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Bai JF, Wang YK, Wang P, Duan WJ, Yuan SH, Sun H, Yuan GL, Ma JX, Wang N, Zhang FT, Zhang LP, Zhao CP. Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1370. [PMID: 28848574 PMCID: PMC5550412 DOI: 10.3389/fpls.2017.01370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/24/2017] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs which play important negative regulatory roles at both the transcriptional and post-transcriptional levels in plants. Wheat is the most commonly cultivated plant species worldwide. In this study, RNA-seq analysis was used to examine the expression profiles of miRNA in the spikelets of photo-thermosenisitive genic male sterile (PTGMS) wheat line BS366 during male fertility transition. Through mapping on their corresponding precursors, 917-7,762 novel miRNAs were found in six libraries. Six novel miRNAs were selected for examination of their secondary structures and confirmation by stem-loop RT-PCR. In a differential expression analysis, 20, 22, and 58 known miRNAs exhibited significant differential expression between developmental stages 1 (secondary sporogenous cells had formed), 2 (all cells layers were present and mitosis had ceased), and 3 (meiotic division stage), respectively, of fertile and sterile plants. Some of these differential expressed miRNAs, such as tae-miR156, tae-miR164, tae-miR171, and tae-miR172, were shown to be associated with their targets. These targets were previously reported to be related to pollen development and/or male sterility, indicating that these miRNAs and their targets may be involved in the regulation of male fertility transition in the PTGMS wheat line BS366. Furthermore, target genes of miRNA cleavage sites were validated by degradome sequencing. In this study, a possible signal model for the miRNA-mediated signaling pathway during the process of male fertility transition in the PTGMS wheat line BS366 was developed. This study provides a new perspective for understanding the roles of miRNAs in male fertility in PTGMS lines of wheat.
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Affiliation(s)
- Jian-Fang Bai
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Yu-Kun Wang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Peng Wang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- College of Plant Science and Technology, Beijing University of AgricultureBeijing, China
| | - Wen-Jing Duan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Shao-Hua Yuan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Hui Sun
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Guo-Liang Yuan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Jing-Xiu Ma
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Na Wang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Feng-Ting Zhang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Li-Ping Zhang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Chang-Ping Zhao
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
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Tong A, Yuan Q, Wang S, Peng J, Lu Y, Zheng H, Lin L, Chen H, Gong Y, Chen J, Yan F. Altered accumulation of osa-miR171b contributes to rice stripe virus infection by regulating disease symptoms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4357-4367. [PMID: 28922766 PMCID: PMC5853540 DOI: 10.1093/jxb/erx230] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/09/2017] [Indexed: 05/03/2023]
Abstract
Viral infection affects the pattern of plant miRNA expression. It has been presumed that reduction of miR171 and several other miRNAs influences viral symptoms in plants. We here experimentally demonstrate the association of osa-miR171b with rice stripe virus (RSV) symptoms in rice. Inhibition of osa-miR171b caused stunting with reduced chlorophyll content in leaves similar to viral symptoms. Overexpression of osa-miR171b by an artificial miRNA extended vegetative growth and enhanced chlorophyll accumulation in leaves. Tillers were thicker, and panicles were longer with more spikelets in plants overexpressing osa-miR171b than in controls, but there were no differences in tiller numbers. Targets of osa-miR171b, OsSCL6-IIa, OsSCL6-IIb, and OsSCL6-IIc, were respectively up- and down-regulated in plants where osa-miR171b was inhibited or overexpressed. In plants overexpressing osa-miR171b, five positive regulators for heading development, Ehd1, Ehd2, Ehd3, Ehd4, and Hd3a were up-regulated, while the negative regulator Ghd7 was down-regulated. Plants overexpressing osa-miR171b were less susceptible to RSV and virus symptoms were attenuated. Taken together, the results reveal that a reduction of osa-miR171b in RSV-infected rice contributes to RSV symptoms, and provide more insight into the roles of osa-miR171b in rice.
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Affiliation(s)
- Aizi Tong
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Quan Yuan
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- School of Marine Sciences, Ningbo University, Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo, China
| | - Shu Wang
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiejun Peng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuwen Lu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongying Zheng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Lin
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hairu Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Yifu Gong
- School of Marine Sciences, Ningbo University, Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo, China
| | - Jianping Chen
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Yan
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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103
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Short tandem target mimic rice lines uncover functions of miRNAs in regulating important agronomic traits. Proc Natl Acad Sci U S A 2017; 114:5277-5282. [PMID: 28461499 DOI: 10.1073/pnas.1703752114] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Improvements in plant agricultural productivity are urgently needed to reduce the dependency on limited natural resources and produce enough food for a growing world population. Human intervention over thousands of years has improved the yield of important crops; however, it is increasingly difficult to find new targets for genetic improvement. MicroRNAs (miRNAs) are promising targets for crop improvement, but their inactivation is technically challenging and has hampered functional analyses. We have produced a large collection of transgenic short tandem target mimic (STTM) lines silencing 35 miRNA families in rice as a resource for functional studies and crop improvement. Visual assessment of field-grown miRNA-silenced lines uncovered alterations in many valuable agronomic traits, including plant height, tiller number, and grain number, that remained stable for up to five generations. We show that manipulation of miR398 can increase panicle length, grain number, and grain size in rice. In addition, we discovered additional agronomic functions for several known miRNAs, including miR172 and miR156. Our collection of STTM lines thus represents a valuable resource for functional analysis of rice miRNAs, as well as for agronomic improvement that can be readily transferred to other important food crops.
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104
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Li S, Castillo-González C, Yu B, Zhang X. The functions of plant small RNAs in development and in stress responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:654-670. [PMID: 27943457 DOI: 10.1111/tpj.13444] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 05/22/2023]
Abstract
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.
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Affiliation(s)
- Shengjun Li
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
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105
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Fan S, Zhang D, Gao C, Zhao M, Wu H, Li Y, Shen Y, Han M. Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica. Front Physiol 2017; 8:253. [PMID: 28503152 PMCID: PMC5408086 DOI: 10.3389/fphys.2017.00253] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/10/2017] [Indexed: 12/02/2022] Open
Abstract
GRAS genes encode plant-specific transcription factors that play important roles in plant growth and development. However, little is known about the GRAS gene family in apple. In this study, 127 GRAS genes were identified in the apple (Malus domestica Borkh.) genome and named MdGRAS1 to MdGRAS127 according to their chromosomal locations. The chemical characteristics, gene structures and evolutionary relationships of the MdGRAS genes were investigated. The 127 MdGRAS genes could be grouped into eight subfamilies based on their structural features and phylogenetic relationships. Further analysis of gene structures, segmental and tandem duplication, gene phylogeny and tissue-specific expression with ArrayExpress database indicated their diversification in quantity, structure and function. We further examined the expression pattern of MdGRAS genes during apple flower induction with transcriptome sequencing. Eight higher MdGRAS (MdGRAS6, 26, 28, 44, 53, 64, 107, and 122) genes were surfaced. Further quantitative reverse transcription PCR indicated that the candidate eight genes showed distinct expression patterns among different tissues (leaves, stems, flowers, buds, and fruits). The transcription levels of eight genes were also investigated with various flowering related treatments (GA3, 6-BA, and sucrose) and different flowering varieties (Yanfu No. 6 and Nagafu No. 2). They all were affected by flowering-related circumstance and showed different expression level. Changes in response to these hormone or sugar related treatments indicated their potential involvement during apple flower induction. Taken together, our results provide rich resources for studying GRAS genes and their potential clues in genetic improvement of apple flowering, which enriches biological theories of GRAS genes in apple and their involvement in flower induction of fruit trees.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Cai Gao
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Ming Zhao
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Haiqin Wu
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Youmei Li
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Yawen Shen
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F UniversityYangling, China
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106
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Huang W, Peng S, Xian Z, Lin D, Hu G, Yang L, Ren M, Li Z. Overexpression of a tomato miR171 target gene SlGRAS24 impacts multiple agronomical traits via regulating gibberellin and auxin homeostasis. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:472-488. [PMID: 27712008 PMCID: PMC5362688 DOI: 10.1111/pbi.12646] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/21/2016] [Accepted: 09/29/2016] [Indexed: 05/20/2023]
Abstract
In Arabidopsis, the miR171-GRAS module has been clarified as key player in meristem maintenance. However, the knowledge about its role in fruit crops like tomato (Solanum lycopersicum) remains scarce. We previously identified tomato SlGRAS24 as a target gene of Sly-miR171. To study the role of this probable transcription factor, we generated transgenic tomato plants underexpressing SlGRAS24, overexpressing SlGRAS24, overexpressing Sly-miR171 and expressing β-glucuronidase (GUS) under the SlGRAS24 promoter (proSlGRAS24-GUS). Plants overexpressing SlGRAS24 (SlGRAS24-OE) had pleiotropic phenotypes associated with multiple agronomical traits including plant height, flowering time, leaf architecture, lateral branch number, root length, fruit set and development. Many GA/auxin-related genes were down-regulated and altered responsiveness to exogenous IAA/NAA or GA3 application was observed in SlGRAS24-OE seedlings. Moreover, compromised fruit set and development in SlGRAS24-OE was also observed. These newly identified phenotypes for SlGRAS24 homologs in tomato were later proved to be caused by impaired pollen sacs and fewer viable pollen grains. At anthesis, the comparative transcriptome results showed altered expression of genes involved in pollen development and hormone signalling. Taken together, our data demonstrate that SlGRAS24 participates in a series of developmental processes through modulating gibberellin and auxin signalling, which sheds new light on the involvement of hormone crosstalk in tomato development.
