Transcriptome analysis of Arabidopsis mature pollen grains from wild type and heterozygous NOT1 mutants
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PROVIDER: PRJNA551613 | ENA |
REPOSITORIES: ENA
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Project description:In flowering plants, pollen development is under a dynamic and well-orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post-mitotic phase skewed to a cell-type specific-transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4-NOT complex is the main evolutionary conserved deadenylase complex in eukaryotes, and its function is essential during germline specification in animals. We hypothesised that the CCR4-NOT complex might play a central role in mRNA turnover during microgametogenesis in Arabidopsis. Disruption of NOT1 gene, which encodes the scaffold protein of the CCR4-NOT complex, showed abnormal seed set. Genetic analysis failed to recover homozygous progeny and reciprocal crosses confirmed reduced transmission through the male and female gametophytes. Concordantly not1 embryo sacs showed delayed development and defects in embryogenesis. not1 pollen grains exhibited abnormal male germ unit configurations and failed to germinate. Transcriptome analysis of pollen from not1/+ mutants revealed that lack of NOT1 leads to an extensive transcriptional deregulation during microgametogenesis. Therefore, our work establishes NOT1 as an important player during gametophyte development in Arabidopsis.
2020-04-24 | GSE133490 | GEO
Project description:Comparative transcriptional profiling of FACS-sorted Arabidopsis thaliana sperm cells versus FACS-sorted mature pollen grains and seedlings
2008-08-01 | E-ATMX-35 | biostudies-arrayexpress
Project description:Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant Arabidopsis thaliana, which has tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip® to perform transcriptional profiling on mature bi-cellular soybean pollen. Results: Compared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean unique transcripts addressed in this study, 10,299 genes (27.46%) are expressed in pollen. Of the pollen-expressed genes, about 9,489 (92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), cell cycle-related transcripts, signal recognition receptors, ethylene responsive factors, chromatin remodeling factors, and members of the ubiquitin proteasome proteolytic pathway. Moreover, we identify several new pollen-specific candidate genes that might play a significant role in pollen biology. Conclusion: This is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. We also demonstrate that pollen is a rich store of regulatory proteins that are essential and sufficient for de novo gene expression. A comparison between transcription factors up-regulated in soybean and those upregulated in Arabidopsis revealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.
2009-03-26 | GSE12286 | GEO
Project description:Pollen germination, along with pollen tube growth, is an essential process for the reproduction of flowering plants. The germinating pollen with tip-growth characteristics provides an ideal model system for the study of cell growth and morphogenesis. As an essential step towards a detailed understanding of this important process, the objective of this study was to comprehensively analyze the transcriptome changes during pollen germination and pollen tube growth. Using Affymetrix Arabidopsis ATH1 Genome Arrays, this study is the first to show the changes in the transcriptome from desiccated mature pollen grains to hydrated pollen grains and then to pollen tubes of Arabidopsis thaliana. The number of expressed genes, either for total expressed genes or for specifically expressed genes, increased significantly from desiccated mature pollen to hydrated pollen and again to growing pollen tubes, which is consistent with the finding that pollen germination and tube growth was significantly inhibited in vitro by a transcriptional inhibitor. The results of GO analyses showed that expression of genes related to cell rescue, transcription, signal transduction and cellular transport were significantly changed, especially for up-regulation, during pollen germination and tube growth, respectively. In particular, genes of the CaM/CML, CHX and Hsp families showed the most significant changes during pollen germination and tube growth. These results demonstrate that the overall transcription of genes, both in the number of expressed genes and in the levels of transcription, was increased. Furthermore, the appearance of many novel transcripts during pollen germination as well as tube growth indicates that these newly expressed genes may function in this complex process. SUBMITTER_CITATION: Yi Wang, Wen-Zheng Zhang, Lian-Fen Song, Jun-Jie Zou, Zhen Su, and Wei-Hua Wu. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol. September 5, 2008; 10.1104/pp.108.126375 Experiment Overall Design: Three samples are analyzed in this experiment. They are desiccated mature pollen grains (MP), hydrated pollen grains (HP) and growing pollen tubes (PT) of Arabidopsis thaliana, respectively. Each sample has two biological replicates, so that there are 6 data sets of ATH1 array in this experiment.
2008-10-25 | E-GEOD-6696 | biostudies-arrayexpress
Project description:Effects of loss-of-function of AtMIKC* MADS-box genes on the mature Arabidopsis pollen transcriptome.
2007-12-04 | E-MEXP-1138 | biostudies-arrayexpress
Project description:Tobacco mature pollen has extremely desiccated cytoplasm, and is metabolically quiescent. Upon re-hydration it becomes metabolically active and that results in later emergence of rapidly growing pollen tube. These changes in cytoplasm hydration and metabolic activity are accompanied by protein phosphorylation. In this study, we subjected mature pollen, 5-min-activated pollen, and 30-min-activated pollen to TCA/acetone protein extraction, trypsin digestion and phosphopeptide enrichment by titanium dioxide. The enriched fraction was subjected to nLC-MS/MS. We identified 471 phosphopeptides that carried 432 phosphorylation sites, position of which was exactly matched by mass spectrometry. These 471 phosphopeptides were assigned to 301 phosphoproteins, since some proteins carried more phosphorylation sites. Of the 13 functional groups, the majority of proteins were put into these categories: transcription, protein synthesis, protein destination and storage, and signal transduction. Many proteins were of unknown function, reflecting the fact that male gametophyte contains many specific proteins that have not been fully functionally annotated. The quantitative data highlighted the dynamics of protein phosphorylation during pollen activation; the identified phosphopeptides were divided into seven groups based on the regulatory trends. The major group comprised mature pollen-specific phosphopeptides that were dephosphorylated during pollen activation. Several phosphopeptides representing the same phosphoprotein had different regulation, which pinpointed the complexity of protein phosphorylation and its clear functional context. Collectively, we showed the first phosphoproteomics data on activated pollen where the position of phosphorylation sites was clearly demonstrated and regulatory kinetics was resolved.
