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Genomics & Informatics May 2024Small auxin-up RNA (SAUR) proteins were known as a large family that supposedly participated in various biological processes in higher plant species. However, the SAUR...
Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao).
Small auxin-up RNA (SAUR) proteins were known as a large family that supposedly participated in various biological processes in higher plant species. However, the SAUR family has been still not explored in cacao (Theobroma cacao L.), one of the most important industrial trees. The present work, as an in silico study, revealed comprehensive aspects of the structure, phylogeny, and expression of TcSAUR gene family in cacao. A total of 90 members of the TcSAUR gene family have been identified and annotated in the cacao genome. According to the physic-chemical features analysis, all TcSAUR proteins exhibited slightly similar characteristics. Phylogenetic analysis showed that these TcSAUR proteins could be categorized into seven distinct groups, with 10 sub-groups. Our results suggested that tandemly duplication events, segmental duplication events, and whole genome duplication events might be important in the growth of the TcSAUR gene family in cacao. By re-analyzing the available transcriptome databases, we found that a number of TcSAUR genes were exclusively expressed during the zygotic embryogenesis and somatic embryogenesis. Taken together, our study will be valuable to further functional characterizations of candidate TcSAUR genes for the genetic engineering of cacao.
PubMed: 38907330
DOI: 10.1186/s44342-024-00003-6 -
The EMBO Journal Jun 2024Cell polarity networks are defined by quantitative features of their constituent feedback circuits, which must be tuned to enable robust and stable polarization, while...
Cell polarity networks are defined by quantitative features of their constituent feedback circuits, which must be tuned to enable robust and stable polarization, while also ensuring that networks remain responsive to dynamically changing cellular states and/or spatial cues during development. Using the PAR polarity network as a model, we demonstrate that these features are enabled by the dimerization of the polarity protein PAR-2 via its N-terminal RING domain. Combining theory and experiment, we show that dimer affinity is optimized to achieve dynamic, selective, and cooperative binding of PAR-2 to the plasma membrane during polarization. Reducing dimerization compromises positive feedback and robustness of polarization. Conversely, enhanced dimerization renders the network less responsive due to kinetic trapping of PAR-2 on internal membranes and reduced sensitivity of PAR-2 to the anterior polarity kinase, aPKC/PKC-3. Thus, our data reveal a key role for a dynamically oligomeric RING domain in optimizing interaction affinities to support a robust and responsive cell polarity network, and highlight how optimization of oligomerization kinetics can serve as a strategy for dynamic and cooperative intracellular targeting.
PubMed: 38907033
DOI: 10.1038/s44318-024-00123-3 -
Plant Physiology Jun 2024Body axis establishment is one of the earliest patterning events in plant embryogenesis. Asymmetric zygote division is critical for apical-basal axis formation in...
Body axis establishment is one of the earliest patterning events in plant embryogenesis. Asymmetric zygote division is critical for apical-basal axis formation in Arabidopsis (Arabidopsis thaliana). However, how the orientation of the cell division plane is regulated and its relation to apical-basal axis establishment and proper position of embryos in grasses remain poorly understood. By characterizing mutants of 3 rice (Oryza sativa) WUSCHEL HOMEOBOX9 (WOX9) genes, whose paralogs in Arabidopsis play essential roles in zygotic asymmetric cell division and cell fate determination, we found 2 kinds of independent embryonic defects: topsy-turvy embryos, in which apical-basal axis twists from being parallel to the longitudinal axis of the seed to being perpendicular; and organ-less embryos. In contrast to their Arabidopsis orthologs, OsWOX9s displayed dynamic distribution during embryo development. Both DWT1/OsWOX9A and DWL2/WOX9C play major roles in the apical-basal axis formation and initiation of stem cells. In addition, DWT1 has a distinct function in regulating the first few embryonic cell divisions to ensure the correct orientation of the embryo in the ovary. In summary, DWT1 acts in 2 steps during rice embryo pattern formation: the initial zygotic division, and with DWL2 to establish the main body axes and stem cell fate 2 to 3 d after pollination.
PubMed: 38905146
DOI: 10.1093/plphys/kiae318 -
Frontiers in Endocrinology 2024Polycystic ovary syndrome with insulin resistance (PCOS-IR) is the most common endocrine and metabolic disease in women of reproductive age, and low fertility in PCOS...
High coverage of targeted lipidomics revealed lipid changes in the follicular fluid of patients with insulin-resistant polycystic ovary syndrome and a positive correlation between plasmalogens and oocyte quality.
BACKGROUND
Polycystic ovary syndrome with insulin resistance (PCOS-IR) is the most common endocrine and metabolic disease in women of reproductive age, and low fertility in PCOS patients may be associated with oocyte quality; however, the molecular mechanism through which PCOS-IR affects oocyte quality remains unknown.
