scholarly journals Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny A. Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Model Organism ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied. We analyzed transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrated that 45% of the genes in the genome were differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionarily conserved transcription factor containing an RWP-RK domain suggested a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in the induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Transcriptional profiling of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP‐RK transcription factors linked to reproduction

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Gametogenesis in the green seaweed Ulva mutabilis coincides with massive transcriptional restructuring

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie Dhondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Model Organism ◽  
Land Plants ◽  
Alternative Source ◽  
Master Regulators ◽  
Energy Applications ◽  
Starting Point ◽  
Green Seaweed

The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Here, gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function

2006 ◽  
Vol 84 (9) ◽  
pp. 1434-1443 ◽  
Author(s):  
Gernot G. Presting
Keyword(s):  
Dna Barcoding ◽  
Plastid Genome ◽  
Rational Design ◽  
Higher Plants ◽  
Dna Barcode ◽  
Single Copy ◽  
Land Plants ◽  
Computer Assisted ◽  
Plastid Genomes ◽  
Starting Point

All oligonucleotides of the sugarcane chloroplast genome that are conserved in one or more of 36 other completed plastid genomes have been identified by computer-assisted sequence comparison. These regions are of interest because they (i) are indicative of strong selection pressures to maintain specific nucleotide sequences that may yield insights into plastid biology and (ii) can be used as priming sites for amplifying intervening sequences that represent potential DNA barcodes for species identification. The majority of conserved sites are located in the inverted repeat (IR) region, but several sites in the single copy region (predominantly in tRNA and psa/psb genes) are conserved among chloroplasts of all higher plants examined here. Of particular interest are protein coding regions that have been conserved at the nucleotide level, as these may be involved in transcript regulation. This analysis also provides the basis for rational design of a DNA barcode for plastids, and several potential barcode regions have been identified. In particular, two oligonucleotides of length 33 and 25, and separated by approximately 362 nucleotides, are found in all cyanobacteria, red, brown and green algae, as well as diatoms, euglenids, apicomplexans and land plants that have been examined to date. Their widespread occurrence makes the intervening sequence a universal marker for all photosynthetic lineages. Analysis of 160 GenBank accessions illustrates that this region discriminates many algae at the species level, but lacks sufficient variation among the more recently diverged land plants to serve as a single DNA barcode for this taxon. However, this marker should be particularly useful for the DNA barcoding of algal lineages and lichens, as well as for environmental sampling. More rapidly evolving regions of the plastid genome also identified here serve as a starting point to design and test barcodes for more narrowly defined lineages, including the more recently diverged angiosperms.

scholarly journals Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

2019 ◽  
Vol 20 (14) ◽  
pp. 3591 ◽  
Author(s):  
Ming-Ming Liu ◽  
Mang-Mang Wang ◽  
Jin Yang ◽  
Jing Wen ◽  
Peng-Cheng Guo ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Higher Plants ◽  
Protein Complexes ◽  
Expression Patterns ◽  
Interaction Network ◽  
Land Plants ◽  
Terrestrial Plants ◽  
Functional Studies ◽  
Transcription Factor Genes ◽  
Tcp Family

The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants’ development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.

scholarly journals Gamete fusion rapidly reconstitutes a bi-partite transcription factor to block re-fertilization

2018 ◽  
Author(s):  
Aleksandar Vještica ◽  
Laura Merlini ◽  
Pedro N’kosi ◽  
Sophie G Martin
Keyword(s):  
Transcription Factor ◽  
Sexual Reproduction ◽  
Model Organism ◽  
Nuclear Accumulation ◽  
M Cell ◽  
Cell Fates ◽  
Gamete Fusion ◽  
Zygotic Transcription ◽  
Distinct Cell ◽  
Homeobox Protein

