liu
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
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64
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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Gaillochet C, Stiehl T, Wenzl C, Ripoll JJ, Bailey-Steinitz LJ, Li L, Pfeiffer A, Miotk A, Hakenjos JP, Forner J, Yanofsky MF, Marciniak-Czochra A, Lohmann JU. Control of plant cell fate transitions by transcriptional and hormonal signals. eLife 2017; 6:30135. [PMID: 29058667 PMCID: PMC5693117 DOI: 10.7554/elife.30135] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/22/2017] [Indexed: 11/24/2022] Open
Abstract
Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate. In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors transcriptionally control and physically interact with MONOPTEROS (MP), a key regulator of auxin signalling, and modulate the autocatalytic stabilization of auxin signalling output. Unlike animals, plants continuously generate new organs that make up their body. At the core of this amazing capacity lie tissues called meristems, which are found at the growing tips of all plants. Meristems contain dividing stem cells. The daughters of these stem cells pass through nearby regions called transition domains. Over time, they change – or differentiate – to go on to become part of tissues like leaves, roots, stems, shoots, flowers or fruits. Stem cell differentiation has a direct impact on a plant’s architecture and eventually its reproductive success. For crops, these factors determine yield. This means that understanding this aspect of plant development is central to basic and applied plant biology. Many factors required for shoot meristem activity have been identified, with a focus so far on the processes that control the identity of the cells produced. Now, Gaillochet et al. have asked which genes are responsible for controlling when stem cells in meristems differentiate. The analysis focused on the meristem that makes all the above ground parts of model plant Arabidopsis thaliana – the shoot apical meristem. Gaillochet et al. found that HECATE genes (or HEC for short) control the timing of stem cell differentiation by regulating the balance between the activities of two plant hormones: cytokinin and auxin. These genes promote cytokinin signals at the centre of the meristem, and dampen auxin response at the edges. This acts to slow down cell differentiation in two key transition domains of the shoot meristem. These new findings provide a molecular framework that now can be further investigated in crop plants to try to improve their yield. The findings also lay the foundation for studies of animals that may define common principles shared among stem cell systems in organisms that diverged over a billion years ago.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Thomas Stiehl
- Institute of Applied Mathematics, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, San Diego, United States
| | - Lindsay J Bailey-Steinitz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, San Diego, United States
| | - Lanxin Li
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Anne Pfeiffer
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Andrej Miotk
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jana P Hakenjos
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Joachim Forner
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Martin F Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, San Diego, United States
| | - Anna Marciniak-Czochra
- Institute of Applied Mathematics, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.,Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
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da Silva EM, Silva GFFE, Bidoia DB, da Silva Azevedo M, de Jesus FA, Pino LE, Peres LEP, Carrera E, López-Díaz I, Nogueira FTS. microRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:95-109. [PMID: 28715118 DOI: 10.1111/tpj.13637] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 05/02/2023]
Abstract
The transition from flowering to fruit production, namely fruit set, is crucial to ensure successful sexual plant reproduction. Although studies have described the importance of hormones (i.e. auxin and gibberellins) in controlling fruit set after pollination and fertilization, the role of microRNA-based regulation during ovary development and fruit set is still poorly understood. Here we show that the microRNA159/GAMYB1 and -2 pathway (the miR159/GAMYB1/2 module) is crucial for tomato ovule development and fruit set. MiR159 and SlGAMYBs were expressed in preanthesis ovaries, mainly in meristematic tissues, including developing ovules. SlMIR159-overexpressing tomato cv. Micro-Tom plants exhibited precocious fruit initiation and obligatory parthenocarpy, without modifying fruit shape. Histological analysis showed abnormal ovule development in such plants, which led to the formation of seedless fruits. SlGAMYB1/2 silencing in SlMIR159-overexpressing plants resulted in misregulation of pathways associated with ovule and female gametophyte development and auxin signalling, including AINTEGUMENTA-like genes and the miR167/SlARF8a module. Similarly to SlMIR159-overexpressing plants, SlGAMYB1 was downregulated in ovaries of parthenocarpic mutants with altered responses to gibberellins and auxin. SlGAMYBs likely contribute to fruit initiation by modulating auxin and gibberellin responses, rather than their levels, during ovule and ovary development. Altogether, our results unveil a novel function for the miR159-targeted SlGAMYBs in regulating an agronomically important trait, namely fruit set.