METHODS
A total of 22 women with PCOS-IR and 23 women without polycystic ovary syndrome (control) who underwent fertilization and embryo transfer were recruited, and clinical information pertaining to oocyte quality was analyzed. Lipid components of follicular fluid (FF) were detected using high-coverage targeted lipidomics, which identified 344 lipid species belonging to 19 lipid classes. The exact lipid species associated with oocyte quality were identified.
RESULTS
The number (rate) of two pronuclear (2PN) zygotes, the number (rate) of 2PN cleaved embryos, and the number of high-quality embryos were significantly lower in the PCOS-IR group. A total of 19 individual lipid classes and 344 lipid species were identified and quantified. The concentrations of the 19 lipid species in the normal follicular fluid (control) ranged between 10 mol/L and 10 mol/L. In addition, 39 lipid species were significantly reduced in the PCOS-IR group, among which plasmalogens were positively correlated with oocyte quality.
CONCLUSIONS
This study measured the levels of various lipids in follicular fluid, identified a significantly altered lipid profile in the FF of PCOS-IR patients, and established a correlation between poor oocyte quality and plasmalogens in PCOS-IR patients. These findings have contributed to the development of plasmalogen replacement therapy to enhance oocyte quality and have improved culture medium formulations for oocyte maturation (IVM).
Topics: Humans; Female; Polycystic Ovary Syndrome; Follicular Fluid; Oocytes; Adult; Lipidomics; Insulin Resistance; Plasmalogens; Fertilization in Vitro; Lipids; Infertility, Female; Lipid Metabolism; Embryo Transfer; Case-Control Studies
PubMed: 38904043
DOI: 10.3389/fendo.2024.1414289 -
International Journal of Molecular... May 2024Global methylation levels differ in in vitro- and in vivo-developed embryos. Follicular fluid (FF) contains extracellular vesicles (EVs) containing miRNAs that affect...
Global methylation levels differ in in vitro- and in vivo-developed embryos. Follicular fluid (FF) contains extracellular vesicles (EVs) containing miRNAs that affect embryonic development. Here, we examined our hypothesis that components in FF affect global DNA methylation and embryonic development. Oocytes and FF were collected from bovine ovaries. Treatment of zygotes with a low concentration of FF induced global DNA demethylation, improved embryonic development, and reduced DNMT1/3A levels. We show that embryos take up EVs containing labeled miRNA secreted from granulosa cells and the treatment of zygotes with EVs derived from FF reduces global DNA methylation in embryos. Furthermore, the methylation levels of in vitro-developed blastocysts were higher than those of in their vivo counterparts. Based on small RNA-sequencing and in silico analysis, we predicted miR-29b, -199a-3p, and -148a to target DNMTs and to induce DNA demethylation, thereby improving embryonic development. Moreover, among FF from 30 cows, FF with a high content of these miRNAs demethylated more DNA in the embryos than FF with a lower miRNA content. Thus, miRNAs in FF play a role in early embryonic development.
Topics: Animals; Female; MicroRNAs; Cattle; Follicular Fluid; Extracellular Vesicles; Embryonic Development; DNA Methylation; DNA Demethylation; Oocytes; Blastocyst; Embryo, Mammalian; Gene Expression Regulation, Developmental; Zygote
PubMed: 38892059
DOI: 10.3390/ijms25115872 -
International Journal of Molecular... May 2024In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their...
Prediction of Pesticide Interactions with Proteins Involved in Human Reproduction by Using a Virtual Screening Approach: A Case Study of Famoxadone Binding CRBP-III and Izumo.
In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their influence on human fertility. In this study, we investigated, by a virtual screening approach, the binding between pesticides and proteins present in human gametes or associated with reproduction, in order to identify new interactions that could affect human fertility. To this aim, we prepared ligand (pesticides) and receptor (proteins) 3D structure datasets from online structural databases (such as PubChem and RCSB), and performed a virtual screening analysis using Autodock Vina. In the comparison of the predicted interactions, we found that famoxadone was predicted to bind Cellular Retinol Binding Protein-III in the retinol-binding site with a better minimum energy value of -10.4 Kcal/mol and an RMSD of 3.77 with respect to retinol (-7.1 Kcal/mol). In addition to a similar network of interactions, famoxadone binding is more stabilized by additional hydrophobic patches including L20, V29, A33, F57, L117, and L118 amino acid residues and hydrogen bonds with Y19 and K40. These results support a possible competitive effect of famoxadone on retinol binding with impacts on the ability of developing the cardiac tissue, in accordance with the literature data on zebrafish embryos. Moreover, famoxadone binds, with a minimum energy value between -8.3 and -8.0 Kcal/mol, to the IZUMO Sperm-Egg Fusion Protein, interacting with a network of polar and hydrophobic amino acid residues in the cavity between the 4HB and Ig-like domains. This binding is more stabilized by a predicted hydrogen bond with the N185 residue of the protein. A hindrance in this position can probably affect the conformational change for JUNO binding, avoiding the gamete membrane fusion to form the zygote. This work opens new interesting perspectives of study on the effects of pesticides on fertility, extending the knowledge to other typologies of interaction which can affect different steps of the reproductive process.