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Affiliation(s)
- Wei Huang
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Shiyuan Peng
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Zhiqiang Xian
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Dongbo Lin
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Guojian Hu
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Lu Yang
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Maozhi Ren
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
| | - Zhengguo Li
- Genetic Engineering Research CenterSchool of Life SciencesChongqing UniversityChongqingChina
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107
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Gao X, Cui Q, Cao QZ, Liu Q, He HB, Zhang DM, Jia GX. Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:753. [PMID: 28572808 PMCID: PMC5435993 DOI: 10.3389/fpls.2017.00753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 05/07/2023]
Abstract
MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.
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Affiliation(s)
- Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qi Cui
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qin-Zheng Cao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qiang Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Heng-Bin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Dong-Mei Zhang
- Shanghai Academy of Landscape Architecture Science and PlanningShanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghai, China
| | - Gui-Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
- *Correspondence: Gui-Xia Jia
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108
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Song C, Zhang D, Zheng L, Zhang J, Zhang B, Luo W, Li Y, Li G, Ma J, Han M. miRNA and Degradome Sequencing Reveal miRNA and Their Target Genes That May Mediate Shoot Growth in Spur Type Mutant "Yanfu 6". FRONTIERS IN PLANT SCIENCE 2017; 8:441. [PMID: 28424721 PMCID: PMC5371658 DOI: 10.3389/fpls.2017.00441] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/14/2017] [Indexed: 05/22/2023]
Abstract
The spur-type growth habit in apple trees is characterized by short internodes, increased number of fruiting spurs, and compact growth that promotes flowering and facilitates management practices, such as pruning. The molecular mechanisms responsible for regulating spur-type growth have not been elucidated. In the present study, miRNAs and the expression of their potential target genes were evaluated in shoot tips of "Nagafu 2" (CF) and spur-type bud mutation "Yanfu 6" (YF). A total of 700 mature miRNAs were identified, including 202 known apple miRNAs and 498 potential novel miRNA candidates. A comparison of miRNA expression in CF and YF revealed 135 differentially expressed genes, most of which were downregulated in YF. YF also had lower levels of GA, ZR, IAA, and ABA hormones, relative to CF. Exogenous applications of GA promoted YF shoot growth. Based on the obtained results, a regulatory network involving plant hormones, miRNA, and their potential target genes is proposed for the molecular mechanism regulating the growth of YF. miRNA164, miRNA166, miRNA171, and their potential targets, and associated plant hormones, appear to regulate shoot apical meristem (SAM) growth. miRNA159, miRNA167, miRNA396, and their potential targets, and associated plant hormones appear to regulate cell division and internode length. This study provides a foundation for further studies designed to elucidate the mechanism underlying spur-type apple architecture.
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Affiliation(s)
- Chunhui Song
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Dong Zhang
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Liwei Zheng
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Jie Zhang
- Tongchuan Fruit Tree Experiment StationTongchuan, China
| | - Baojuan Zhang
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Wenwen Luo
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Youmei Li
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Guangfang Li
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
| | - Mingyu Han
- College of Horticulture, Yangling Subsidiary Center Project of National Apple Improvement Center, Collaborative Innovation Center of Shaanxi Fruit Industry Development, Northwest A&F UniversityYangling, China
- *Correspondence: Mingyu Han
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109
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Atabekova AK, Pankratenko AV, Makarova SS, Lazareva EA, Owens RA, Solovyev AG, Morozov SY. Phylogenetic and functional analyses of a plant protein related to human B-cell receptor-associated proteins. Biochimie 2017; 132:28-37. [PMID: 27770627 DOI: 10.1016/j.biochi.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 10/17/2016] [Indexed: 12/20/2022]
Abstract
Human B-cell receptor-associated protein BAP31 (HsBAP31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. Plant orthologs of HsBAP31 termed 'plant BAP-like proteins' (PBL proteins) have thus far remained unstudied. Recently, the PBL protein from Nicotiana tabacum (NtPBL) was identified as an interactor of Nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of potato spindle tuber viroid (PSTVd) via the phloem. Here, we have compared the sequences of PBL proteins and studied the biochemical properties of NtPBL. Analysis of a number of fully sequenced plant genomes revealed that PBL-encoding genes represent a small multigene family with up to six members per genome. Two conserved motifs were identified in the C-terminal region of PBL proteins. The NtPBL C-terminal hydrophilic region (NtPBL-C) was expressed in bacterial cells, purified, and used for analysis of its RNA binding properties in vitro. In gel shift experiments, NtPBL-C was found to bind several tested RNAs, showing the most efficient binding to microRNA precursors (pre-miRNA) and less efficient interaction with PSTVd. Mutational analysis suggested that NtPBL-C has a composite RNA-binding site, with two conserved lysine residues in the most C-terminal protein region being involved in binding of pre-miRNA but not PSTVd RNA. Virus-mediated transient expression of NtPBL-C in plants resulted in stunting and leaf malformation, developmental abnormalities similar to those described previously for blockage of miRNA biogenesis/function. We hypothesize that the NtPBL protein represents a previously undiscovered component of the miRNA pathway.
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Affiliation(s)
- Anastasia K Atabekova
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - Anna V Pankratenko
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - Svetlana S Makarova
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - Ekaterina A Lazareva
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Andrey G Solovyev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119992, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia.
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Hendelman A, Kravchik M, Stav R, Frank W, Arazi T. Tomato HAIRY MERISTEM genes are involved in meristem maintenance and compound leaf morphogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6187-6200. [PMID: 27811085 PMCID: PMC5100029 DOI: 10.1093/jxb/erw388] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The HAIRY MERISTEM (HAM) genes function in meristem maintenance but play minor roles in the morphogenesis of a simple leaf that is determinate. Here, we functionally analyzed HAM genes in tomato and uncovered their involvement in compound leaf morphogenesis. Tomato encodes three HAM homologs, of which SlHAM and SlHAM2 (SlHAMs) are guided for cleavage by microRNA171 and are abundant in the shoot and floral meristems as well as in the compound leaf primordia. We found that SlHAMs silencing led to overproliferation of cells in the periphery of the meristems where SlHAM is localized. As in meristems, leaf-specific silencing of SlHAMs provoked overproliferation of meristematic cells in the organogenic compound leaf rachis. We further demonstrate that the meristematic cell overproliferation in both meristems and leaves was in part due to the misexpression of the stem cell regulator WUSCHEL, previously shown to be induced by cytokinin. Strikingly, reduction of cytokinin levels in SlHAMs-silenced leaves completely suppressed the overproliferation phenotype, suggesting a regulatory link between SlHAMs and cytokinin, a key hormone found to promote indeterminacy in meristems and leaves. Taken together, our data provide evidence that in addition to their conserved function in meristem maintenance, SlHAMs are also required for the proper morphogenesis of the compound leaf.
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Affiliation(s)
- Anat Hendelman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159 Rishon LeZion 7505101, Israel
| | - Michael Kravchik
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159 Rishon LeZion 7505101, Israel
| | - Ran Stav
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159 Rishon LeZion 7505101, Israel
| | - Wolfgang Frank
- Ludwig-Maximilians-Universität München, Department Biology I, Plant Molecular Cell Biology, LMU Biocenter, Grosshadernerstr. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159 Rishon LeZion 7505101, Israel
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111
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Li Z, Zhang X, Liu X, Zhao Y, Wang B, Zhang J. miRNA alterations are important mechanism in maize adaptations to low-phosphate environments. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:103-117. [PMID: 27717445 DOI: 10.1016/j.plantsci.2016.07.009] [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] [Received: 12/16/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 05/26/2023]
Abstract
Maize is a globally important crop, and a low phosphate (LP) supply frequently limits maize yields in many areas. microRNAs (miRNAs) play important roles in plant development and environmental adaptation. In this study, spatio-temporal miRNA transcript profiling and some of the target genes in the roots and leaves of the maize inbred line Q319 were analyzed in response to LP. Complex small RNA populations were detected after LP culture, and they displayed different patterns in the roots and leaves. Differentially expressed miRNAs can be grouped into 'early' miRNAs, which respond rapidly and are often non-specific to phosphate deficiency, and 'late' miRNAs, which alter the morphology, physiology or metabolism of plants upon prolonged phosphate deficiency. miR827 and miR399-mediated posttranscriptional pathway responses to phosphate availability were conserved and species-specific in maize. Abiotic stress-related miRNAs were engaged in interactions with different signaling and/or metabolic pathways. Auxin-related miRNAs and their targets' expression may be involved in root architecture modification and upland growth retardation in maize when subjected to LP. The changes that were found in the expression of miRNAs and their target genes suggested that miRNA regulation/alterations are pivotal mechanisms in maize adaptations to LP environments. A complex regulatory mechanism involving miRNAs in response to the LP environment is present in maize.