2016-01-27 | PXD003042 | Pride
Project description:In this study, we investigated the differential metabolic pathway enrichment among mature, hydrated, and germinated pollen using untargeted metabolomics analysis. Integration of publicly available transcriptome with presented metabolome data revealed starch and sucrose metabolism was significantly increased during pollen hydration and germination. The alterations in central metabolism focusing on sugar, fatty acids, and lipids were analyzed in detail. Several metabolites, including palmitic acid, oleic acid, linolenic acid, quercetin, luteolin/kaempferol, and γ-aminobutyric acid (GABA), were elevated in the hydrated pollen, suggesting a potential role in activating pollen tube emergence. The metabolite levels of mature, hydrated, and germinated pollen, presented in this work provide insights on the molecular basis of pollen germination.
2022-01-17 | ST002060 | MetabolomicsWorkbench
Project description:Upon germination, pollen forms a tube that elongates dramatically through female tissues in order to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We used Affymetrix Arabidopsis ATH1 Genome Arrays covering more than 80% of the Arabidopsis genome to compare transcriptomes of cell-sorted, hydrated pollen grains with those of flowers, leaves, seedlings and siliques (all samples with duplicates). This comparison revealed that pollen expresses a reduced set of genes with increased proportions of enriched and selectively-expressed transcripts. Relative gene ontology (GO) category representations in pollen and vegetative tissues revealed a functional skew of the pollen transcriptome towards signaling, vesicle transport and cytoskeleton, suggestive of a commitment towards germination and tube growth. Relative gene ontology (GO) category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome towards signaling, vesicle transport and cytoskeleton, suggestive of a commitment towards germination and tube growth. Relative gene ontology (GO) category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome towards signaling, vesicle transport and cytoskeleton, suggestive of a commitment towards germination and tube growth. Gene family and pathway analysis allowed formulation of novel hypotheses for the role of non-classical MADS-box genes, small RNA pathways and cell cycle components in pollen.
2005-06-01 | E-MEXP-285 | biostudies-arrayexpress
Project description:Pollen germination, along with pollen tube growth, is an essential process for the reproduction of flowering plants. The germinating pollen with tip-growth characteristics provides an ideal model system for the study of cell growth and morphogenesis. As an essential step towards a detailed understanding of this important process, the objective of this study was to comprehensively analyze the transcriptome changes during pollen germination and pollen tube growth. Using Affymetrix Arabidopsis ATH1 Genome Arrays, this study is the first to show the changes in the transcriptome from desiccated mature pollen grains to hydrated pollen grains and then to pollen tubes of Arabidopsis thaliana. The number of expressed genes, either for total expressed genes or for specifically expressed genes, increased significantly from desiccated mature pollen to hydrated pollen and again to growing pollen tubes, which is consistent with the finding that pollen germination and tube growth was significantly inhibited in vitro by a transcriptional inhibitor. The results of GO analyses showed that expression of genes related to cell rescue, transcription, signal transduction and cellular transport were significantly changed, especially for up-regulation, during pollen germination and tube growth, respectively. In particular, genes of the CaM/CML, CHX and Hsp families showed the most significant changes during pollen germination and tube growth. These results demonstrate that the overall transcription of genes, both in the number of expressed genes and in the levels of transcription, was increased. Furthermore, the appearance of many novel transcripts during pollen germination as well as tube growth indicates that these newly expressed genes may function in this complex process.
2008-09-08 | GSE6696 | GEO
Project description:Successful pollination brings together the mature pollen grain and stigma papilla to initiate an intricate series of molecular processes meant to eventually enable sperm cell delivery for fertilization and reproduction. At maturity, the pollen and stigma cells have acquired proteomes comprising the primary molecular effectors required upon their meeting. In Brassica species, knowledge of the roles and global composition of these proteomes is largely lacking. To address this gap, gel-free shotgun proteomics was performed on the mature pollen and stigma of Brassica carinata, a representative of the Brassica family and its many crop species (e.g. B. napus, B. oleracea, B. rapa), which holds considerable potential as a bio-industrial crop. 5608 and 7703 B. carinata mature pollen and stigma proteins were identified, respectively. The pollen and stigma proteomes were found to reflect not only their many common functional and developmental objectives, but also important differences underlying their cellular specialization. Isobaric tag for relative and absolute quantification (iTRAQ) was exploited in the first analysis of a developing Brassicaceae stigma, and uncovered 251 B. carinata proteins that were differentially abundant during stigma maturation, providing insight into proteins involved in the initial phases of pollination.
2021-03-13 | PXD017953 | Pride