Topics: Humans; Molecular Docking Simulation; Protein Binding; Pesticides; Retinol-Binding Proteins, Cellular; Binding Sites; Reproduction; Animals; Hydrogen Bonding; Ligands
PubMed: 38891976
DOI: 10.3390/ijms25115790 -
International Journal of Molecular... May 2024Species of the genus have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are...
Species of the genus have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing females and males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, and , the functional RDC complex in hybrid ovaries was not assembled. However, the activity of the RDC complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial piRNA targeting of the allele and a significant zygotic delay in expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.
Topics: Animals; Female; Drosophila melanogaster; Male; Drosophila simulans; Drosophila Proteins; RNA, Small Interfering; DNA Transposable Elements; Ovary; Hybridization, Genetic; Oogenesis; Infertility; Crosses, Genetic; DEAD-box RNA Helicases
PubMed: 38891872
DOI: 10.3390/ijms25115681 -
International Journal of Molecular... May 2024The testis-specific double sex and mab-3-related transcription factor 1 () has long been recognized as a crucial player in sex determination across vertebrates, and its...
The testis-specific double sex and mab-3-related transcription factor 1 () has long been recognized as a crucial player in sex determination across vertebrates, and its essential role in gonadal development and the regulation of spermatogenesis is well established. Here, we report the cloning of the key spermatogenesis-related cDNA, named , from the gonads of (), with a molecular weight of 41.93 kDa and an isoelectric point of 7.83 (pI). Our hypothesis is that machinery governs spermatogenesis and regulates gonadogenesis. RNAi-mediated knockdown revealed its critical role in hindering spermatogenesis and reducing expression levels in boring giant clams. A histological analysis showed structural changes, with normal sperm cell counts in the control group (ds-EGFP) but significantly lower concentrations of sperm cells in the experimental group (). transcripts during embryogenesis exhibited a significantly high expression pattern ( < 0.05) during the early zygote stage, and whole-embryo in-situ hybridization confirmed its expression pattern throughout embryogenesis. A qRT-PCR analysis of various reproductive stages revealed an abundant expression of in the gonads during the male reproductive stage. In-situ hybridization showed tissue-specific expression of , with a positive signal detected in male-stage gonadal tissues comprising sperm cells, while no signal was detected in other stages. Our study findings provide an initial understanding of the molecular machinery controlling spermatogenesis and its specificity in male-stage gonads of the key bivalve species, , and suggest that predominantly functions as a key regulator of spermatogenesis in giant clams.
Topics: Animals; Spermatogenesis; Transcription Factors; Male; Testis; Bivalvia; Gene Expression Regulation, Developmental; Gonads; Hermaphroditic Organisms; Cloning, Molecular; Phylogeny; Amino Acid Sequence
PubMed: 38891762
DOI: 10.3390/ijms25115574 -
Nature Reviews. Genetics Jun 2024Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules.... (Review)
Review
Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
PubMed: 38890558
DOI: 10.1038/s41576-024-00744-8 -
Frontiers in Cell and Developmental... 2024What is the utilization rate of embryos that exert inadequate zygote cleavage into three daughter cells?
RESEARCH QUESTION
What is the utilization rate of embryos that exert inadequate zygote cleavage into three daughter cells?
DESIGN
This study used a retrospective dataset from a single IVF Unit. A total of 3,060 embryos from 1,811 fresh IVF cycles were analyzed. The cleavage pattern, morphokinetics, and outcome were recorded. Only 2pn embryos, fertilized by ejaculated sperm, and cultured in a time-lapse system for at least 5 days were included. We generated three study groups according to the embryo's cleavage pattern: (I) Control, normal cleavage ( = 551); (II) fast cleavage, zygote to three cells within 5 h ( = 1,587); and (III) instant direct tripolar cleavage (IDC) from zygote to three cells ( = 922).
RESULTS
The rate of usable fast cleavage blastocysts was 108/1,587 (6.81%) and usable control blastocysts was 180/551 (32.67%). The time of PN fading and from fading to first cleavage differed significantly between the three groups. Although the pregnancy rate of control and fast cleavage blastocysts were comparable (40.35% and 42.55%, respectively), the amount of instant direct cleavage embryos that reached blastocyst stage was neglectable (only four embryos out of 922 analyzed IDC embryos) and unsuitable for statistical comparison of pregnancy rates.
CONCLUSION
Our results indicate the need to culture instant direct cleavage embryos for 5 days, up to the blastocyst stage, and avoid transfer of embryos that are fated to arrest even when their morphological grade on day 3 is acceptable, whereas fast cleavage embryos could be transferred on day 3 when there is no alternative.
PubMed: 38887513
DOI: 10.3389/fcell.2024.1398684