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Affiliation(s)
- Zhaoxia Li
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Xinrui Zhang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Xiuxia Liu
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Yajie Zhao
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Baomei Wang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Juren Zhang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
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112
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Li L, Xue M, Yi H. Uncovering microRNA-mediated response to SO2 stress in Arabidopsis thaliana by deep sequencing. JOURNAL OF HAZARDOUS MATERIALS 2016; 316:178-85. [PMID: 27232729 DOI: 10.1016/j.jhazmat.2016.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/24/2016] [Accepted: 05/04/2016] [Indexed: 05/20/2023]
Abstract
Sulfur dioxide (SO2) is a major air pollutant and has significant impacts on plants. MicroRNAs (miRNAs) are a class of gene expression regulators that play important roles in response to environmental stresses. In this study, deep sequencing was used for genome-wide identification of miRNAs and their expression profiles in response to SO2 stress in Arabidopsis thaliana shoots. A total of 27 conserved miRNAs and 5 novel miRNAs were found to be differentially expressed under SO2 stress. qRT-PCR analysis showed mostly negative correlation between miRNA accumulation and target gene mRNA abundance, suggesting regulatory roles of these miRNAs during SO2 exposure. The target genes of SO2-responsive miRNAs encode transcription factors and proteins that regulate auxin signaling and stress response, and the miRNAs-mediated suppression of these genes could improve plant resistance to SO2 stress. Promoter sequence analysis of genes encoding SO2-responsive miRNAs showed that stress-responsive and phytohormone-related cis-regulatory elements occurred frequently, providing additional evidence of the involvement of miRNAs in adaption to SO2 stress. This study represents a comprehensive expression profiling of SO2-responsive miRNAs in Arabidopsis and broads our perspective on the ubiquitous regulatory roles of miRNAs under stress conditions.
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Affiliation(s)
- Lihong Li
- School of Life Science, Shanxi University, Taiyuan, China
| | - Meizhao Xue
- School of Life Science, Shanxi University, Taiyuan, China
| | - Huilan Yi
- School of Life Science, Shanxi University, Taiyuan, China.
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113
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Couzigou JM, Combier JP. Plant microRNAs: key regulators of root architecture and biotic interactions. THE NEW PHYTOLOGIST 2016; 212:22-35. [PMID: 27292927 DOI: 10.1111/nph.14058] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/08/2016] [Indexed: 05/24/2023]
Abstract
Contents 22 I. 22 II. 24 III. 25 IV. 27 V. 29 VI. 10 31 References 32 SUMMARY: Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions. In this context, the roots have taken over nutritional aspects and the root system architecture can be modulated in response to nutrient availability or biotic interactions with soil microorganisms. This adaptability requires a fine tuning of gene expression. Indeed, root specification and development are highly complex processes requiring gene regulatory networks involved in hormonal regulations and cell identity. Among the different molecular partners governing root development, microRNAs (miRNAs) are key players for the fast regulation of gene expression. miRNAs are small RNAs involved in most developmental processes and are required for the normal growth of organisms, by the negative regulation of key genes, such as transcription factors and hormone receptors. Here, we review the known roles of miRNAs in root specification and development, from the embryonic roots to the establishment of root symbioses, highlighting the major roles of miRNAs in these processes.
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Affiliation(s)
- Jean-Malo Couzigou
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Jean-Philippe Combier
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
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114
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Chiang CP, Yim WC, Sun YH, Ohnishi M, Mimura T, Cushman JC, Yen HE. Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings. FRONTIERS IN PLANT SCIENCE 2016; 7:1143. [PMID: 27555850 PMCID: PMC4977306 DOI: 10.3389/fpls.2016.01143] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/18/2016] [Indexed: 05/03/2023]
Abstract
The halophyte Mesembryanthemum crystallinum (common or crystalline ice plant) is a useful model for studying molecular mechanisms of salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied and large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. A rapid root growth to a sudden increase in salinity was observed in ice plant seedlings. Using a fluorescent dye to detect Na(+), we found that ice plant roots respond to an increased flux of Na(+) by either secreting or storing Na(+) in specialized cells. High-throughput sequencing was used to identify small RNA profiles in 3-day-old seedlings treated with or without 200 mM NaCl. In total, 135 conserved miRNAs belonging to 21 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. After 6 h of salt stress, the expression of most mcr-miRNAs showed decreased relative abundance, whereas the expression of their corresponding target genes showed increased mRNA relative abundance. The cognate target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity are likely to be enhanced in roots under salt stress. The expression of eleven conserved miRNAs and two novel miRNAs were correlated reciprocally with predicted targets within hours after salt stress exposure. Several conserved miRNAs have been known to regulate root elongation, root apical meristem activity, and lateral root formation. Based upon the expression pattern of miRNA and target genes in combination with the observation of Na(+) distribution, ice plant likely responds to increased salinity by using Na(+) as an osmoticum for cell expansion and guard cell opening. Excessive Na(+) could either be secreted through the root epidermis or stored in specialized leaf epidermal cells. These responses are regulated in part at the miRNA-mediated post-transcriptional level.
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Affiliation(s)
- Chih-Pin Chiang
- Department of Life Sciences, National Chung Hsing UniversityTaichung, Taiwan
| | - Won C. Yim
- Department of Biochemistry and Molecular Biology, University of NevadaReno, NV, USA
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing UniversityTaichung, Taiwan
| | - Miwa Ohnishi
- Graduate School of Science, Kobe UniversityKobe, Japan
| | | | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of NevadaReno, NV, USA
| | - Hungchen E. Yen
- Department of Life Sciences, National Chung Hsing UniversityTaichung, Taiwan
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115
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Zhang H, Hu J, Qian Q, Chen H, Jin J, Ding Y. Small RNA Profiles of the Rice PTGMS Line Wuxiang S Reveal miRNAs Involved in Fertility Transition. FRONTIERS IN PLANT SCIENCE 2016; 7:514. [PMID: 27148335 PMCID: PMC4837141 DOI: 10.3389/fpls.2016.00514] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/01/2016] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) play key roles in the regulation of plant growth and developmental processes. In this study, RNA-seq was used to examine the expression profiles of miRNAs in a novel, photo-thermosensitive genic male sterile (PTGMS) rice line, Wuxiang S (WXS), during fertility transition. A total of 497 known miRNAs and 273 novel miRNAs were identified. In a differential expression analysis, 26 miRNAs exhibited significant differential expression between WXS (Sterile, S) and WXS (Fertile, F). Some of these miRNAs were validated by quantitative real-time PCR. Among these miRNAs, 11 showed decreased expression levels, and 15 showed increased expression levels in WXS (S) compared to WXS (F). Some of these miRNAs, such as osa-miR156a-j, osa-miR164d, and osa-miR528, were shown to be negatively correlated with their targets. These targets have previously been reported to be related to pollen development and male sterility, suggesting that these miRNAs may be involved in the regulation of pollen development in the rice PTGMS line WXS. Furthermore, miRNA-mediated editing events were also observed. In this study, a possible model for the control of signaling pathways during the process of fertility transition in the rice PTGMS line WXS by miRNAs was developed. These findings contribute to our understanding of the roles of miRNAs during anther development in PTGMS lines in rice.
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Affiliation(s)
| | | | | | | | | | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan UniversityWuhan, China
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116
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Sun X, Xie Z, Zhang C, Mu Q, Wu W, Wang B, Fang J. A characterization of grapevine of GRAS domain transcription factor gene family. Funct Integr Genomics 2016; 16:347-63. [PMID: 26842940 DOI: 10.1007/s10142-016-0479-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/21/2015] [Accepted: 01/19/2016] [Indexed: 11/30/2022]
Abstract
GRAS domain genes are a group of important plant-specific transcription factors that have been reported to be involved in plant development. In order to know the roles of GRAS genes in grapevine, a widely cultivated fruit crop, the study on grapevine GRAS (VvGRAS) was carried out, and from which, 43 were identified from 12× assemble grapevine genomic sequences. Further, the genomic structures, synteny, phylogeny, expression profiles in different tissues of these genes, and their roles in response to stress were investigated. Among the genes, two potential target genes (VvSCL15 and VvSCL22) for VvmiR171 were experimentally verified by PPM-RACE and RLM-RACE, in that not only the cleavage sites of miR171 on the target mRNA were mapped but also the cleaved fragments and their expressing patterns were detected. Transgenic Arabidopsis plants over expression VvSCL15 showed lower tolerance to drought and salt treatments.
