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Lohani N, Golicz AA, Allu AD, Bhalla PL, Singh MB. Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development. PLANT CELL REPORTS 2023; 42:337-354. [PMID: 36653661 DOI: 10.1007/s00299-022-02960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The genomic location and stage-specific expression pattern of many long non-coding RNAs reveal their critical role in regulating protein-coding genes crucial in pollen developmental progression and male germ line specification. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with no apparent protein-coding potential. Multiple investigations have revealed high expression of lncRNAs in plant reproductive organs in a cell and tissue-specific manner. However, their potential role as essential regulators of molecular processes involved in sexual reproduction remains largely unexplored. We have used developing field mustard (Brassica rapa) pollen as a model system for investigating the potential role of lncRNAs in reproductive development. Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- School of Science, Western Sydney University, Richmond, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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Babaei S, Singh MB, Bhalla PL. Role of long non-coding RNAs in rice reproductive development. FRONTIERS IN PLANT SCIENCE 2022; 13:1040366. [PMID: 36457537 PMCID: PMC9705774 DOI: 10.3389/fpls.2022.1040366] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/28/2022] [Indexed: 05/13/2023]
Abstract
Rice is a staple crop, feeding over half of the global population. The future demand of population growth and climate change requires substantial rice improvement. Recent advances in rice genomics have highlighted the vital role of the non-coding part of the genome. The protein-coding regions account for only a tiny portion of the eukaryotic genome, and most of the genomic regions transcribe copious amounts of non-coding RNAs. Of these, the long non-coding RNAs, including linear non-coding RNAs (lncRNAs) and circular non-coding RNAs (circRNAs), have been shown to play critical roles in various developmental processes by regulating the expression of genes and functions of proteins at transcriptional, post-transcriptional and post-translational levels. With the advances in next-generation sequencing technologies, a substantial number of long non-coding RNAs have been found to be expressed in plant reproductive organs in a cell- and tissue-specific manner suggesting their reproductive development-related functions. Accumulating evidence points towards the critical role of these non-coding RNAs in flowering, anther, and pollen development, ovule and seed development and photoperiod and temperature regulation of male fertility. In this mini review, we provide a brief overview of the role of the linear and circular long non-coding RNAs in rice reproductive development and control of fertility and crop yield.
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Affiliation(s)
| | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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3
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Golicz AA, Allu AD, Li W, Lohani N, Singh MB, Bhalla PL. A dynamic intron retention program regulates the expression of several hundred genes during pollen meiosis. PLANT REPRODUCTION 2021; 34:225-242. [PMID: 34019149 DOI: 10.1007/s00497-021-00411-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/19/2021] [Indexed: 05/12/2023]
Abstract
Intron retention is a stage-specific mechanism of functional attenuation of a subset of co-regulated, functionally related genes during early stages of pollen development. To improve our understanding of the gene regulatory mechanisms that drive developmental processes, we performed a genome-wide study of alternative splicing and isoform switching during five key stages of pollen development in field mustard, Brassica rapa. Surprisingly, for several hundred genes (12.3% of the genes analysed), isoform switching results in stage-specific expression of intron-retaining transcripts at the meiotic stage of pollen development. In such cases, we report temporally regulated switching between expression of a canonical, translatable isoform and an intron-retaining transcript that is predicted to produce a truncated and presumably inactive protein. The results suggest a new pervasive mechanism underlying modulation of protein levels in a plant developmental program. The effect is not based on gene expression induction but on the type of transcript produced. We conclude that intron retention is a stage-specific mechanism of functional attenuation of a subset of co-regulated, functionally related genes during meiosis, especially genes related to ribosome biogenesis, mRNA transport and nuclear envelope architecture. We also propose that stage-specific expression of a non-functional isoform of Brassica rapa BrSDG8, a non-redundant member of histone methyltransferase gene family, linked to alternative splicing regulation, may contribute to the intron retention observed.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Wei Li
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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4
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Singh MB, Lohani N, Bhalla PL. The Role of Endoplasmic Reticulum Stress Response in Pollen Development and Heat Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2021; 12:661062. [PMID: 33936150 PMCID: PMC8079734 DOI: 10.3389/fpls.2021.661062] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/15/2021] [Indexed: 05/15/2023]
Abstract
Endoplasmic reticulum (ER) stress is defined by a protracted disruption in protein folding and accumulation of unfolded or misfolded proteins in the ER. This accumulation of unfolded proteins can result from excessive demands on the protein folding machinery triggered by environmental and cellular stresses such as nutrient deficiencies, oxidative stress, pathogens, and heat. The cell responds to ER stress by activating a protective pathway termed unfolded protein response (UPR), which comprises cellular mechanisms targeted to maintain cellular homeostasis by increasing the ER's protein folding capacity. The UPR is especially significant for plants as being sessile requires them to adapt to multiple environmental stresses. While multiple stresses trigger the UPR at the vegetative stage, it appears to be active constitutively in the anthers of unstressed plants. Transcriptome analysis reveals significant upregulation of ER stress-related transcripts in diploid meiocytes and haploid microspores. Interestingly, several ER stress-related genes are specifically upregulated in the sperm cells. The analysis of gene knockout mutants in Arabidopsis has revealed that defects in ER stress response lead to the failure of normal pollen development and enhanced susceptibility of male gametophyte to heat stress conditions. In this mini-review, we provide an overview of the role of ER stress and UPR in pollen development and its protective roles in maintaining male fertility under heat stress conditions.
