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Percival S, Onyenedum JG, Chitwood DH, Husbands AY. Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae). PLoS Comput Biol 2024; 20:e1011845. [PMID: 38315720 PMCID: PMC10868772 DOI: 10.1371/journal.pcbi.1011845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 02/15/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Leaves are often described in language that evokes a single shape. However, embedded in that descriptor is a multitude of latent shapes arising from evolutionary, developmental, environmental, and other effects. These confounded effects manifest at distinct developmental time points and evolve at different tempos. Here, revisiting datasets comprised of thousands of leaves of vining grapevine (Vitaceae) and maracuyá (Passifloraceae) species, we apply a technique from the mathematical field of topological data analysis to comparatively visualize the structure of heteroblastic and ontogenetic effects on leaf shape in each group. Consistent with a morphologically closer relationship, members of the grapevine dataset possess strong core heteroblasty and ontogenetic programs with little deviation between species. Remarkably, we found that most members of the maracuyá family also share core heteroblasty and ontogenetic programs despite dramatic species-to-species leaf shape differences. This conservation was not initially detected using traditional analyses such as principal component analysis or linear discriminant analysis. We also identify two morphotypes of maracuyá that deviate from the core structure, suggesting the evolution of new developmental properties in this phylogenetically distinct sub-group. Our findings illustrate how topological data analysis can be used to disentangle previously confounded developmental and evolutionary effects to visualize latent shapes and hidden relationships, even ones embedded in complex, high-dimensional datasets.
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Affiliation(s)
- Sarah Percival
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Joyce G. Onyenedum
- Department of Environmental Studies, New York University, New York, New York, United States of America
| | - Daniel H. Chitwood
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Horticulture, Michigan State University, Michigan State University, East Lansing, Michigan, United States of America
| | - Aman Y. Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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2
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Lyu J, Cai Z, Li Y, Suo H, Yi R, Zhang S, Nian H. The Floral Repressor GmFLC-like Is Involved in Regulating Flowering Time Mediated by Low Temperature in Soybean. Int J Mol Sci 2020; 21:E1322. [PMID: 32075331 PMCID: PMC7072909 DOI: 10.3390/ijms21041322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/09/2023] Open
Abstract
Soybean is an important crop that is grown worldwide. Flowering time is a critical agricultural trait determining successful reproduction and yields. For plants, light and temperature are important environmental factors that regulate flowering time. Soybean is a typical short-day (SD) plant, and many studies have elucidated the fine-scale mechanisms of how soybean responds to photoperiod. Low temperature can delay the flowering time of soybean, but little is known about the detailed mechanism of how temperature affects soybean flowering. In this study, we isolated GmFLC-like from soybean, which belongs to the FLOWERING LOCUS C clade of the MADS-box family and is intensely expressed in soybean leaves. Heterologous expression of GmFLC-like results in a delayed-flowering phenotype in Arabidopsis. Additional experiments revealed that GmFLC-like is involved in long-term low temperature-triggered late flowering by inhibiting FT gene expression. In addition, yeast one-hybrid, dual-luciferase reporter assay, and electrophoretic mobility shift assay revealed that the GmFLC-like protein could directly repress the expression of FT2a by physically interacting with its promoter region. Taken together, our results revealed that GmFLC-like functions as a floral repressor involved in flowering time during treatments with various low temperature durations. As the only the FLC gene in soybean, GmFLC-like was meaningfully retained in the soybean genome over the course of evolution, and this gene may play an important role in delaying flowering time and providing protective mechanisms against sporadic and extremely low temperatures.