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Affiliation(s)
- Xin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Zhengqiang Xie
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.,Department of Agronomy and Horticulture, Jiangsu Polytechnic College of Agriculture and Forestry, Jurong, 212400, Jiangsu Province, People's Republic of China
| | - Cheng Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Qian Mu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Weimin Wu
- Institute of Horticulture, Jiangsu Academy of Agriculture Sciences, Nanjing, 210014, Jiangsu Province, People's Republic of China
| | - Baoju Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.
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Khatabi B, Arikit S, Xia R, Winter S, Oumar D, Mongomake K, Meyers BC, Fondong VN. High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics 2016; 17:85. [PMID: 26822616 PMCID: PMC4730657 DOI: 10.1186/s12864-016-2391-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 01/13/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research.
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Affiliation(s)
- Behnam Khatabi
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.
| | - Rui Xia
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Doungous Oumar
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Ekona Research Centre, Southwest, Cameroon.
| | - Kone Mongomake
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Université Nangui Abrogoua, Abidjan, Côte d'Ivoire.
| | - Blake C Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Vincent N Fondong
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
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118
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Guo R, Chen X, Lin Y, Xu X, Thu MK, Lai Z. Identification of Novel and Conserved miRNAs in Leaves of In vitro Grown Citrus reticulata "Lugan" Plantlets by Solexa Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 6:1212. [PMID: 26779240 PMCID: PMC4705231 DOI: 10.3389/fpls.2015.01212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/16/2015] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in plant development, but the roles in the in vitro plant development are unknown. Leaves of ponkan plantlets derived from mature embryos at in vitro culture conditions were used to sequence small RNA fraction via Solexa sequencing, and the miRNAs expression was analyzed. The results showed that there were 3,065,625 unique sequences in ponkan, of which 0.79% were miRNAs. The RNA sequences with lengths of 18-25 nt derived from the library were analyzed, leading to the identification of 224 known miRNAs, of which the most abundant were miR157, miR156, and miR166. Three hundred and fifty-eight novel miRNA candidates were also identified, and the number of reads of ponkan novel miRNAs varied from 5 to 168,273. The expression of the most known miRNAs obtained was at low levels, which varied from 5 to 4,946,356. To better understand the role of miRNAs during the preservation of ponkan in vitro plantlet, the expression patterns of cre-miR156a/159b/160a/166a/167a/168a/171/398b were validated by quantitative real-time PCR (qPCR). The results showed that not only the development-associated miRNAs, e.g., cre-miR156/159/166/396, expressed highly at the early preservation period in the in vitro ponkan plantlet leaves but also the stress-related miRNAs, e.g., cre-miR171 and cre-miR398b, expressed highly at the same time. The expression levels of most tested miRNAs were found to decrease after 6 months and the amounts of these miRNAs were kept at low levels at 18 months. After analyzing the expression level of their targets during the reservation of the ponkan in vitro plantlet, development-associated cre-ARF6 and stress-related cre-CSD modules exhibited negative correlation with miR167 and miR398, respectively, indicating an involvement of the miRNAs in the in vitro development of ponkan and function in the conservation of ponkan germplasm.
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Affiliation(s)
- Rongfang Guo
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xiaodong Chen
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yuling Lin
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xuhan Xu
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institut de la Recherche Interdisciplinaire de ToulouseToulouse, France
| | - Min Kyaw Thu
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhongxiong Lai
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
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119
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Kobayashi K, Masuda T. Transcriptional Regulation of Tetrapyrrole Biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1811. [PMID: 27990150 PMCID: PMC5130987 DOI: 10.3389/fpls.2016.01811] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/16/2016] [Indexed: 05/17/2023]
Abstract
Biosynthesis of chlorophyll (Chl) involves many enzymatic reactions that share several first steps for biosynthesis of other tetrapyrroles such as heme, siroheme, and phycobilins. Chl allows photosynthetic organisms to capture light energy for photosynthesis but with simultaneous threat of photooxidative damage to cells. To prevent photodamage by Chl and its highly photoreactive intermediates, photosynthetic organisms have developed multiple levels of regulatory mechanisms to coordinate tetrapyrrole biosynthesis (TPB) with the formation of photosynthetic and photoprotective systems and to fine-tune the metabolic flow with the varying needs of Chl and other tetrapyrroles under various developmental and environmental conditions. Among a wide range of regulatory mechanisms of TPB, this review summarizes transcriptional regulation of TPB genes during plant development, with focusing on several transcription factors characterized in Arabidopsis thaliana. Key TPB genes are tightly coexpressed with other photosynthesis-associated nuclear genes and are induced by light, oscillate in a diurnal and circadian manner, are coordinated with developmental and nutritional status, and are strongly downregulated in response to arrested chloroplast biogenesis. LONG HYPOCOTYL 5 and PHYTOCHROME-INTERACTING FACTORs, which are positive and negative transcription factors with a wide range of light signaling, respectively, target many TPB genes for light and circadian regulation. GOLDEN2-LIKE transcription factors directly regulate key TPB genes to fine-tune the formation of the photosynthetic apparatus with chloroplast functionality. Some transcription factors such as FAR-RED ELONGATED HYPOCOTYL3, REVEILLE1, and scarecrow-like transcription factors may directly regulate some specific TPB genes, whereas other factors such as GATA transcription factors are likely to regulate TPB genes in an indirect manner. Comprehensive transcriptional analyses of TPB genes and detailed characterization of key transcriptional regulators help us obtain a whole picture of transcriptional control of TPB in response to environmental and endogenous cues.
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120
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Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:353. [PMID: 27065316 PMCID: PMC4811876 DOI: 10.3389/fpls.2016.00353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | | | - Rita T. Teixeira
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
| | - Jose M. Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
- Instituto de Tecnologia de Química Biológica, Biotecnologia de Células VegetaisOeiras, Portugal
- *Correspondence: Ana M. Fortes
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121
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Cheah BH, Nadarajah K, Divate MD, Wickneswari R. Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage. BMC Genomics 2015; 16:692. [PMID: 26369665 PMCID: PMC4570225 DOI: 10.1186/s12864-015-1851-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
Background Developing drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success of rice molecular breeding programmes. microRNAs have received tremendous attention recently due to its importance in negative regulation. In plants, apart from regulating developmental and physiological processes, microRNAs have also been associated with different biotic and abiotic stresses. Hence here we chose to analyze the differential expression profiles of microRNAs in three drought treated rice varieties: Vandana (drought-tolerant), Aday Sel (drought-tolerant) and IR64 (drought-susceptible) in greenhouse conditions via high-throughput sequencing. Results Twenty-six novel microRNA candidates involved in the regulation of diverse biological processes were identified based on the detection of miRNA*. Out of their 110 predicted targets, we confirmed 16 targets from 5 novel microRNA candidates. In the differential expression analysis, mature microRNA members from 49 families of known Oryza sativa microRNA were differentially expressed in leaf and stem respectively with over 28 families having at least a similar mature microRNA member commonly found to be differentially expressed between both tissues. Via the sequence profiling data of leaf samples, we identified osa-miR397a/b, osa-miR398b, osa-miR408-5p and osa-miR528-5p as being down-regulated in two drought-tolerant rice varieties and up-regulated in the drought-susceptible variety. These microRNAs are known to be involved in regulating starch metabolism, antioxidant defence, respiration and photosynthesis. A wide range of biological processes were found to be regulated by the target genes of all the identified differentially expressed microRNAs between both tissues, namely root development (5.3–5.7 %), cell transport (13.2–18.4 %), response to stress (10.5–11.3 %), lignin catabolic process (3.8–5.3 %), metabolic processes (32.1–39.5 %), oxidation-reduction process (9.4–13.2 %) and DNA replication (5.7–7.9 %). The predicted target genes of osa-miR166e-3p, osa-miR166h-5p*, osa-miR169r-3p* and osa-miR397a/b were found to be annotated to several of the aforementioned biological processes. Conclusions The experimental design of this study, which features rice varieties with different drought tolerance and tissue specificity (leaf and stem), has provided new microRNA profiling information. The potentially regulatory importance of the microRNA genes mentioned above and their target genes would require further functional analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1851-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boon Huat Cheah
- School of Biotechnology and Bioscience, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Kalaivani Nadarajah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Mayur Dashrath Divate
- Bionivid Technology [P] Ltd., 401-4AB Cross, 1st Main, NGEF East Kasturi Nagar, Bangalore, 560043, India.
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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122
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Pan L, Wang X, Jin J, Yu X, Hu J. Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps.1500046. [PMID: 26421251 PMCID: PMC4578376 DOI: 10.3732/apps.1500046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/12/2015] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Sacred lotus (Nelumbo nucifera) is a perennial aquatic herbaceous plant of ecological, ornamental, and economic importance. MicroRNAs (miRNAs) play an important role in plant development. However, reports of miRNAs and their role in sacred lotus have been limited. METHODS Using the homology search of known miRNAs with genome and transcriptome contig sequences, we employed a pipeline to identify miRNAs in N. nucifera. We also predicted the targets of these miRNAs. RESULTS We found 106 conserved miRNAs in N. nucifera, and 456 of their miRNA targets were annotated. Quantitative real-time PCR (qRT-PCR) analysis revealed the different expression levels of the 10 selected conserved miRNAs in tissues of young leaves, stems, and flowers of N. nucifera. Negative correlation of expression level between five miRNAs and their target genes was also revealed. DISCUSSION Combining bioinformatics and experiment analysis, we identified the miRNAs in N. nucifera. The results can be used as a workbench for further investigation of the roles of miRNAs in N. nucifera.