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Affiliation(s)
| | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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6
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Lazare S, Burgos A, Brotman Y, Zaccai M. The metabolic (under)groundwork of the lily bulb toward sprouting. PHYSIOLOGIA PLANTARUM 2018; 163:436-449. [PMID: 29274128 DOI: 10.1111/ppl.12685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Large bulbs of Lilium longiflorum have an obligatory cold requirement to flower. Bulb cooling is widely used to induce and accelerate flowering. However, in-depth investigations of the effect of bulb cooling on major landmarks of plant development are lacking. It has been demonstrated that low temperature induces carbohydrate degradation, yet integrative studies on metabolic changes occurring in the bulb are not available. We detected that cold exposure mainly hastened bulb sprouting, rather than floral transition or blooming. Metabolite profiling of cooled and non-cooled bulbs was carried out, revealing cold-induced accumulation of soluble sugars, lipids and specific amino acids, and a significant reduction in tricarboxylic acid (TCA)-cycle elements. We observed that metabolic pathways located in the cytosol - including glycolysis, lipid synthesis and part of the gamma-Aminobutyric acid (GABA) shunt - were enhanced by cold exposure, while mitochondrial metabolism - namely the TCA cycle - was reduced by cold. We suggest a physiological model accounting for this metabolic discrepancy.
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Affiliation(s)
- Silit Lazare
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Asdrubal Burgos
- Laboratorio de Biotecnología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, CP 15110, Zapopan, Jalisco, Mexico
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michele Zaccai
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
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7
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Shi S, Duan G, Li D, Wu J, Liu X, Hong B, Yi M, Zhang Z. Two-dimensional analysis provides molecular insight into flower scent of Lilium 'Siberia'. Sci Rep 2018; 8:5352. [PMID: 29599431 PMCID: PMC5876372 DOI: 10.1038/s41598-018-23588-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/16/2018] [Indexed: 11/10/2022] Open
Abstract
Lily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods. By overlapping differentially-expressed genes (DEGs) that responded to flower scent changes in flower development and circadian rhythm, 3,426 DEGs were initially identified to be candidates for flower scent production, of which 1,270 were predicted as transcriptional factors (TFs). The DEGs were further correlated to individual flower volatiles by WGCNA. Finally, 37, 41 and 90 genes were identified as candidate TFs likely regulating terpenoids, phenylpropanoids and fatty acid derivatives productions, respectively. Moreover, by WGCNA several genes related to auxin, gibberellins and ABC transporter were revealed to be responsible for flower scent production. Thus, this strategy provides an important foundation for future studies on the molecular mechanisms involved in floral scent production.
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Affiliation(s)
- Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Guangyou Duan
- Energy Plant Research Center, School of Life Sciences, Qilu Normal University, Jinan, China
| | - Dandan Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jie Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Bo Hong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China.
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China.