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Affiliation(s)
- Jing Lyu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Zhandong Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Yonghong Li
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Haicui Suo
- Crop Research Institute, Guangdong Academy of Agriculture, Guangzhou 510642, China;
| | - Rong Yi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shuai Zhang
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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3
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Foerster JM, Beissinger T, de Leon N, Kaeppler S. Large effect QTL explain natural phenotypic variation for the developmental timing of vegetative phase change in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:529-38. [PMID: 25575839 DOI: 10.1007/s00122-014-2451-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/20/2014] [Indexed: 05/16/2023]
Abstract
Natural variation for the timing of vegetative phase change in maize is controlled by several large effect loci, one corresponding to Glossy15 , a gene known for regulating juvenile tissue traits. Vegetative phase change is an intrinsic component of developmental programs in plants. Juvenile and adult vegetative tissues in grasses differ dramatically in their anatomical and biochemical composition affecting the utility of specific genotypes as animal feed and biofuel feedstock. The molecular network controlling the process of developmental transition is incompletely characterized. In this study, we used scoring for juvenile and adult epicuticular wax as an entry point to discover quantitative trait loci (QTL) controlling phenotypic variation for the developmental timing of juvenile to adult transition in maize. We scored the last leaf with juvenile wax on 25 recombinant inbred line families of the B73 reference Nested Association Mapping (NAM) population and the intermated B73×Mo17 (IBM) population across multiple seasons. A total of 13 unique QTL were identified through genome-wide association analysis across the NAM populations, three of which have large effects. A QTL located on chromosome nine had the most significant SNPs within Glossy15, a gene controlling expression of juvenile leaf traits. The second large effect QTL is located on chromosome two. The most significant SNP in this QTL is located adjacent to a homolog of the Arabidopsis transcription factor, enhanced downy mildew-2, which has been shown to promote the transition from juvenile to adult vegetative phase. Overall, these results show that several major QTL and potential candidate genes underlie the extensive natural variation for this developmental trait.
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Affiliation(s)
- Jillian M Foerster
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr., Madison, WI, 53706, USA
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4
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Bellini C, Pacurar DI, Perrone I. Adventitious roots and lateral roots: similarities and differences. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:639-66. [PMID: 24555710 DOI: 10.1146/annurev-arplant-050213-035645] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation.
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Affiliation(s)
- Catherine Bellini
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE90187 Umeå, Sweden; , ,
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5
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Wilson DC, Carella P, Isaacs M, Cameron RK. The floral transition is not the developmental switch that confers competence for the Arabidopsis age-related resistance response to Pseudomonas syringae pv. tomato. PLANT MOLECULAR BIOLOGY 2013; 83:235-46. [PMID: 23722504 PMCID: PMC3777159 DOI: 10.1007/s11103-013-0083-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 05/27/2013] [Indexed: 05/29/2023]
Abstract
Age-related resistance (ARR) is a plant defense response characterized by enhanced resistance to certain pathogens in mature plants relative to young plants. In Arabidopsis thaliana the transition to flowering is associated with ARR competence, suggesting that this developmental event is the switch that initiates ARR competence in mature plants (Rusterucci et al. in Physiol Mol Plant Pathol 66:222-231, 2005). The association of ARR and the floral transition was examined using flowering-time mutants and photoperiod-induced flowering to separate flowering from other developmental events that occur as plants age. Under short-day conditions, late-flowering plant lines ld-1 (luminidependens-1), soc1-2 (suppressor of overexpression of co 1-2), and FRI (+) (FRIGIDA) displayed ARR before the transition to flowering occurred. Early-flowering svp-31, svp-32 (short vegetative phase), and Ws-2 were ARR-defective, whereas early-flowering tfl1-14 (terminal flower 1-14) displayed ARR at the same time as Col-0. While svp-31, svp-32 and Ws-2 produced few rosette leaves, tfl1-14 produced a rosette leaf number similar to Col-0, suggesting that the development of a minimum number of rosette leaves is necessary to initiate ARR competence under short-day conditions. Photoperiod-induced transient expression of FT (FLOWERING LOCUS T) caused precocious flowering in short-day-grown Col-0 but this was not associated with ARR competence. Under long-day conditions co-9 (constans-9) mutants did not flower but displayed an ARR response at the same time as Col-0. This study suggests that SVP is required for the ARR response and that the floral transition is not the developmental event that regulates ARR competence.
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Affiliation(s)
- Daniel C. Wilson
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, ON L8S 4L8 Canada
| | - Philip Carella
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, ON L8S 4L8 Canada
| | - Marisa Isaacs
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, ON L8S 4L8 Canada
| | - Robin K. Cameron
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, ON L8S 4L8 Canada
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6
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Moreno AB, Martínez de Alba AE, Bardou F, Crespi MD, Vaucheret H, Maizel A, Mallory AC. Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants. Nucleic Acids Res 2013; 41:4699-708. [PMID: 23482394 PMCID: PMC3632135 DOI: 10.1093/nar/gkt152] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic RNA quality control (RQC) uses both endonucleolytic and exonucleolytic degradation to eliminate dysfunctional RNAs. In addition, endogenous and exogenous RNAs are degraded through post-transcriptional gene silencing (PTGS), which is triggered by the production of double-stranded (ds)RNAs and proceeds through short-interfering (si)RNA-directed ARGONAUTE-mediated endonucleolytic cleavage. Compromising cytoplasmic or nuclear 5'-3' exoribonuclease function enhances sense-transgene (S)-PTGS in Arabidopsis, suggesting that these pathways compete for similar RNA substrates. Here, we show that impairing nonsense-mediated decay, deadenylation or exosome activity enhanced S-PTGS, which requires host RNA-dependent RNA polymerase 6 (RDR6/SGS2/SDE1) and SUPPRESSOR OF GENE SILENCING 3 (SGS3) for the transformation of single-stranded RNA into dsRNA to trigger PTGS. However, these RQC mutations had no effect on inverted-repeat-PTGS, which directly produces hairpin dsRNA through transcription. Moreover, we show that these RQC factors are nuclear and cytoplasmic and are found in two RNA degradation foci in the cytoplasm: siRNA-bodies and processing-bodies. We propose a model of single-stranded RNA tug-of-war between RQC and S-PTGS that ensures the correct partitioning of RNA substrates among these RNA degradation pathways.