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Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Xiaolu Yu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Jihong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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123
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Huang W, Xian Z, Kang X, Tang N, Li Z. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC PLANT BIOLOGY 2015; 15:209. [PMID: 26302743 PMCID: PMC4549011 DOI: 10.1186/s12870-015-0590-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/11/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits. RESULTS In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated. CONCLUSIONS This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
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Affiliation(s)
- Wei Huang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhiqiang Xian
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Xia Kang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Ning Tang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
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Zhu X, Leng X, Sun X, Mu Q, Wang B, Li X, Wang C, Fang J. Discovery of Conservation and Diversification of miR171 Genes by Phylogenetic Analysis based on Global Genomes. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0076. [PMID: 33228325 DOI: 10.3835/plantgenome2014.10.0076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/03/2015] [Indexed: 05/24/2023]
Abstract
The microRNA171 (miR171) family is widely distributed and highly conserved in a range of species and plays critical roles in regulating plant growth and development through repressing expression of SCARECROW-LIKE (SCL) transcription factors. However, information on the evolutionary conservation and functional diversification of the miRNA171 family members remains scanty. We reconstructed the phylogenetic relationships among miR171 precursor and mature sequences so as to investigate the extent and degree of evolutionary conservation of miR171 in Arabidopsis thaliana (L.) Heynh. (ath), grape (Vitis vinifera L.) (vvi), poplar (Populus trichocarpa Torr. & A.Gray ex Hook.) (ptc), and rice (Oryza sativa L.) (osa). Despite strong conservation of over 80%, some mature miR171 sequences, such as ptc-miR171j -l, and -m and osa-miR171g, -h, and -i, have undergone critical sequence variation, leading to functional diversification, since they target non-SCL gene transcript(s). Phylogenetic analyses revealed a combination of old ancestral relationships and recent lineage-specific diversification in the miR171 family within the four model plants. The cis-regulatory motifs on the upstream promoter sequences of miR171 genes were highly divergent and shared some similar elements, indicating their possible contribution to the functional variation observed within the miR171 family. This study will buttress our understanding of the functional differentiation of miRNAs and the relationships of miRNA-target pairs based on the evolutionary history of miRNA genes.
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Affiliation(s)
- Xudong Zhu
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Xin Sun
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Qian Mu
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Baoju Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Xiaopeng Li
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, Weigang 1 Hao, China
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125
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Gao MJ, Li X, Huang J, Gropp GM, Gjetvaj B, Lindsay DL, Wei S, Coutu C, Chen Z, Wan XC, Hannoufa A, Lydiate DJ, Gruber MY, Chen ZJ, Hegedus DD. SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme. Nat Commun 2015; 6:7243. [PMID: 26129778 PMCID: PMC4507008 DOI: 10.1038/ncomms8243] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/22/2015] [Indexed: 01/20/2023] Open
Abstract
Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a histone deacetylase19 (HDA19)-associated regulator, scarecrow-like15 (SCL15), is essential for repressing the seed maturation programme in vegetative tissues. SCL15 is expressed in and GFP-tagged SCL15 predominantly localizes to, the vascular bundles particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds. In scl15 seedlings, many genes involved in seed maturation are markedly derepressed with concomitant accumulation of seed 12S globulin; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci. SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies reveal that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings.
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Affiliation(s)
- Ming-Jun Gao
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Xiang Li
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Jun Huang
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Gordon M Gropp
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Branimir Gjetvaj
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Donna L Lindsay
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Shu Wei
- Key Laboratory of Tea Biochemistry and Biotechnology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Zhixiang Chen
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Xiao-Chun Wan
- Key Laboratory of Tea Biochemistry and Biotechnology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, Canada N5V 4T3
| | - Derek J Lydiate
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Margaret Y Gruber
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
| | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas 78712, USA
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
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126
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Das A, Chaudhury S, Kalita MC, Mondal TK. In silico identification, characterization and expression analysis of miRNAs in Cannabis sativa L. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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127
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Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors. PLoS One 2015; 10:e0125833. [PMID: 26023934 PMCID: PMC4449180 DOI: 10.1371/journal.pone.0125833] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/25/2015] [Indexed: 12/20/2022] Open
Abstract
Phase change from vegetative to reproductive development is one of the critical developmental steps in plants, and it is regulated by both environmental and endogenous factors. The maintenance of shoot apical meristem (SAM) identity, miRNAs and flowering integrators are involved in this phase change process. Here, we report that the miRNA osa-miR171c targets four GRAS (GAI-RGA-SCR) plant-specific transcription factors (OsHAM1, OsHAM2, OsHAM3, and OsHAM4) to control the floral transition and maintenance of SAM indeterminacy in rice (Oryza sativa). We characterized a rice T-DNA insertion delayed heading (dh) mutant, where the expression of OsMIR171c gene is up-regulated. This mutant showed pleiotropic phenotypic defects, including especially prolonged vegetative phase, delayed heading date, and bigger shoot apex. Parallel expression analysis showed that osa-miR171c controlled the expression change of four OsHAMs in the shoot apex during floral transition, and responded to light. In the dh mutant, the expression of the juvenile-adult phase change negative regulator osa-miR156 was up-regulated, expression of the flowering integrators Hd3a and RFT1 was inhibited, and expression of FON4 negative regulators involved in the maintenance of SAM indeterminacy was also inhibited. From these data, we propose that the inhibition of osa-miR171c-mediated OsHAM transcription factors regulates the phase transition from vegetative to reproductive development by maintaining SAM indeterminacy and inhibiting flowering integrators.
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128
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Ye X, Song T, Liu C, Feng H, Liu Z. Identification of fruit related microRNAs in cucumber (Cucumis sativus L.) using high-throughput sequencing technology. Hereditas 2015; 151:220-8. [PMID: 25588308 DOI: 10.1111/hrd2.00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/09/2014] [Indexed: 12/01/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 21 nt noncoding RNAs that influence the phenotypes of different species through the post-transcriptional regulation of gene expression. Although many miRNAs have been identified in a few model plants, less is known about miRNAs specific to cucumber (Cucumis sativus L.). In this study, two libraries of cucumber RNA, one based on fruit samples and another based on mixed samples from leaves, stems, and roots, were prepared for deep-sequencing. A total of 110 sequences were matched to known miRNAs in 47 families, while 56 sequences in 46 families are newly identified in cucumber. Of these, 77 known and 44 new miRNAs were differentially expressed, with a fold-change of at least 2 and p-value < 0.05. In addition, we predicted the potential targets of known and new miRNAs. The identification and characterization of known and new miRNAs will enable us to better understand the role of these miRNAs in the formation of cucumber fruit.
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Affiliation(s)
- Xueling Ye
- College of Horticulture, Shenyang Agriculture University, Shenyang, China
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129
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Teotia S, Tang G. To bloom or not to bloom: role of microRNAs in plant flowering. MOLECULAR PLANT 2015; 8:359-77. [PMID: 25737467 DOI: 10.1016/j.molp.2014.12.018] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/01/2014] [Accepted: 12/15/2014] [Indexed: 05/02/2023]
Abstract
During the course of their life cycles, plants undergo various morphological and physiological changes underlying juvenile-to-adult and adult-to-flowering phase transitions. To flower or not to flower is a key step of plasticity of a plant toward the start of its new life cycle. In addition to the previously revealed intrinsic genetic programs, exogenous cues, and endogenous cues, a class of small non-coding RNAs, microRNAs (miRNAs), plays a key role in plants making the decision to flower by integrating into the known flowering pathways. This review highlights the age-dependent flowering pathway with a focus on a number of timing miRNAs in determining such a key process. The contributions of other miRNAs which exist mainly outside the age pathway are also discussed. Approaches to study the flowering-determining miRNAs, their interactions, and applications are presented.
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Affiliation(s)
- Sachin Teotia
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India; Department of Biological Sciences and Biotechnology Research Center (BRC), Michigan Technological University, Houghton, MI 49931, USA
| | - Guiliang Tang
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences and Biotechnology Research Center (BRC), Michigan Technological University, Houghton, MI 49931, USA.