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8
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Higo A, Niwa M, Yamato KT, Yamada L, Sawada H, Sakamoto T, Kurata T, Shirakawa M, Endo M, Shigenobu S, Yamaguchi K, Ishizaki K, Nishihama R, Kohchi T, Araki T. Transcriptional Framework of Male Gametogenesis in the Liverwort Marchantia polymorpha L. PLANT & CELL PHYSIOLOGY 2016; 57:325-38. [PMID: 26858289 DOI: 10.1093/pcp/pcw005] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/31/2015] [Indexed: 05/19/2023]
Abstract
In land plants, there are two types of male gametes: one is a non-motile sperm cell which is delivered to the egg cell by a pollen tube, and the other is a motile sperm cell with flagella. The molecular mechanism underlying the sexual reproduction with the egg and pollen-delivered sperm cell is well understood from studies using model plants such as Arabidopsis and rice. On the other hand, the sexual reproduction with motile sperm has remained poorly characterized, due to the lack of suitable models. Marchantia polymorpha L. is a model basal land plant with sexual reproduction involving an egg cell and bi-flagellated motile sperm. To understand the differentiation process of plant motile sperm, we analyzed the gene expression profile of developing antheridia of M. polymorpha. We performed RNA-sequencing experiments and compared transcript profiles of the male sexual organ (antheridiophore and antheridium contained therein), female sexual organ (archegoniophore) and a vegetative organ (thallus). Transcriptome analysis showed that the antheridium expresses nearly half of the protein-coding genes predicted in the genome, but it also has unique features. The antheridium transcriptome shares some common features with male gamete transcriptomes of angiosperms and animals, and homologs of genes involved in male gamete formation and function in angiosperms and animals were identified. In addition, we showed that some of them had distinct expression patterns in the spermatogenous tissue of developing antheridia. This study provides a transcriptional framework on which to study the molecular mechanism of plant motile sperm development in M. polymorpha as a model.
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Affiliation(s)
- Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Masaki Niwa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Kinokawa, 649-6493 Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004 Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004 Japan
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan Present address: Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555 Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan Present address: Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan Present address: Department of Botany, Faculty of Science, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, 444-8585 Japan
| | | | | | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
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Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods ("omics") now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis). Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.
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Affiliation(s)
| | | | - Ueli Grossniklaus
- Department of Plant & Microbial Biology and Zurich-Basel Plant Science Center, University of ZurichZurich, Switzerland
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10
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Rutley N, Twell D. A decade of pollen transcriptomics. PLANT REPRODUCTION 2015; 28:73-89. [PMID: 25761645 PMCID: PMC4432081 DOI: 10.1007/s00497-015-0261-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/24/2015] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Overview of pollen transcriptome studies. Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.
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Affiliation(s)
- Nicholas Rutley
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
| | - David Twell
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
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Lang V, Usadel B, Obermeyer G. De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species. PLANT MOLECULAR BIOLOGY 2015; 87:69-80. [PMID: 25341867 DOI: 10.1007/s11103-014-0261-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Pollen grains of Lilium longiflorum are a long-established model system for pollen germination and tube tip growth. Due to their size, protein content and almost synchronous germination in synthetic media, they provide a simple system for physiological measurements as well as sufficient material for biochemical studies like protein purifications, enzyme assays, organelle isolation or determination of metabolites during germination and pollen tube elongation. Despite recent progresses in molecular biology techniques, sequence information of expressed proteins or transcripts in lily pollen is still scarce. Using a next generation sequencing strategy (RNAseq), the lily pollen transcriptome was investigated resulting in more than 50 million high quality reads with a length of 90 base pairs. Sequenced transcripts were assembled and annotated, and finally visualized with MAPMAN software tools and compared with other RNAseq or genome data including Arabidopsis pollen, Lilium vegetative tissues and the Amborella trichopoda genome. All lily pollen sequence data are provided as open access files with suitable tools to search sequences of interest.
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Affiliation(s)
- Veronika Lang
- Molecular Plant Biophysics and Biochemistry, Depatment of Molecular Biology, University of Salzburg, Billrothstr.11, 5020, Salzburg, Austria
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Li X, Wang C, Cheng J, Zhang J, da Silva JAT, Liu X, Duan X, Li T, Sun H. Transcriptome analysis of carbohydrate metabolism during bulblet formation and development in Lilium davidii var. unicolor. BMC PLANT BIOLOGY 2014; 14:358. [PMID: 25524032 PMCID: PMC4302423 DOI: 10.1186/s12870-014-0358-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/27/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The formation and development of bulblets are crucial to the Lilium genus since these processes are closely related to carbohydrate metabolism, especially to starch and sucrose metabolism. However, little is known about the transcriptional regulation of both processes. To gain insight into carbohydrate-related genes involved in bulblet formation and development, we conducted comparative transcriptome profiling of Lilium davidii var. unicolor bulblets at 0 d, 15 d (bulblets emerged) and 35 d (bulblets formed a basic shape with three or four scales) after scale propagation. RESULTS Analysis of the transcriptome revealed that a total of 52,901 unigenes with an average sequence size of 630 bp were generated. Based on Clusters of Orthologous Groups (COG) analysis, 8% of the sequences were attributed to carbohydrate transport and metabolism. The results of KEGG pathway enrichment analysis showed that starch and sucrose metabolism constituted the predominant pathway among the three library pairs. The starch content in mother scales and bulblets decreased and increased, respectively, with almost the same trend as sucrose content. Gene expression analysis of the key enzymes in starch and sucrose metabolism suggested that sucrose synthase (SuSy) and invertase (INV), mainly hydrolyzing sucrose, presented higher gene expression in mother scales and bulblets at stages of bulblet appearance and enlargement, while sucrose phosphate synthase (SPS) showed higher expression in bulblets at morphogenesis. The enzymes involved in the starch synthetic direction such as ADPG pyrophosphorylase (AGPase), soluble starch synthase (SSS), starch branching enzyme (SBE) and granule-bound starch synthase (GBSS) showed a decreasing trend in mother scales and higher gene expression in bulblets at bulblet appearance and enlargement stages while the enzyme in the cleavage direction, starch de-branching enzyme (SDBE), showed higher gene expression in mother scales than in bulblets. CONCLUSIONS An extensive transcriptome analysis of three bulblet development stages contributes considerable novel information to our understanding of carbohydrate metabolism-related genes in Lilium at the transcriptional level, and demonstrates the fundamentality of carbohydrate metabolism in bulblet emergence and development at the molecular level. This could facilitate further investigation into the molecular mechanisms underlying these processes in lily and other related species.