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Affiliation(s)
- Ana Beatriz Moreno
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, 91198 Gif-sur-Yvette, France
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7
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Li S, Yang X, Wu F, He Y. HYL1 controls the miR156-mediated juvenile phase of vegetative growth. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2787-98. [PMID: 22268150 PMCID: PMC3346236 DOI: 10.1093/jxb/err465] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/23/2011] [Accepted: 12/27/2011] [Indexed: 05/18/2023]
Abstract
HYL1 is an important regulator of microRNA (miRNA) biogenesis. A loss-of-function mutation of HYL1 causes the reduced accumulation of some miRNAs but fails to display the miRNA-deficient phenotypes of these miRNAs. In Arabidopsis, miR156 mediates phase transition through repression of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) genes. However, it remains unknown whether, and if so how, HYL1 enables phase transition through miR156. This study showed that a loss-of-function mutation of the HYL1 gene caused defects in the timing of the juvenile phase. In the primary leaves of hyl1-2 mutants, abaxial trichomes were generated prematurely, the leaf blades elongated, and the blade base angles enlarged, as is observed for adult leaves. In hyl1-2 p35S::miR156a and hyl1-2 spl9-4 spl15-1 plants, increased accumulation of miR156a and repressed expression of the SPL genes were concomitant with a complete or partial rescue of the hyl1-2 phenotype in phase defects. In contrast, overexpression of the SPL9 gene in hyl1-2 mutants led to total disappearance of the juvenile phase. Moreover, HYL1 prevented the premature accumulation of adult-related transcripts in the primary leaves. Taken together, these results suggest that HYL1 controls the expression levels of miR156-targeted SPL genes and enables plants to undergo the juvenile phase, an important and critical step during plant development to ensure maximum growth and productivity.
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Affiliation(s)
| | | | | | - Yuke He
- To whom correspondence should be addressed. E-mail:
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8
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Kaufmann K, Pajoro A, Angenent GC. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet 2010; 11:830-42. [PMID: 21063441 DOI: 10.1038/nrg2885] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Unlike animals, plants produce new organs throughout their life cycle using pools of stem cells that are organized in meristems. Although many key regulators of meristem and organ identities have been identified, it is still not well understood how they function at the molecular level and how they can switch an entire developmental programme in which thousands of genes are involved. Recent advances in the genome-wide identification of target genes controlled by key plant transcriptional regulators and their interactions with epigenetic factors provide new insights into general transcriptional regulatory mechanisms that control switches of developmental programmes and cell fates in complex organisms.
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9
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Li H, Deng Y, Wu T, Subramanian S, Yu O. Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. PLANT PHYSIOLOGY 2010; 153:1759-70. [PMID: 20508137 PMCID: PMC2923892 DOI: 10.1104/pp.110.156950] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Accepted: 05/20/2010] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of plant growth and development. Previously, we identified a group of conserved and novel miRNA families from soybean (Glycine max) roots. Many of these miRNAs are specifically induced during soybean-Bradyrhizobium japonicum interactions. Here, we examined the gene expression levels of six families of novel miRNAs and investigated their functions in nodule development. We used northern-blot analyses to study the tissue specificity and time course of miRNA expression. Transgenic expression of miR482, miR1512, and miR1515 led to significant increases of nodule numbers, while root length, lateral root density, and the number of nodule primordia were not altered in all tested miRNA lines. We also found differential expression of these miRNAs in nonnodulating and supernodulating soybean mutants. The expression levels of 22 predicted target genes regulated by six novel miRNAs were studied by real-time polymerase chain reaction and quantitative real-time polymerase chain reaction. These results suggested that miRNAs play important roles in soybean nodule development.