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Affiliation(s)
- Eder Marques da Silva
- Bioscience Institute, State University of Sao Paulo, Botucatu, Sao Paulo, 18618-970, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz', University of Sao Paulo, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Geraldo Felipe Ferreira E Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz', University of Sao Paulo, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Débora Brussolo Bidoia
- Bioscience Institute, State University of Sao Paulo, Botucatu, Sao Paulo, 18618-970, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz', University of Sao Paulo, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Mariana da Silva Azevedo
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Frederico Almeida de Jesus
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Lilian Ellen Pino
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Lázaro Eustáquio Pereira Peres
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elío s/n, Valencia, 46022, Spain
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elío s/n, Valencia, 46022, Spain
| | - Fabio Tebaldi Silveira Nogueira
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz', University of Sao Paulo, Piracicaba, Sao Paulo, 13418-900, Brazil
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Reyes-Olalde JI, Zúñiga-Mayo VM, Serwatowska J, Chavez Montes RA, Lozano-Sotomayor P, Herrera-Ubaldo H, Gonzalez-Aguilera KL, Ballester P, Ripoll JJ, Ezquer I, Paolo D, Heyl A, Colombo L, Yanofsky MF, Ferrandiz C, Marsch-Martínez N, de Folter S. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet 2017; 13:e1006726. [PMID: 28388635 PMCID: PMC5400277 DOI: 10.1371/journal.pgen.1006726] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/21/2017] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
Fruits and seeds are the major food source on earth. Both derive from the gynoecium and, therefore, it is crucial to understand the mechanisms that guide the development of this organ of angiosperm species. In Arabidopsis, the gynoecium is composed of two congenitally fused carpels, where two domains: medial and lateral, can be distinguished. The medial domain includes the carpel margin meristem (CMM) that is key for the production of the internal tissues involved in fertilization, such as septum, ovules, and transmitting tract. Interestingly, the medial domain shows a high cytokinin signaling output, in contrast to the lateral domain, where it is hardly detected. While it is known that cytokinin provides meristematic properties, understanding on the mechanisms that underlie the cytokinin signaling pattern in the young gynoecium is lacking. Moreover, in other tissues, the cytokinin pathway is often connected to the auxin pathway, but we also lack knowledge about these connections in the young gynoecium. Our results reveal that cytokinin signaling, that can provide meristematic properties required for CMM activity and growth, is enabled by the transcription factor SPATULA (SPT) in the medial domain. Meanwhile, cytokinin signaling is confined to the medial domain by the cytokinin response repressor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFERASE 6 (AHP6), and perhaps by ARR16 (a type-A ARR) as well, both present in the lateral domains (presumptive valves) of the developing gynoecia. Moreover, SPT and cytokinin, probably together, promote the expression of the auxin biosynthetic gene TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and the gene encoding the auxin efflux transporter PIN-FORMED 3 (PIN3), likely creating auxin drainage important for gynoecium growth. This study provides novel insights in the spatiotemporal determination of the cytokinin signaling pattern and its connection to the auxin pathway in the young gynoecium.
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Affiliation(s)
- J. Irepan Reyes-Olalde
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Víctor M. Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Joanna Serwatowska
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Ricardo A. Chavez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Karla L. Gonzalez-Aguilera
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan José Ripoll
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Dario Paolo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Alexander Heyl
- Biology Department, Adelphi University, Garden City, New York, United States of America
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Martin F. Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Cristina Ferrandiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
- * E-mail:
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Ballester P, Ferrándiz C. Shattering fruits: variations on a dehiscent theme. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:68-75. [PMID: 27888713 DOI: 10.1016/j.pbi.2016.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 05/18/2023]
Abstract
Fruits are seed dispersal units, and for that they have evolved different strategies to facilitate separation and dispersal of the progeny from the mother plant. A great proportion of fruits from different clades are dry and dehiscent, opening upon maturity to disperse the seeds. In the last two decades, intense research mainly in Arabidopsis has uncovered the basic network that controls the differentiation of the Arabidopsis fruit dehiscence zone. This review focuses on recent discoveries that have helped to complete the picture, as well as the insights from evo-devo and crop domestication studies that show how the conservation/variation of the elements of this network across species accounts for its evolutionary plasticity and the origin of evolutionary innovations.
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Affiliation(s)
- Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia 46022, Spain.