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Affiliation(s)
- XueYan Li
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - ChunXia Wang
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - JinYun Cheng
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - Jing Zhang
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | | | - XiaoYu Liu
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - Xin Duan
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - TianLai Li
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - HongMei Sun
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
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13
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Lipinska AP, D’hondt S, Van Damme EJM, De Clerck O. Uncovering the genetic basis for early isogamete differentiation: a case study of Ectocarpus siliculosus. BMC Genomics 2013; 14:909. [PMID: 24359479 PMCID: PMC3879662 DOI: 10.1186/1471-2164-14-909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 12/17/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The phenomenon of sexual reproduction characterizes nearly all eukaryotes, with anisogamy being the most prevalent form of gamete discrimination. Since dimorphic gametes most likely descend from equal-sized specialized germ cells, identifying the genetic bases of the early functional diversification in isogametes can provide better understanding of the evolution of sexual dimorphism. However, despite the potential importance to the evolutionary biology field, no comprehensive survey of the transcriptome profiling in isomorphic gametes has been reported hitherto. RESULTS Gamete differentiation on the genomic level was investigated using Ectocarpus siliculosus, a model organism for brown algal lineage which displays an isogamous sexual reproduction cycle. Transcriptome libraries of male and female gametes were generated using Next Generation Sequencing technology (SOLiD) and analyzed to identify differentially regulated genes and pathways with potential roles in fertilization and gamete specialization. Gamete transcriptomes showed a high level of complexity with a large portion of gender specific gene expression. Our results indicate that over 4,000 of expressed genes are differentially regulated between male and female, including sequences related to cell movement, carbohydrate and lipid metabolism, signaling, transport and RNA processing. CONCLUSIONS This first comprehensive transcriptomic study of protist isogametes describes considerable adaptation to distinct sexual roles, suggesting that functional anisogamy precedes morphological differentiation. Several sex-biased genes and pathways with a putative role in reproduction were identified, providing the basis for more detailed investigations of the mechanisms underlying evolution of mating types and sexual dimorphism.
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Affiliation(s)
- Agnieszka P Lipinska
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Sofie D’hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Els JM Van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
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14
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Zhao X, Yang N, Wang T. Comparative proteomic analysis of generative and sperm cells reveals molecular characteristics associated with sperm development and function specialization. J Proteome Res 2013; 12:5058-71. [PMID: 23879389 DOI: 10.1021/pr400291p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In flowering plants, two sperm cells (SCs) are generated from a generative cell (GC) in the developing pollen grain or growing pollen tube and are then delivered to the embryo sac to initiate double fertilization. SC development and function specialization involve the strict control of the protein (gene) expression program and coordination of diverse cellular processes. However, because methods for collecting a large amount of highly purified GCs and SCs for proteomic and transcriptomic studies from a plant are not available, molecular information about the program and the interconnections is lacking. Here, we describe a method for obtaining a large quantity of highly purified GCs and SCs from just-germinated lily pollen grains and growing pollen tubes for proteomic analysis. Our observation showed that SCs had less condensed chromatin and more vacuole-like structures than GCs and that mature SCs were arrested at the G2 phase. Comparison of SC and GC proteomes revealed 101 proteins differentially expressed in the two proteomes. These proteins are involved in diverse cellular and metabolic processes, with preferential involvement in metabolism, the cell cycle, signaling, the ubiquitin/proteasome pathway, and chromatin remodeling. Impressively, almost all proteins in SCF complex-mediated proteolysis and the cell cycle were up-regulated in SCs, whereas those in chromatin remodeling and stress response were down-regulated. Our data also reveal the coordination of SCF complex-mediated proteolysis, cell cycle progression, and DNA repair in SC development and function specialization. This study revealed for the first time a difference in protein profiles between GCs and SCs.