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Affiliation(s)
| | | | | | | | - Oliver Yu
- Shanghai JiaoTong University, School of Agriculture and Biology, Shanghai 200240, China (H.L., T.W.); Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (Y.D., S.S., O.Y.); Plant Science Department, South Dakota State University, Brookings, South Dakota 57007 (S.S.)
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10
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Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2010; 2:225-39. [PMID: 20624728 PMCID: PMC2997538 DOI: 10.1093/gbe/evq012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2010] [Indexed: 01/01/2023] Open
Abstract
We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
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Affiliation(s)
- Angélica Cibrián-Jaramillo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
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11
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Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet 2009; 5:e1000716. [PMID: 19936050 PMCID: PMC2773440 DOI: 10.1371/journal.pgen.1000716] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/12/2009] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Zhijie Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Apurva Narechania
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Christopher A. Maher
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Katherine Guill
- Plant Genetics Research Unit, United States Department of Agriculture–Agriculture Research Service, Columbia, Missouri, United States of America
| | - Michael D. McMullen
- Plant Genetics Research Unit, United States Department of Agriculture–Agriculture Research Service, Columbia, Missouri, United States of America
- Division of Plant Sciences, University of Missouri Columbia, Columbia, Missouri, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Plant, Soil, and Nutrition Research Unit, United States Department of Agriculture–Agriculture Research Service, Ithaca, New York, United States of America
- * E-mail:
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12
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Chuck G, Candela H, Hake S. Big impacts by small RNAs in plant development. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:81-6. [PMID: 18980858 DOI: 10.1016/j.pbi.2008.09.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 09/12/2008] [Accepted: 09/17/2008] [Indexed: 05/09/2023]
Abstract
The identification and study of small RNAs, including microRNAs and trans-acting small interfering RNAs, have added a layer of complexity to the many pathways that regulate plant development. These molecules, which function as negative regulators of gene expression, are now known to have greatly expanded roles in a variety of developmental processes affecting all major plant structures, including meristems, leaves, roots, and inflorescences. Mutants with specific developmental phenotypes have also advanced our knowledge of the biogenesis and mode of action of these diverse small RNAs. In addition, previous models on the cell autonomy of microRNAs may have to be revised as more data accumulate supporting their long distance transport. As many of these small RNAs appear to be conserved across different species, knowledge gained from one species is expected to have general application. However, a few surprising differences in small RNA function seem to exist between monocots and dicots regarding meristem initiation and sex determination. Integrating these unique functions into the overall scheme for plant growth will give a more complete picture of how they have evolved as unique developmental systems.
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Affiliation(s)
- George Chuck
- Plant Gene Expression Center, United States Department of Agriculture-Agriculture Research Service and the University of California, Albany, CA 94710, USA.
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13
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Trebbi D, McGrath JM. Functional differentiation of the sugar beet root system as indicator of developmental phase change. PHYSIOLOGIA PLANTARUM 2009; 135:84-97. [PMID: 19121102 DOI: 10.1111/j.1399-3054.2008.01169.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Developmental phase transitions in the plant root system have not been well characterized. In this study we compared the dynamics of sucrose accumulation with changes in gene expression analyzed with cDNA-amplified fragment length polymorphism (AFLP) in the developing tap root of sugar beet (Beta vulgaris, L.) during the first 9 weeks after emergence (WAE). Although differences between lines were evident as soon as 9 WAE, sucrose showed a marked increase in the rate of accumulation between 4 and 6 WAE and a remarkable shift in gene expression was observed between 5 and 6 WAE. These changes were evident in two unrelated genetic backgrounds and suggest that physiological and gene expression changes represent a functional differentiation of the tap root. These changes were considered as indicators of a developmental change in the sugar beet root system. To identify genes and metabolic pathways involved in this developmental shift, a root cDNA library was hybridized with probes enriched for 3- and 7-WAE transcripts and differentially expressed transcripts were analyzed by cDNA microarray. Several genes involved in the regulation of tissue development were found to be differentially regulated. Genes involved in protein metabolism, disease-related and secretory system were upregulated before the functional differentiation transition, while genes under hormonal control were upregulated after the functional differentiation transition. This developmental phase change of the root system is important to understand plant developmental regulation at the whole-plant level and will likely be useful as early selection parameter in breeding programs.
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Affiliation(s)
- Daniele Trebbi
- Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824-1325, USA.