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130
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Gentile A, Dias LI, Mattos RS, Ferreira TH, Menossi M. MicroRNAs and drought responses in sugarcane. FRONTIERS IN PLANT SCIENCE 2015; 6:58. [PMID: 25755657 PMCID: PMC4337329 DOI: 10.3389/fpls.2015.00058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 01/22/2015] [Indexed: 05/03/2023]
Abstract
There is a growing demand for renewable energy, and sugarcane is a promising bioenergy crop. In Brazil, the largest sugarcane producer in the world, sugarcane plantations are expanding into areas where severe droughts are common. Recent evidence has highlighted the role of miRNAs in regulating drought responses in several species, including sugarcane. This review summarizes the data from miRNA expression profiles observed in a wide array of experimental conditions using different sugarcane cultivars that differ in their tolerance to drought. We uncovered a complex regulation of sugarcane miRNAs in response to drought and discussed these data with the miRNA profiles observed in other plant species. The predicted miRNA targets revealed different transcription factors, proteins involved in tolerance to oxidative stress, cell modification, as well as hormone signaling. Some of these proteins might regulate sugarcane responses to drought, such as reduction of internode growth and shoot branching and increased leaf senescence. A better understanding on the regulatory network from miRNAs and their targets under drought stress has a great potential to contribute to sugarcane improvement, either as molecular markers as well as by using biotechnological approaches.
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Affiliation(s)
| | | | | | | | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, São Paulo, Brazil
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131
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Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 2015; 517:377-80. [PMID: 25363783 PMCID: PMC4297503 DOI: 10.1038/nature13853] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 09/10/2014] [Indexed: 11/08/2022]
Abstract
Plant stem cells in the shoot apical meristem (SAM) and root apical meristem are necessary for postembryonic development of aboveground tissues and roots, respectively, while secondary vascular stem cells sustain vascular development. WUSCHEL (WUS), a homeodomain transcription factor expressed in the rib meristem of the Arabidopsis SAM, is a key regulatory factor controlling SAM stem cell populations, and is thought to establish the shoot stem cell niche through a feedback circuit involving the CLAVATA3 (CLV3) peptide signalling pathway. WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the root quiescent centre, defines quiescent centre identity and functions interchangeably with WUS in the control of shoot and root stem cell niches. WOX4, expressed in Arabidopsis procambial cells, defines the vascular stem cell niche. WUS/WOX family proteins are evolutionarily and functionally conserved throughout the plant kingdom and emerge as key actors in the specification and maintenance of stem cells within all meristems. However, the nature of the genetic regime in stem cell niches that centre on WOX gene function has been elusive, and molecular links underlying conserved WUS/WOX function in stem cell niches remain unknown. Here we demonstrate that the Arabidopsis HAIRY MERISTEM (HAM) family of transcription regulators act as conserved interacting cofactors with WUS/WOX proteins. HAM and WUS share common targets in vivo and their physical interaction is important in driving downstream transcriptional programs and in promoting shoot stem cell proliferation. Differences in the overlapping expression patterns of WOX and HAM family members underlie the formation of diverse stem cell niche locations, and the HAM family is essential for all of these stem cell niches. These findings establish a new framework for the control of stem cell production during plant development.
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Affiliation(s)
- Yun Zhou
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Xing Liu
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Eric M. Engstrom
- Biology Department, College of William and Mary, Williamsburg, Virginia 23187–8795, United States
| | - Zachary L. Nimchuk
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Jose L. Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul T. Tarr
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - An Yan
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Steve A. Kay
- University of Southern California, Molecular and Computational Biology, Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Science, Los Angeles, CA 90089, United States
| | - Elliot M. Meyerowitz
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
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132
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Fang J, Sun X. A method for validating microRNAs in plants by miR-RACE. Methods Mol Biol 2015; 1287:139-145. [PMID: 25740362 DOI: 10.1007/978-1-4939-2453-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
miRNA prediction algorithms often fail to predict the accurate location of the mature miRNA in a precursor sequence with nucleotide-level precision. miRNAs-rapid amplification of cDNA ends (miR-RACE) is an efficient method to determine the precise sequences of computationally predicted microRNAs (miRNAs). miR-RACE includes the following steps: miRNA-enriched library preparation, two specific 5'- and 3'-miRNA RACE (miR-RACE) PCR reactions, and sequence-directed cloning. The most challenging step is the two gene-specific primers designed for the two RACE reactions. The miR-RACE protocol is rapid and can be executed and completed in 2-3 days.
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Affiliation(s)
- Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China,
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Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R. NPK macronutrients and microRNA homeostasis. FRONTIERS IN PLANT SCIENCE 2015; 6:451. [PMID: 26136763 PMCID: PMC4468412 DOI: 10.3389/fpls.2015.00451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/02/2015] [Indexed: 05/02/2023]
Abstract
Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.
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Affiliation(s)
- Franceli R. Kulcheski
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
| | - Régis Côrrea
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Igor A. Gomes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Júlio C. de Lima
- Laboratório de Genética Molecular, Instituto de Ciências Biológicas, Universidade de Passo Fundo, Passo FundoBrazil
| | - Rogerio Margis
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
- *Correspondence: Rogerio Margis, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Setor IV, Prédio 43431, Sala 213, Porto Alegre, RS, CEP, Brazil
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134
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Sun Z, He Y, Li J, Wang X, Chen J. Genome-Wide Characterization of Rice Black Streaked Dwarf Virus-Responsive MicroRNAs in Rice Leaves and Roots by Small RNA and Degradome Sequencing. ACTA ACUST UNITED AC 2014; 56:688-99. [DOI: 10.1093/pcp/pcu213] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 12/16/2014] [Indexed: 11/14/2022]
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135
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Xian Z, Huang W, Yang Y, Tang N, Zhang C, Ren M, Li Z. miR168 influences phase transition, leaf epinasty, and fruit development via SlAGO1s in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6655-66. [PMID: 25378580 DOI: 10.1093/jxb/eru387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In Arabidopsis thaliana, Argonaute1 (AGO1) interacts with miR168 to modulate the small RNA regulatory pathway. However, the underlying mechanism of regulation and relationship between AGO1 and miR168 is poorly understood in the cash crop Solanum lycopersicum (tomato). We previously found that SlAGO1A and SlAGO1B were cleaved by miR168 in tomato. In this study, we show that SlAGO1A and SlAGO1B accumulate in miR168-sponge transgenic plants, and that expression of miR168-resistant SlAGO1A (4m-SlAGO1A) and SlAGO1B (4m-SlAGO1B) in tomato results in a series of defects affecting growth rate, floral timing, leaves, and fruit. Accumulation of miR156 was found when 4m-SlAGO1A was at an early developmental stage compared to the wild type and original SlAGO1A transgenic plants, and miR172 was highly expressed in adult 4m-SlAGO1A compared to the controls. In addition, the expression of multiple small RNAs was altered in 4m-SlAGO1A. Taken together, our data provide novel insights into the interaction between SlAGO1s and miR168 in determining growth rate, phase change, leaf epinasty, fruit initiation and expansion, and other developmental processes in tomato.
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Affiliation(s)
- Zhiqiang Xian
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Wei Huang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yingwu Yang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Ning Tang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Chao Zhang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Maozhi Ren
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zhengguo Li
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
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136
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Sun X, Zhang Y, Zhu X, Korir NK, Tao R, Wang C, Fang J. Advances in identification and validation of plant microRNAs and their target genes. PHYSIOLOGIA PLANTARUM 2014; 152:203-18. [PMID: 24641625 DOI: 10.1111/ppl.12191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 01/19/2014] [Accepted: 02/12/2014] [Indexed: 05/27/2023]
Abstract
Developments in the field of molecular biology and genetics, such as microarray, gene transfer and discovery of small regulatory RNAs, have led to significant advances in plant biotechnology. Among the small RNAs, microRNAs (miRNAs) have elicited much interest as key post-transcriptional regulators in eukaryotic gene expression. Advances in genome and transcriptome sequencing of plants have facilitated the generation of a huge wealth of sequence information that can find much use in the discovery of novel miRNAs and their target genes. In this review, we present an overview of the developments in the strategies and methods used to identify and study miRNAs, their target genes and the mechanisms by which these miRNAs interact with their target genes since the discovery of the first miRNA. The approaches discussed include both reverse and forward genetics. We observed that despite the availability of advanced methods, certain limitations ranging from the cost of materials, equipment and personnel to the availability of genome sequences for many plant species present a number of challenges for the development and utilization of modern scientific methods for the elucidation and development of miRNAs in many important plant species.