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Affiliation(s)
- Xin Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences and National Center for Plant Gene Research , Beijing 100093, China
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15
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Schmidt A, Schmid MW, Grossniklaus U. Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:18-29. [PMID: 22449040 DOI: 10.1111/j.1365-313x.2012.04897.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reproduction is a crucial step in the life cycle of plants. The male and female germline lineages develop in the reproductive organs of the flower, which in higher plants are the anthers and ovules, respectively. Development of the germline lineage initiates from a dedicated sporophytic cell that undergoes meiosis to form spores that subsequently give rise to the gametophytes through mitotic cell divisions. The mature male and female gametophytes harbour the male (sperm cells) and female gametes (egg and central cell), respectively. Those unite during double fertilization to initiate embryo and endosperm development in sexually reproducing higher plants. While cytological changes involved in development of the germline lineages have been well characterized in a number of species, investigation of the transcriptional basis underlying their development and the specification of the gametes proved challenging. This is largely due to the inaccessibility of the cells constituting the germline lineages, which are enclosed by sporophytic tissues. Only recently, these technical limitations could be overcome by combining new methods to isolate the relevant cells with powerful transcriptional profiling methods, such as microarrays or high-throughput sequencing of RNA. This review focuses on these technical advances and the new insights gained from them concerning the transcriptional basis and molecular mechanisms underlying germline development.
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Affiliation(s)
- Anja Schmidt
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, Zürich, Switzerland.
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16
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Deveshwar P, Bovill WD, Sharma R, Able JA, Kapoor S. Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC PLANT BIOLOGY 2011; 11:78. [PMID: 21554676 PMCID: PMC3112077 DOI: 10.1186/1471-2229-11-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/09/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed in many plant species at progressive stages of development by using microarray and sequence-by synthesis-technologies to identify genes that regulate anther development. Here we report a comprehensive analysis of rice anther transcriptomes at four distinct stages, focusing on identifying regulatory components that contribute to male meiosis and germline development. Further, these transcriptomes have been compared with the transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. RESULTS Transcriptome profiling of four stages of anther development in rice including pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA) revealed about 22,000 genes expressing in at least one of the anther developmental stages, with the highest number in MA (18,090) and the lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes specifically expressed in anther stages. From this sub-set, 453 genes were specific to TPA, while 78 and 184 genes were expressed specifically in MA and SCP, respectively. The expression pattern of selected genes has been validated using real time PCR and in situ hybridizations. Gene ontology and pathway analysis of stage-specific genes revealed that those encoding transcription factors and components of protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. CONCLUSIONS Not only have we provided the transcriptome constituents of four landmark stages of anther development in rice but we have also identified genes that express exclusively in these stages. It is likely that many of these candidates may therefore contribute to specific aspects of anther and/or male gametophyte development in rice. In addition, the gene sets that have been produced will assist the plant reproductive community in building a deeper understanding of underlying regulatory networks and in selecting gene candidates for functional validation.
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Affiliation(s)
- Priyanka Deveshwar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi-110021, India
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17
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Houben A, Kumke K, Nagaki K, Hause G. CENH3 distribution and differential chromatin modifications during pollen development in rye (Secale cereale L.). Chromosome Res 2011; 19:471-80. [PMID: 21503764 DOI: 10.1007/s10577-011-9207-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/24/2011] [Accepted: 02/24/2011] [Indexed: 11/30/2022]
Abstract
Microgametogenesis in angiosperms results in two structurally and functionally different cells, one generative cell, which subsequently forms the sperm cells, and the vegetative cell. We analysed the chromatin properties of both types of nuclei after first and second pollen mitosis in rye (Secale cereale). The condensed chromatin of generative nuclei is earmarked by an enhanced level of histone H3K4/K9 dimethylation and H3K9 acetylation. The less condensed vegetative nuclei are RNA polymerase II positive. Trimethylation of H3K27 is not involved in transcriptional downregulation of genes located in generative nuclei as H3K27me3 was exclusively detected in the vegetative nuclei. The global level of DNA methylation does not differ between both types of pollen nuclei. In rye, unlike in Arabidopsis thaliana (Ingouff et al. Curr Biol 17:1032-1037 2007; Schoft et al. EMBO Rep 10:1015-1021 2009), centromeric histone H3 is not excluded from the chromatin of the vegetative nucleus and the condensation degree of centromeric and subtelomeric regions did not differ between the generative and vegetative nuclei. Differences between rye and A. thaliana data suggest that the chromatin organization in mature nuclei of pollen grains is not universal across angiosperms.