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14
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Abstract
Photoperiod controls many developmental responses in animals, plants and even fungi. The response to photoperiod has evolved because daylength is a reliable indicator of the time of year, enabling developmental events to be scheduled to coincide with particular environmental conditions. Much progress has been made towards understanding the molecular mechanisms involved in the response to photoperiod in plants. These mechanisms include the detection of the light signal in the leaves, the entrainment of circadian rhythms, and the production of a mobile signal which is transmitted throughout the plant. Flowering, tuberization and bud set are just a few of the many different responses in plants that are under photoperiodic control. Comparison of what is known of the molecular mechanisms controlling these responses shows that, whilst common components exist, significant differences in the regulatory mechanisms have evolved between these responses.
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Affiliation(s)
- Stephen D Jackson
- Warwick HRI, University of Warwick, Wellesbourne, Warwickshire CV35 9EF, UK.
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15
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Mallard S, Nègre S, Pouya S, Gaudet D, Lu ZX, Dedryver F. Adult plant resistance-related gene expression in 'Camp Remy' wheat inoculated with Puccinia striiformis. MOLECULAR PLANT PATHOLOGY 2008; 9:213-25. [PMID: 18705853 PMCID: PMC6640271 DOI: 10.1111/j.1364-3703.2007.00459.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The French wheat variety 'Camp Remy' (CR) possesses a durable, adult plant resistance to yellow rust (YR), caused by the pathogen Puccinia striiformis. Using cDNA-AFLP on different sets of heterogeneous inbred families (HIFs) derived from the cross CR x Récital, we compared gene expression profiles during one seedling and two adult developmental stages following inoculation with P. striiformis. Transcripts differentially expressed in response to YR infection were isolated and cloned. Sequence analysis of the resultant clones revealed several classes of putative genes, including those related to resistance/defence responses, transcription and signal transduction, and primary metabolism. The expression profiles of seven selected genes were obtained using real-time PCR in CR leaves at the same three stages of development. The results confirmed the stage-specific expression of the genes at one or two specific stages in response to P. striiformis infection and demonstrated that CR modifies the expression of some resistance/defence-related genes during its transition from the seedling to adult growth stages. These results provided the first clue to understand the molecular basis of quantitative trait loci for adult plant resistance to YR and connect it with durability.
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Affiliation(s)
- Stéphanie Mallard
- INRA, Agrocampus Rennes, UMR118, Amélioration des Plantes et Biotechnologies Végétales, 35650 Le Rheu, France
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16
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Dykxhoorn DM, Chowdhury D, Lieberman J. RNA interference and cancer: endogenous pathways and therapeutic approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 615:299-329. [PMID: 18437900 DOI: 10.1007/978-1-4020-6554-5_14] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The endogenous RNA interference (RNAi) pathway regulates cellular differentiation and development using small noncoding hairpin RNAs, called microRNAs. This chapter will review the link between mammalian microRNAs and genes involved in cellular proliferation, differentiation, and apoptosis. Some microRNAs act as oncogenes or tumor suppressor genes, but the target gene networks they regulate are just beginning to be described. Cancer cells have altered atterns of microRNA expression, which can be used to identify the cell of origin and to subtype cancers. RNAi has also been used to identify novel genes involved in cellular transformation using forward genetic screening methods previously only possible in invertebrates. Possible strategies and obstacles to harnessing RNAi for cancer therapy will also be discussed.
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Affiliation(s)
- Derek M Dykxhoorn
- Institute for Biomedical Research and Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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17
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Schmitz RJ, Hong L, Fitzpatrick KE, Amasino RM. DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics 2007; 176:1359-62. [PMID: 17579240 PMCID: PMC1894598 DOI: 10.1534/genetics.107.070649] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In Arabidopsis thaliana, DICER-LIKE 1 and DICER-LIKE 3 are involved in the generation of small RNAs. Double mutants between dicer-like 1 and dicer-like 3 exhibit a delay in flowering that is caused by increased expression of the floral repressor FLOWERING LOCUS C. This delayed-flowering phenotype is similar to that of autonomous-pathway mutants, and the flowering delay can be overcome by vernalization.
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Affiliation(s)
- Robert J. Schmitz
- Laboratory of Genetics and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lewis Hong
- Laboratory of Genetics and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kathleen E. Fitzpatrick
- Laboratory of Genetics and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard M. Amasino
- Laboratory of Genetics and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
- Corresponding author: Department of Biochemistry, 433 Babcock Dr., University of Wisconsin, Madison, WI 53706. E-mail:
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18
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Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. THE PLANT CELL 2007; 19:926-42. [PMID: 17400893 PMCID: PMC1867363 DOI: 10.1105/tpc.107.050062] [Citation(s) in RCA: 292] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.