AbstractThe ploidy cycle, integral to sexual reproduction, requires not only meiosis to halve the number of chromosomes, but also mechanisms that ensure zygotes are formed by exactly two partners1–5. During sexual reproduction of the fungal model organism Schizosaccharomyces pombe, haploid P- and M-cells normally fuse to form a diploid zygote that immediately enters meiosis6. Here, we reveal that fast post-fusion reconstitution of a bi-partite transcription factor actively blocks re-fertilization. We first identify mutants that undergo transient cell fusion involving cytosol exchange but not karyogamy, and show this drives distinct cell fates in the two gametes: The P-partner undergoes lethal, haploid meiosis while the M-cell persists in mating. Consistently, we find that the zygotic transcription that drives meiosis is initiated rapidly only from the P-parental genome, even in wild type cells. This asymmetric gene expression depends on a bi-partite complex formed post-fusion between the nuclear P-cell-specific homeobox protein Pi and a cytosolic M-specific peptide Mi7,8, which is captured by Pi in the P-nucleus. Zygotic transcription is thus poised to initiate in the P-nucleus as fast as Mi reaches it. The asymmetric nuclear accumulation is inherent to the transcription factor design, and is reconstituted by a pair of synthetic interactors, one localized to the nucleus of one gamete and the other in the cytosol of its partner. Strikingly, imposing a delay in zygotic transcription, by postponing Mi expression or deleting its transcriptional target in the P-genome, leads to zygotes fusing with additional gametes, thus forming polyploids and eventually aneuploid progeny. We further show that the signaling cascade to block re-fertilization shares components with, but bifurcates from, meiotic induction9–11. Thus, cytoplasmic connection upon gamete fusion leads to rapid reconstitution of a bi-partite transcription factor in one partner to block re-fertilization and induce meiosis, thus ensuring genome maintenance during sexual reproduction.

scholarly journals Health and longevity studies in C. elegans: the “healthy worm database” reveals strengths, weaknesses and gaps of test compound-based studies

2021 ◽  
Vol 22 (2) ◽  
pp. 215-236
Author(s):  
Nadine Saul ◽  
Steffen Möller ◽  
Francesca Cirulli ◽  
Alessandra Berry ◽  
Walter Luyten ◽  
...  
Keyword(s):  
Healthy Aging ◽  
Model Organism ◽  
Research Field ◽  
Aging Research ◽  
Genetic Manipulations ◽  
C Elegans ◽  
Starting Point ◽  
Health Related ◽  
Phenotype Measurement ◽  
Or Gene

AbstractSeveral biogerontology databases exist that focus on genetic or gene expression data linked to health as well as survival, subsequent to compound treatments or genetic manipulations in animal models. However, none of these has yet collected experimental results of compound-related health changes. Since quality of life is often regarded as more valuable than length of life, we aim to fill this gap with the “Healthy Worm Database” (http://healthy-worm-database.eu). Literature describing health-related compound studies in the aging model Caenorhabditis elegans was screened, and data for 440 compounds collected. The database considers 189 publications describing 89 different phenotypes measured in 2995 different conditions. Besides enabling a targeted search for promising compounds for further investigations, this database also offers insights into the research field of studies on healthy aging based on a frequently used model organism. Some weaknesses of C. elegans-based aging studies, like underrepresented phenotypes, especially concerning cognitive functions, as well as the convenience-based use of young worms as the starting point for compound treatment or phenotype measurement are discussed. In conclusion, the database provides an anchor for the search for compounds affecting health, with a link to public databases, and it further highlights some potential shortcomings in current aging research.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

scholarly journals Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes

2014 ◽  
Vol 65 (15) ◽  
pp. 4433-4449 ◽  
Author(s):  
Kazuya Koyama ◽  
Mineyo Numata ◽  
Ikuko Nakajima ◽  
Nami Goto-Yamamoto ◽  
Hideo Matsumura ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Functional Characterization ◽  
Myb Transcription Factor

scholarly journals Gene targeting facilitated by engineered sequence-specific nucleases and its potential for applications in crop improvement

2021 ◽  
Author(s):  
Daisuke Miki ◽  
Rui Wang ◽  
Jing Li ◽  
Dali Kong ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Gene Targeting ◽  
Agronomic Traits ◽  
Higher Plants ◽  
Crop Improvement ◽  
Strand Break ◽  
End Joining ◽  
Homology Directed Repair ◽  
Target Dna ◽  
Targeted Gene Editing ◽  
Non Homologous End Joining

Abstract Humans are currently facing the problem of how to ensure that there is enough food to feed all of the world’s population. Ensuring that the food supply is sufficient will likely require the modification of crop genomes to improve their agronomic traits. The development of engineered sequence-specific nucleases (SSNs) paved the way for targeted gene editing in organisms, including plants. SSNs generate a double-strand break (DSB) at the target DNA site in a sequence-specific manner. These DSBs are predominantly repaired via error-prone non-homologous end joining (NHEJ), and are only rarely repaired via error-free homology-directed repair (HDR) if an appropriate donor template is provided. Gene targeting (GT), i.e., the integration or replacement of a particular sequence, can be achieved with combinations of SSNs and repair donor templates. Although its efficiency is extremely low, GT has been achieved in some higher plants. Here, we provide an overview of SSN-facilitated GT in higher plants and discuss the potential of GT as a powerful tool for generating crop plants with desirable features.

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