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Affiliation(s)
- Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany.
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18
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Xin HP, Peng XB, Ning J, Yan TT, Ma LG, Sun MX. Expressed sequence-tag analysis of tobacco sperm cells reveals a unique transcriptional profile and selective persistence of paternal transcripts after fertilization. SEXUAL PLANT REPRODUCTION 2011; 24:37-46. [PMID: 20981558 DOI: 10.1007/s00497-010-0151-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 10/11/2010] [Indexed: 11/26/2022]
Abstract
Transcript analysis of male gametes of Nicotiana tabacum was conducted to gather gene expression data regarding the specialization of male germ cells and transmission of paternal transcripts during fertilization. We constructed a tobacco sperm cell cDNA library yielding 1,864 expressed sequence tags representing 1,050 clusters; 37.2% of these clusters have no homologs in GenBank, and 42% did not match any functionally classified protein. A comparative analysis of tobacco sperm transcripts with those of Arabidopsis and maize confirms that some genes are conserved in sperm specialization, while some are distinct to tobacco germline cells. Using reverse transcription-PCR (RT-PCR) of selected transcripts, we evaluated expression of sperm-obtained sequences in vegetative tissue, isolated egg cells, zygotes, and two-celled proembryos, identifying sperm cell-specific transcripts as potential markers for fertilization analysis. We further confirmed that two clusters of sperm transcripts were detected in zygotes about 10 h after fertilization, offering new examples of apparently paternally transmitted transcripts that may be involved in egg cell activation and/or early embryogenesis.
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Affiliation(s)
- Hai-Ping Xin
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, China
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19
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Baroux C, Raissig MT, Grossniklaus U. Epigenetic regulation and reprogramming during gamete formation in plants. Curr Opin Genet Dev 2011; 21:124-33. [PMID: 21324672 DOI: 10.1016/j.gde.2011.01.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 01/18/2011] [Indexed: 11/29/2022]
Abstract
Plants and animals reproduce sexually via specialized, highly differentiated gametes. Yet, gamete formation drastically differs between the two kingdoms. In flowering plants, the specification of cells destined to enter meiosis occurs late in development, gametic and accessory cells are usually derived from the same meiotic product, and two distinct female gametes involved in double fertilization differentiate. This poses fascinating questions in terms of gamete development and the associated epigenetic processes. Although studies in this area remain at their infancy, it becomes clear that large-scale epigenetic reprogramming, involving RNA-directed DNA methylation, chromatin modifications, and nucleosome remodeling, contributes to the establishment of transcriptionally repressive or permissive epigenetic landscapes. Furthermore, a role for small RNAs in the regulation of transposable elements during gametogenesis is emerging.
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Affiliation(s)
- Célia Baroux
- Institute of Plant Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
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20
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Techniques of cell type-specific transcriptome analysis and applications in researches of sexual plant reproduction. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11515-011-1090-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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21
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Xin H, Sun M. What we have learned from transcript profile analyses of male and female gametes in flowering plants. SCIENCE CHINA-LIFE SCIENCES 2010; 53:927-33. [PMID: 20821291 DOI: 10.1007/s11427-010-4033-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 06/21/2010] [Indexed: 11/30/2022]
Abstract
Double fertilization is one of the predominant features of sexual reproduction in flowering plants but, because of the physical inaccessibility of gametes, the essential molecular mechanisms in these processes are largely unknown. Based on the techniques for isolating highly purified gametes from several species and well-developed methods for manipulating RNA from limited quantities of gametes, genome-wide investigations of gamete transcription profiles were recently conducted in flowering plants. In this review, we survey the accumulated knowledge on gamete collection and purification, cDNA library construction, and transcript profile analysis to assess our understanding of the molecular mechanisms of gamete specialization and fertilization.