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69
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Bemer M, van Dijk ADJ, Immink RGH, Angenent GC. Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation. TRENDS IN PLANT SCIENCE 2017; 22:66-80. [PMID: 27814969 DOI: 10.1016/j.tplants.2016.10.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/03/2016] [Accepted: 10/07/2016] [Indexed: 05/09/2023]
Abstract
Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein-protein interactions between members of a particular plant TF family has long been recognised; however, a significant number of interfamily TF interactions has recently been reported. The biological implications and the molecular mechanisms involved in cross-family interactions have now started to be elucidated and the examples illustrate potential roles in the bridging of biological processes. Hence, cross-family TF interactions expand the molecular toolbox for plants with additional mechanisms to control and fine-tune robust gene expression patterns and to adapt to their continuously changing environment.
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Affiliation(s)
- Marian Bemer
- Wageningen University and Research, Bioscience, Plant Developmental Systems, Wageningen, The Netherlands; Wageningen University and Research, Laboratory of Molecular Biology, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Wageningen University and Research, Bioscience, Applied Bioinformatics, Wageningen, The Netherlands
| | - Richard G H Immink
- Wageningen University and Research, Bioscience, Plant Developmental Systems, Wageningen, The Netherlands; Wageningen University and Research, Laboratory of Molecular Biology, Wageningen, The Netherlands
| | - Gerco C Angenent
- Wageningen University and Research, Bioscience, Plant Developmental Systems, Wageningen, The Netherlands; Wageningen University and Research, Laboratory of Molecular Biology, Wageningen, The Netherlands.
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70
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Farinati S, Rasori A, Varotto S, Bonghi C. Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective. FRONTIERS IN PLANT SCIENCE 2017; 8:1247. [PMID: 28769956 PMCID: PMC5511831 DOI: 10.3389/fpls.2017.01247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/30/2017] [Indexed: 05/06/2023]
Abstract
Rosaceae is a family with an extraordinary spectrum of fruit types, including fleshy peach, apple, and strawberry that provide unique contributions to a healthy diet for consumers, and represent an excellent model for studying fruit patterning and development. In recent years, many efforts have been made to unravel regulatory mechanism underlying the hormonal, transcriptomic, proteomic and metabolomic changes occurring during Rosaceae fruit development. More recently, several studies on fleshy (tomato) and dry (Arabidopsis) fruit model have contributed to a better understanding of epigenetic mechanisms underlying important heritable crop traits, such as ripening and stress response. In this context and summing up the results obtained so far, this review aims to collect the available information on epigenetic mechanisms that may provide an additional level in gene transcription regulation, thus influencing and driving the entire Rosaceae fruit developmental process. The whole body of information suggests that Rosaceae fruit could become also a model for studying the epigenetic basis of economically important phenotypes, allowing for their more efficient exploitation in plant breeding.
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Affiliation(s)
- Silvia Farinati
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
| | - Angela Rasori
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura e Enologia, University of PadovaConegliano, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura e Enologia, University of PadovaConegliano, Italy
- *Correspondence: Claudio Bonghi,
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71
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Marsch-Martínez N, de Folter S. Hormonal control of the development of the gynoecium. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:104-14. [PMID: 26799132 DOI: 10.1016/j.pbi.2015.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 05/03/2023]
Abstract
Flowering plants are called angiosperms and most of their flowers produce at their center a pistil or a gynoecium, which is the female reproductive structure. After a double fertilization event, the gynoecium develops into a fruit with great importance for the plant because it protects and helps the dispersion of a new generation, and, for humans is a key nutritional source. Over 20 years, Arabidopsis thaliana has been used to discover important genes for gynoecium development, and in the early years, auxin was already proposed to play a role. More recently, new discoveries are unveiling the importance of other hormones, particularly cytokinins, and providing insights about the action of these hormones in gynoecium development, which is the focus of this review. One of the next challenges is to further refine the knowledge about the mechanisms by which hormones shape the gynoecium, understand the communication among them and their interactions with transcription factors that altogether guide gynoecium development.
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Affiliation(s)
- Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Gto, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Gto, Mexico.