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Affiliation(s)
- Xin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, PR China
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137
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Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet 2014; 10:e1004519. [PMID: 25101599 PMCID: PMC4125095 DOI: 10.1371/journal.pgen.1004519] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/02/2014] [Indexed: 11/29/2022] Open
Abstract
An extraordinarily precise regulation of chlorophyll biosynthesis is essential for plant growth and development. However, our knowledge on the complex regulatory mechanisms of chlorophyll biosynthesis is very limited. Previous studies have demonstrated that miR171-targeted scarecrow-like proteins (SCL6/22/27) negatively regulate chlorophyll biosynthesis via an unknown mechanism. Here we showed that SCLs inhibit the expression of the key gene encoding protochlorophyllide oxidoreductase (POR) in light-grown plants, but have no significant effect on protochlorophyllide biosynthesis in etiolated seedlings. Histochemical analysis of β-glucuronidase (GUS) activity in transgenic plants expressing pSCL27::rSCL27-GUS revealed that SCL27-GUS accumulates at high levels and suppresses chlorophyll biosynthesis at the leaf basal proliferation region during leaf development. Transient gene expression assays showed that the promoter activity of PORC is indeed regulated by SCL27. Consistently, chromatin immunoprecipitation and quantitative PCR assays showed that SCL27 binds to the promoter region of PORC in vivo. An electrophoretic mobility shift assay revealed that SCL27 is directly interacted with G(A/G)(A/T)AA(A/T)GT cis-elements of the PORC promoter. Furthermore, genetic analysis showed that gibberellin (GA)-regulated chlorophyll biosynthesis is mediated, at least in part, by SCLs. We demonstrated that SCL27 interacts with DELLA proteins in vitro and in vivo by yeast-two-hybrid and coimmunoprecipitation analysis and found that their interaction reduces the binding activity of SCL27 to the PORC promoter. Additionally, we showed that SCL27 activates MIR171 gene expression, forming a feedback regulatory loop. Taken together, our data suggest that the miR171-SCL module is critical for mediating GA-DELLA signaling in the coordinate regulation of chlorophyll biosynthesis and leaf growth in light. Chlorophyll biosynthesis is essential for plant growth and development. To date, the regulatory mechanisms of chlorophyll biosynthesis have been well understood only in dark conditions. Previous reports showed that miR171-targeted SCL6/22/27 proteins were involved in chlorophyll biosynthesis. However, the molecular mechanism of SCL action remains unclear. In this study, we found that SCLs negatively regulated chlorophyll biosynthesis though suppressing the expression of the key gene PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR). SCL27 is highly expressed at the basal cell proliferation region of young leaves, suggesting an important role of SCLs in inhibiting chloroplast development before cell expansion. In addition, GT-cis elements were required for SCL27 directly binding to the PORC promoter. Furthermore, we showed that SCLs mediated GA-regulated chlorophyll biosynthesis through direct interaction with DELLA proteins. The interaction between SCLs and DELLAs reduced the DNA binding activity of SCL27. Our uncovered GA-DELLA-SCL module and its DNA binding targets provide new insights into molecular mechanisms by which chlorophyll biosynthesis and cell proliferation are coordinately regulated during leaf development in response to developmental and environmental cues.
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138
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Xue XY, Zhao B, Chao LM, Chen DY, Cui WR, Mao YB, Wang LJ, Chen XY. Interaction between two timing microRNAs controls trichome distribution in Arabidopsis. PLoS Genet 2014; 10:e1004266. [PMID: 24699192 PMCID: PMC3974651 DOI: 10.1371/journal.pgen.1004266] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/11/2014] [Indexed: 12/18/2022] Open
Abstract
The miR156-targeted squamosa promoter binding protein like (SPL) transcription factors function as an endogenous age cue in regulating plant phase transition and phase-dependent morphogenesis, but the control of SPL output remains poorly understood. In Arabidopsis thaliana the spatial pattern of trichome is a hallmark of phase transition and governed by SPLs. Here, by dissecting the regulatory network controlling trichome formation on stem, we show that the miR171-targeted lost meristems 1 (LOM1), LOM2 and LOM3, encoding GRAS family members previously known to maintain meristem cell polarity, are involved in regulating the SPL activity. Reduced LOM abundance by overexpression of miR171 led to decreased trichome density on stems and floral organs, and conversely, constitutive expression of the miR171-resistant LOM (rLOM) genes promoted trichome production, indicating that LOMs enhance trichome initiation at reproductive stage. Genetic analysis demonstrated LOMs shaping trichome distribution is dependent on SPLs, which positively regulate trichome repressor genes TRICHOMELESS 1 (TCL1) and TRIPTYCHON (TRY). Physical interaction between the N-terminus of LOMs and SPLs underpins the repression of SPL activity. Importantly, other growth and developmental events, such as flowering, are also modulated by LOM-SPL interaction, indicating a broad effect of the LOM-SPL interplay. Furthermore, we provide evidence that MIR171 gene expression is regulated by its targeted LOMs, forming a homeostatic feedback loop. Our data uncover an antagonistic interplay between the two timing miRNAs in controlling plant growth, phase transition and morphogenesis through direct interaction of their targets.
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Affiliation(s)
- Xue-Yi Xue
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zhao
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu-Men Chao
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian-Yang Chen
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Rui Cui
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Bo Mao
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
- * E-mail:
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139
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Jia KP, Luo Q, He SB, Lu XD, Yang HQ. Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways in Arabidopsis. MOLECULAR PLANT 2014; 7:528-40. [PMID: 24126495 DOI: 10.1093/mp/sst093] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Seedling development including hypocotyl elongation is a critical phase in the plant life cycle. Light regulation of hypocotyl elongation is primarily mediated through the blue light photoreceptor cryptochrome and red/far-red light photoreceptor phytochrome signaling pathways, comprising regulators including COP1, HY5, and phytochrome-interacting factors (PIFs). The novel phytohormones, strigolactones, also participate in regulating hypocotyl growth. However, how strigolactone coordinates with light and photoreceptors in the regulation of hypocotyl elongation is largely unclear. Here, we demonstrate that strigolactone inhibition of hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways. The photoreceptor mutants cry1 cry2, phyA, and phyB are hyposensitive to strigolactone analog GR24 under the respective monochromatic light conditions, while cop1 and pif1 pif3 pif4 pif5 (pifq) quadruple mutants are hypersensitive to GR24 in darkness. Genetic studies indicate that the enhanced responsiveness of cop1 to GR24 is dependent on HY5 and MAX2, while that of pifq is independent of HY5. Further studies demonstrate that GR24 constitutively up-regulates HY5 expression in the dark and light, whereas GR24-promoted HY5 protein accumulation is light- and cryptochrome and phytochrome photoreceptor-dependent. These results suggest that the light dependency of strigolactone regulation of hypocotyl elongation is likely mediated through MAX2-dependent promotion of HY5 expression, light-dependent accumulation of HY5, and PIF-regulated components.
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Affiliation(s)
- Kun-Peng Jia
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agricultural and Biological Sciences, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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140
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Li Z, Czarnecki O, Chourey K, Yang J, Tuskan GA, Hurst GB, Pan C, Chen JG. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis. J Proteome Res 2014; 13:1359-72. [DOI: 10.1021/pr400925t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhou Li
- Graduate
School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, F337 Walters Life Science, Knoxville, Tennessee 37996, United States
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141
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Huang X, Ding J, Effgen S, Turck F, Koornneef M. Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis. THE NEW PHYTOLOGIST 2013; 199:843-57. [PMID: 23668187 DOI: 10.1111/nph.12306] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 05/02/2023]
Abstract
Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control.
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Affiliation(s)
- Xueqing Huang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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142
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Ortiz-Morea FA, Vicentini R, Silva GF, Silva EM, Carrer H, Rodrigues AP, Nogueira FT. Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2307-20. [PMID: 23564956 PMCID: PMC3654421 DOI: 10.1093/jxb/ert089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth.
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Affiliation(s)
- Fausto A. Ortiz-Morea
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- These authors contributed equally to this work
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
- These authors contributed equally to this work
| | - Geraldo F.F. Silva
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Eder M. Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Helaine Carrer
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
| | - Ana P. Rodrigues
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Fabio T.S. Nogueira
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- To whom correspondence should be addressed.
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143
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David-Schwartz R, Borovsky Y, Zemach H, Paran I. CaHAM is autoregulated and regulates CaSTM expression and is required for shoot apical meristem organization in pepper. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:8-16. [PMID: 23415323 DOI: 10.1016/j.plantsci.2012.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/28/2012] [Accepted: 12/01/2012] [Indexed: 05/26/2023]
Abstract
The angiosperm shoot apical meristem (SAM) is characterized by tightly organized cell layers and zones. The SAM's organization allows it to maintain its indeterminate nature while producing determinate lateral organs. Alterations in SAM gene expression partly account for the immense diversity in plant architecture. The GRAS protein family gene HAIRY MERISTEM (HAM) is an important regulator of SAM organization in Petunia and Arabidopsis. Here we describe CaHAM loss-of-function pepper mutants characterized by an arrested SAM following the formation of several leaves on the primary stem, complete inhibition of axillary meristem development, an expanded tunica domain and trichome formation on the SAM epidermis. CaHAM is expressed in the periphery of the SAM and in the vasculature of young leaves throughout plant development, reaching its highest level in the reproductive growth stage. Analysis of the effect of CaHAM loss-of-function on its own expression showed that CaHAM is negatively autoregulated. Furthermore, CaHAM negatively regulates the expression level and pattern of pepper SHOOT MERISTEMLESS (CaSTM), which is required to maintain the SAM in an undifferentiated state. We conclude that CaHAM is regulated to achieve adjusted functional levels and has a conserved role in controlling SAM maintenance, organization and axillary meristem formation.