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Affiliation(s)
- HaiPing Xin
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, China
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22
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Ron M, Alandete Saez M, Eshed Williams L, Fletcher JC, McCormick S. Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev 2010; 24:1010-21. [PMID: 20478994 DOI: 10.1101/gad.1882810] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Natural cis-antisense siRNAs (cis-nat-siRNAs) are a recently characterized class of small regulatory RNAs that are widespread in eukaryotes. Despite their abundance, the importance of their regulatory activity is largely unknown. The only functional role for eukaryotic cis-nat-siRNAs that has been described to date is in environmental stress responses in plants. Here we demonstrate that cis-nat-siRNA-based regulation plays key roles in Arabidopsis reproductive function, as it facilitates gametophyte formation and double fertilization, a developmental process of enormous agricultural value. We show that male gametophytic kokopelli (kpl) mutants display frequent single-fertilization events, and that KPL and a inversely transcribed gene, ARIADNE14 (ARI14), which encodes a putative ubiquitin E3 ligase, generate a sperm-specific nat-siRNA pair. In the absence of KPL, ARI14 RNA levels in sperm are increased and fertilization is impaired. Furthermore, ARI14 transcripts accumulate in several siRNA biogenesis pathway mutants, and overexpression of ARI14 in sperm phenocopies the reduced seed set of the kokopelli mutants. These results extend the regulatory capacity of cis-nat-siRNAs to development by identifying a role for cis-nat-siRNAs in controlling sperm function during double fertilization.
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Affiliation(s)
- Mily Ron
- Department of Plant and Microbial Biology, Plant Gene Expression Center, US Department of Agriculture/Agricultural Research Service, University of California at Berkeley, Albany, California 94710, USA
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23
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Pertl H, Schulze WX, Obermeyer G. The Pollen Organelle Membrane Proteome Reveals Highly Spatial−Temporal Dynamics during Germination and Tube Growth of Lily Pollen. J Proteome Res 2009; 8:5142-52. [DOI: 10.1021/pr900503f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Heidi Pertl
- Molecular Plant Biophysics and Biochemistry, Deptartment of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria, and Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
| | - Waltraud X. Schulze
- Molecular Plant Biophysics and Biochemistry, Deptartment of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria, and Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
| | - Gerhard Obermeyer
- Molecular Plant Biophysics and Biochemistry, Deptartment of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria, and Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
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24
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Borg M, Brownfield L, Twell D. Male gametophyte development: a molecular perspective. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1465-78. [PMID: 19213812 DOI: 10.1093/jxb/ern355] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Pollen grains represent the highly reduced haploid male gametophyte generation in flowering plants, consisting of just two or three cells when released from the anthers. Their role is to deliver twin sperm cells to the embryo sac to undergo fusion with the egg and central cell. This double fertilization event along with the functional specialization of the male gametophyte, are considered to be key innovations in the evolutionary success of flowering plants. This review encompasses important recent advances in our understanding of the molecular mechanisms controlling male gametophyte development. A brief overview of pollen development is presented, followed by a discussion of genome-wide transcriptomic studies of haploid gene expression. The progress achieved through genetic analysis of landmark events of male gametogenesis is discussed, with a focus on sperm cell production, and an emerging model of the regulatory network governing male germline development is presented. The review concludes with a perspective of the impact these data will have on future research strategies to further develop our understanding of the gametophytic control of pollen development.
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Affiliation(s)
- Michael Borg
- Department of Biology, University of Leicester, UK
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25
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Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijó JA, Becker JD. Comparative transcriptomics of Arabidopsis sperm cells. PLANT PHYSIOLOGY 2008; 148:1168-81. [PMID: 18667720 PMCID: PMC2556834 DOI: 10.1104/pp.108.125229] [Citation(s) in RCA: 286] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 07/27/2008] [Indexed: 05/19/2023]
Abstract
In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.
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Affiliation(s)
- Filipe Borges
- Instituto Gulbenkian de Ciência, Centro de Biologia do Desenvolvimento, Oeiras, Portugal
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26
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Epigenetic marks in the mature pollen of Quercus suber L. (Fagaceae). ACTA ACUST UNITED AC 2008; 22:1-7. [PMID: 20033450 DOI: 10.1007/s00497-008-0083-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 09/13/2008] [Indexed: 12/28/2022]
Abstract
We have analysed the distribution of epigenetic marks for histone modifications at lysine residues H3 and H4, and DNA methylation, in the nuclei of mature pollen cells of the Angiosperm tree Quercus suber; a monoecious wind pollinated species with a protandrous system, and a long post-pollination period. The ultrasonic treatment developed for the isolation of pollen nuclei proved to be a fast and reliable method, preventing the interference of cell wall autofluorescence in the in situ immunolabelling assays. In contrast with previous studies on herbaceous species with short progamic phases, our results are consistent with a high level of silent (5-mC and H3K9me2) epigenetic marks on chromatin of the generative nucleus, and the prevalence of active marks (H3K9me3 and H4Kac) in the vegetative nucleus. The findings are discussed in terms of the pollination/fertilization timing strategy adopted by this plant species.