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Affiliation(s)
- Miya D Howell
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
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19
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Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V. CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic Acids Res 2006; 35:D829-33. [PMID: 17169981 PMCID: PMC1781248 DOI: 10.1093/nar/gkl991] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Plant small RNAs (smRNAs), which include microRNAs (miRNAs), short interfering RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs), are emerging as significant components of epigenetic processes and of gene networks involved in development and in homeostasis. Here we present a bioinformatics resource for cereal crops, the Cereal Small RNA Database (CSRDB), consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing. The smRNA sequences have been mapped to the rice genome and to the available maize genome sequence and these results are presented in two genome browser datasets using the Generic Genome Browser. Potential RNA targets for the smRNAs have been predicted and access to the resulting smRNA/RNA target pair dataset has been made available through a MySQL based relational database. Various ways to access the data are provided including links from the genome browser to the target database. Data linking and integration are the main focus for this interface, and internal as well as external links are present. The resource is available at and will be updated as more sequences become available.
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Affiliation(s)
- Cameron Johnson
- Section of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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20
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Abstract
Plants rely heavily on environmental cues to control the timing of developmental transitions. We are beginning to better understand what determines the timing of two of these transitions, the switch from juvenile to adult vegetative development and the transition to flowering. In this review, we discuss how RNA silencing mechanisms may influence the juvenile-to-adult vegetative switch. We also describe the discovery and regulation of a component of "florigen," the mobile flowering promotion signal that is involved in the transition to flowering. Parallel themes are beginning to emerge from a molecular comparison of these two developmental transitions.
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Affiliation(s)
- Isabel Bäurle
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
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21
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Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 2006; 16:939-44. [PMID: 16682356 DOI: 10.1016/j.cub.2006.03.065] [Citation(s) in RCA: 398] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 03/12/2006] [Accepted: 03/21/2006] [Indexed: 10/24/2022]
Abstract
MicroRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) in plants form through distinct pathways, although they function as negative regulators of mRNA targets by similar mechanisms . Three ta-siRNA gene families (TAS1, TAS2, and TAS3) are known in Arabidopsis thaliana. Biogenesis of TAS3 ta-siRNAs, which target mRNAs encoding several AUXIN RESPONSE FACTORs (including ARF3/ETTIN and ARF4 ) involves miR390-guided processing of primary transcripts, conversion of a precursor to dsRNA through RNA-DEPENDENT RNA POLYMERASE6 (RDR6) activity, and sequential DICER-LIKE4 (DCL4)-mediated cleavage events. We show that the juvenile-to-adult phase transition is normally suppressed by TAS3 ta-siRNAs, in an ARGONAUTE7-dependent manner, through negative regulation of ARF3 mRNA. Expression of a nontargeted ARF3 mutant (ARF3mut) in a wild-type background reproduced the phase-change phenotypes detected in rdr6-15 and dcl4-2 mutants, which lose all ta-siRNAs. Expression of either ARF3 or ARF3mut in rdr6-15 plants, in which both endogenous and transgenic copies of ARF3 were derepressed, resulted in further acceleration of phase change and severe morphological and patterning defects of leaves and floral organs. In light of the functions of ARF3 and ARF4 in organ asymmetry, these data reveal multiple roles for TAS3 ta-siRNA-mediated regulation of ARF genes in developmental timing and patterning.
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Affiliation(s)
- Noah Fahlgren
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97330, USA
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22
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Abstract
Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective of nanoscience and nanotechnology. 'RNA tectonics' is the design of modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- and meso-scopic architectures of desired size and shape. We report the three-dimensional design of tectoRNAs incorporating modular 4-way junction (4WJ) motifs, hairpin loops and their cognate loop-receptors to create extended, programmable interaction interfaces. Specific and directional RNA-RNA interactions at these interfaces enable conformational, topological and orientational control of tectoRNA self-assembly. The interacting motifs are precisely positioned within the helical arms of the 4WJ to program assembly from only one helical stacking conformation of the 4WJ. TectoRNAs programmed to assemble with orientational compensation produce micrometer-scale RNA filaments through supra-molecular equilibrium polymerization. As visualized by transmission electron microscopy, these RNA filaments resemble actin filaments from the protein world. This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins.
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Affiliation(s)
- Lorena Nasalean
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Stéphanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
- To whom correspondence should be addressed. Tel: +1 805 893 3628; Fax: +1 805 893 4210;
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