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Affiliation(s)
- Rakefet David-Schwartz
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel
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144
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MicroRNAs and their cross-talks in plant development. J Genet Genomics 2013; 40:161-70. [PMID: 23618399 DOI: 10.1016/j.jgg.2013.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 01/10/2023]
Abstract
Plant development is a complex process influenced by exogenous and endogenous elements. A series of postembryonic developmental events is involved to form the final architecture and contend with the changing environment. MicroRNA (miRNA) is one of endogenous non-coding RNAs, which plays an important role in plant developmental regulation. In this review, we summarized 34 miRNA families that are closely associated with plant development. Among these families, nine are expressed only in specific organs, whereas 20 families are expressed in at least two different organs. It is known that some miRNAs are expressed across most processes of plant growth, while some appear only at particular developmental stages or under special environmental conditions such as drought, waterlogging and short-day time. These miRNAs execute their diverse functions by regulating developmental gene expression levels, interacting with phytohormone signaling response, participating in the biogenesis of ta-siRNAs and affecting the production of miRNAs.
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145
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Curaba J, Talbot M, Li Z, Helliwell C. Over-expression of microRNA171 affects phase transitions and floral meristem determinancy in barley. BMC PLANT BIOLOGY 2013; 13:6. [PMID: 23294862 PMCID: PMC3547705 DOI: 10.1186/1471-2229-13-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/02/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The transitions from juvenile to adult and adult to reproductive phases of growth are important stages in the life cycle of plants. The regulators of these transitions include miRNAs, in particular miR156 and miR172 which are part of a regulatory module conserved across the angiosperms. In Arabidopsis miR171 represses differentiation of axillary meristems by repressing expression of SCARECROW-LIKE(SCL) transcription factors, however the role of miR171 has not been examined in other plants. RESULTS To investigate the roles of mir171 and its target genes in a monocot, the Hvu pri-miR171a was over-expressed in barley (Hordeum vulgare L. cv. Golden promise) leading to reduced expression of at least one HvSCL gene. The resulting transgenic plants displayed a pleiotropic phenotype which included branching defects, an increased number of short vegetative phytomers and late flowering. These phenotypes appear to be the consequence of changes in the organisation of the shoot meristem. In addition, the data show that miR171 over-expression alters the vegetative to reproductive phase transition by activating the miR156 pathway and repressing the expression of the TRD (THIRD OUTER GLUME) and HvPLA1 (Plastochron1) genes. CONCLUSIONS Our data suggest that some of the roles of miR171 and its target genes that have been determined in Arabidopsis are conserved in barley and that they have additional functions in barley including activation of the miR156 pathway.
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Affiliation(s)
- Julien Curaba
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Mark Talbot
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Zhongyi Li
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Chris Helliwell
- Current address: School of Agriculture and Food Systems, University of Melbourne, Parkville, Victoria, 3010, Australia
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146
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de Lima JC, Loss-Morais G, Margis R. MicroRNAs play critical roles during plant development and in response to abiotic stresses. Genet Mol Biol 2012; 35:1069-77. [PMID: 23412556 PMCID: PMC3571433 DOI: 10.1590/s1415-47572012000600023] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) have been identified as key molecules in regulatory networks. The fine-tuning role of miRNAs in addition to the regulatory role of transcription factors has shown that molecular events during development are tightly regulated. In addition, several miRNAs play crucial roles in the response to abiotic stress induced by drought, salinity, low temperatures, and metals such as aluminium. Interestingly, several miRNAs have overlapping roles with regard to development, stress responses, and nutrient homeostasis. Moreover, in response to the same abiotic stresses, different expression patterns for some conserved miRNA families among different plant species revealed different metabolic adjustments. The use of deep sequencing technologies for the characterisation of miRNA frequency and the identification of new miRNAs adds complexity to regulatory networks in plants. In this review, we consider the regulatory role of miRNAs in plant development and abiotic stresses, as well as the impact of deep sequencing technologies on the generation of miRNA data.
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Affiliation(s)
- Júlio César de Lima
- Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. ; Laboratório de Fisiologia Vegetal, Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. ; Programa de Pósgraduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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147
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Liang G, He H, Yu D. Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS One 2012; 7:e48951. [PMID: 23155433 PMCID: PMC3498362 DOI: 10.1371/journal.pone.0048951] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 10/02/2012] [Indexed: 01/23/2023] Open
Abstract
microRNAs (miRNAs) are a class of negative regulators that take part in many processes such as growth and development, stress responses, and metabolism in plants. Recently, miRNAs were shown to function in plant nutrient metabolism. Moreover, several miRNAs were identified in the response to nitrogen (N) deficiency. To investigate the functions of other miRNAs in N deficiency, deep sequencing technology was used to detect the expression of small RNAs under N-sufficient and -deficient conditions. The results showed that members from the same miRNA families displayed differential expression in response to N deficiency. Upon N starvation, the expression of miR169, miR171, miR395, miR397, miR398, miR399, miR408, miR827, and miR857 was repressed, whereas those of miR160, miR780, miR826, miR842, and miR846 were induced. miR826, a newly identified N-starvation-induced miRNA, was found to target the AOP2 gene. Among these N-starvation-responsive miRNAs, several were involved in cross-talk among responses to different nutrient (N, P, S, Cu) deficiencies. miR160, miR167, and miR171 could be responsible for the development of Arabidopsis root systems under N-starvation conditions. In addition, twenty novel miRNAs were identified and nine of them were significantly responsive to N-starvation. This study represents comprehensive expression profiling of N-starvation-responsive miRNAs and advances our understanding of the regulation of N homeostasis mediated by miRNAs.
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Affiliation(s)
- Gang Liang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hua He
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- The Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Diqiu Yu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail:
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148
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Arazi T. MicroRNAs in the moss Physcomitrella patens. PLANT MOLECULAR BIOLOGY 2012; 80:55-65. [PMID: 21373961 DOI: 10.1007/s11103-011-9761-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/25/2011] [Indexed: 05/10/2023]
Abstract
Having diverged from the lineage that lead to flowering plants shortly after plants have established on land, mosses, which share fundamental processes with flowering plants but underwent little morphological changes by comparison with the fossil records, can be considered as an evolutionary informative place. Hence, they are especially useful for the study of developmental evolution and adaption to life on land. The transition to land exposed early plants to harsh physical conditions that resulted in key physiological and developmental changes. MicroRNAs (miRNAs) are an important class of small RNAs (sRNAs) that act as master regulators of development and stress in flowering plants. In recent years several groups have been engaged in the cloning of sRNAs from the model moss Physcomitrella patens. These studies have revealed a wealth of miRNAs, including novel and conserved ones, creating a unique opportunity to broaden our understanding of miRNA functions in land plants and their contribution to the latter's evolution. Here we review the current knowledge of moss miRNAs and suggest approaches for their functional analysis in P. patens.
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Affiliation(s)
- Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel.
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149
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Xu MY, Dong Y, Zhang QX, Zhang L, Luo YZ, Sun J, Fan YL, Wang L. Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics 2012; 13:421. [PMID: 22920854 PMCID: PMC3599582 DOI: 10.1186/1471-2164-13-421] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 07/25/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Oilseed rape (Brassica napus) is one of the most important crops in China, Europe and other Asian countries with publicly available expressed sequence tags (ESTs) and genomic survey sequence (GSS) databases, but little is known about its miRNAs and their targets. To date, only 46 miRNAs have been identified in B. napus. RESULTS Forty-one conserved and 62 brassica-specific candidate B. napus miRNAs, including 20 miRNA* sequences, were identified using Solexa sequencing technology. Furthermore, 33 non-redundant mRNA targets of conserved brassica miRNAs and 19 new non-redundant mRNA targets of novel brassica-specific miRNAs were identified by genome-scale sequencing of mRNA degradome. CONCLUSIONS This study describes large scale cloning and characterization of B. napus miRNAs and their potential targets, providing the foundation for further characterization of miRNA function in the regulation of diverse physiological processes in B. napus.
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Affiliation(s)
- Miao Y Xu
- Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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150
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Abstract
HAIRY MERISTEM (HAM) proteins, members of the GRAS family of transcriptional regulators, are essential for maintenance of indeterminate growth in flowering plant shoots, loss-of-function ham mutants exhibiting a strikingly novel phenotype of shoot meristem arrest and differentiation. Specific cellular/molecular functions of HAM proteins underlying meristem maintenance are unknown. In this review, I highlight findings from recent analyses of Arabidopsis ham (Atham) loss-of-function phenotypes, including that HAM function limits the generation of clonally-derived meristem layers and that HAM function regulates CLAVATA3 expression. I consider how this new information both refines our understanding of the role of HAM proteins in regulating meristem structure and function, and may also suggest possible downstream HAM protein transcriptional targets. Finally, I note the significant phenotypic overlap between Atham phenotypes, and aintegumenta/anintegumenta-like6 double mutant phenotypes, suggesting meristem regulatory functions common to, and possible genetic interactions between, HAM and AINTEGUMENTA.
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Affiliation(s)
- Eric M Engstrom
- Biology Department, The College of William and Mary, Williamsburg, VA, USA.
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