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27
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Zienkiewicz K, Zienkiewicz A, Rodriguez-Garcia MI, Smoliński DJ, Swidziński M, Bednarska E. Transcriptional activity and distribution of splicing machinery elements during Hyacinthus orientalis pollen tube growth. PROTOPLASMA 2008; 233:129-139. [PMID: 18615237 DOI: 10.1007/s00709-008-0298-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 11/05/2007] [Indexed: 05/26/2023]
Abstract
The localization of newly formed transcripts and molecules participating in pre-mRNA splicing, i.e., small nuclear ribonucleoproteins (snRNPs) and SC35 protein, in growing pollen tubes of Hyacinthus orientalis L. were analyzed in vitro and in vivo. The results indicated that the restart of RNA synthesis occurred first in the vegetative and then in the generative nucleus of both in vitro and in vivo growing pollen tubes. Changes in RNA synthesis were accompanied by the redistribution of splicing machinery elements in both vegetative and generative nuclei of the growing pollen tube. At stages of pollen tube growth when the vegetative and generative nuclei were transcriptionally active, clear differences in the distribution pattern of the splicing system components were observed in both pollen nuclei. While both small nuclear RNA with a trimethylguanosine cap on the 5' end and SC35 protein were diffusely distributed in the nucleoplasm in the vegetative nucleus, the studied antigens were only present in the areas between condensed chromatin in the generative nucleus. When the transcriptional activity of both pollen nuclei could no longer be observed at later stages of pollen tube growth, snRNPs and SC35 protein were still present in the vegetative nuclei but not in the generative nuclei. We, therefore, investigated potential differences in the spatial organization of splicing system elements during pollen tube growth. They clearly reflect differences in gene expression patterns in the vegetative and the generative cells, which may be determined by the different biological roles of angiosperm male gametophyte cells.
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Affiliation(s)
- K Zienkiewicz
- Department of Cell Biology, Institute of General and Molecular Biology, Nicolaus Copernicus University, Ulica Gagarina 9, Toruń, Poland.
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28
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Peng XB, Sun MX. Gamete recognition in higher plants: an abstruse but charming mystery. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2008; 50:868-874. [PMID: 18713397 DOI: 10.1111/j.1744-7909.2008.00706.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Although much effort has been made to uncover the mechanism underlying double fertilization, little knowledge has been acquired for understanding the molecular base of gamete recognition, mainly because of technical limitations. Still, progress has been made in terms of the mechanism, including the identification of candidate molecules that are involved in gamete recognition in angiosperms. New cues for gamete recognition have been found by the successful separation of the gametes and construction of gamete-specific cDNA libraries in several species, and the application of molecular approaches for studying this process by mutations. Thus, the topic is considered an abstruse but charming mystery.
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Affiliation(s)
- Xiong-Bo Peng
- Key Laboratory of Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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29
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Cartagena JA, Matsunaga S, Seki M, Kurihara D, Yokoyama M, Shinozaki K, Fujimoto S, Azumi Y, Uchiyama S, Fukui K. The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen. Dev Biol 2008; 315:355-68. [PMID: 18252252 DOI: 10.1016/j.ydbio.2007.12.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 12/14/2007] [Accepted: 12/17/2007] [Indexed: 11/29/2022]
Abstract
Plant SET domain proteins are known to be involved in the epigenetic control of gene expression during plant development. Here, we report that the Arabidopsis SET domain protein, SDG4, contributes to the epigenetic regulation of pollen tube growth, thus affecting fertilization. Using an SDG4-GFP fusion construct, the chromosomal localization of SDG4 was established in tobacco BY-2 cells. In Arabidopsis, sdg4 knockout showed reproductive defects. Tissue-specific expression analyses indicated that SDG4 is the major ASH1-related gene expressed in the pollen. Immunological analyses demonstrated that SDG4 was involved in the methylation of histone H3 in the inflorescence and pollen grains. The significant reduction in the amount of methylated histone H3 K4 and K36 in sdg4 pollen vegetative nuclei resulted in suppression of pollen tube growth. Our results indicate that SDG4 is capable of modulating the expression of genes that function in the growth of pollen tube by methylation of specific lysine residues of the histone H3 in the vegetative nuclei.
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Affiliation(s)
- Joyce A Cartagena
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
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