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72
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Stewart D, Graciet E, Wellmer F. Molecular and regulatory mechanisms controlling floral organ development. FEBS J 2016; 283:1823-30. [DOI: 10.1111/febs.13640] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/25/2015] [Accepted: 12/30/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Darragh Stewart
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | | | - Frank Wellmer
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
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73
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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74
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Yao JL, Tomes S, Xu J, Gleave AP. How microRNA172 affects fruit growth in different species is dependent on fruit type. PLANT SIGNALING & BEHAVIOR 2016; 11:e1156833. [PMID: 26926448 PMCID: PMC4883839 DOI: 10.1080/15592324.2016.1156833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
microRNA172 (miR172) expression has been shown to have a positive effect on Arabidopsis fruit (siliques) growth. In contrast, over-expression of miR172 has a negative influence on fruit growth in apple, resulting in a dramatic reduction in fruit size. This negative influence is supported by the results of analyzing a transposable element (TE) insertional allele of a MIR172 gene that has reduced expression of the miRNA and is associated with an increase in fruit size. Arabidopsis siliques are a dry fruit derived from ovary tissues, whereas apple is a fleshy pome fruit derived mostly from hypanthium tissues. A model has been developed to explain the contrasting impact of miR172 expression in these two plant species based on the differences in their fruit structure. Transgenic apple plants with extremely high levels of miR172 overexpression produced flowers consisting of carpel tissues only, which failed to produce fruit. By comparison, in tomato, a fleshy berry fruit derived from the ovary, high level over-expression of the same miR172 resulted in carpel-only flowers which developed into parthenocarpic fruit. These results further indicate that the influence of miR172 on fruit growth in different plant species depends on its fruit type.
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Affiliation(s)
- Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Auckland , New Zealand
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research Limited, Auckland , New Zealand
| | - Juan Xu
- The New Zealand Institute for Plant & Food Research Limited, Auckland , New Zealand
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Andrew P. Gleave
- The New Zealand Institute for Plant & Food Research Limited, Auckland , New Zealand
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75
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Dai Z, Wang J, Zhu M, Miao X, Shi Z. OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1891. [PMID: 28066457 PMCID: PMC5167762 DOI: 10.3389/fpls.2016.01891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/30/2016] [Indexed: 05/20/2023]
Abstract
Specification of floral organ identity is critical for the establishment of floral morphology and inflorescence architecture. Although multiple genes are involved in the regulation of floral organogenesis, our understanding of the underlying regulating network is still fragmentary. MADs-box genes are principle members in the ABCDE model that characterized floral organs. OsMADS1 specifies the determinacy of spikelet meristem and lemma/palea identity in rice. However, the pathway through which OsMADS1 regulates floral organs remains elusive; here, we identified the microRNA172 (miR172) family as possible regulators downstream of OsMADS1. Genetic study revealed that overexpression of each miR172 gene resulted in elongated lemma/palea and indeterminacy of the floret, which resemble the phenotype of osmads1 mutant. On the contrary, overexpression of each target APETALA2 (AP2) genes resulted in shortened palea/lemma. Expression level and specificity of miR172 was greatly influenced by OsMADS1, as revealed by Northern blot analysis and In situ hybridization. Genetically, AP2-3 and AP2-2 over expression rescued the elongation and inconsistent development of the lemma/palea in OsMADS1RNAi transgenic plants. Our results suggested that in rice, OsMADS1 and miR172s/AP2s formed a regulatory network involved in floral organ development, particularly the elongation of the lemma and the palea.
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76
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Auxin signaling modules regulate maize inflorescence architecture. Proc Natl Acad Sci U S A 2015; 112:13372-7. [PMID: 26464512 DOI: 10.1073/pnas.1516473112] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, small groups of pluripotent stem cells called axillary meristems are required for the formation of the branches and flowers that eventually establish shoot architecture and drive reproductive success. To ensure the proper formation of new axillary meristems, the specification of boundary regions is required for coordinating their development. We have identified two maize genes, BARREN INFLORESCENCE1 and BARREN INFLORESCENCE4 (BIF1 and BIF4), that regulate the early steps required for inflorescence formation. BIF1 and BIF4 encode AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins, which are key components of the auxin hormone signaling pathway that is essential for organogenesis. Here we show that BIF1 and BIF4 are integral to auxin signaling modules that dynamically regulate the expression of BARREN STALK1 (BA1), a basic helix-loop-helix (bHLH) transcriptional regulator necessary for axillary meristem formation that shows a striking boundary expression pattern. These findings suggest that auxin signaling directly controls boundary domains during axillary meristem formation and define a fundamental mechanism that regulates inflorescence architecture in one of the most widely grown crop species.
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78
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Zlotorynski E. Epigenetics: Characterizing enhancers with dCas9. Nat Rev Mol Cell Biol 2015; 16:266-7. [PMID: 25874740 DOI: 10.1038/nrm3983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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