Biology subjects

Mironova, V.

Publications and source records attributed to Mironova, V..

10 recordsLinked to original sources

bioRxiv2024

MONOPTEROS isoform MP11ir role during somatic embryogenesis in Arabidopsis thaliana

Auxin is crucial for plant morphogenesis, including in vivo and in vitro embryo development. Exogenous auxin application is necessary for inducing embryogenic responses in in vitro cultured explants of Arabidopsis and other plants. Thus, components of auxin transport, signaling, and metabolism are key to somatic embryogenesis. AUXIN RESPONSE FACTOR (ARF) transcription factors bind to auxin response elements to control auxin-responsive gene expression and are vital in somatic embryo regeneration. ARFs are often repressed by AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs). MONOPTEROS (MP)/ARF5 is especially important in the embryogenic transition, being highly expressed during somatic embryogenesis; its mutant cannot develop somatic embryos. The MP11ir transcript, an alternatively spliced variant of MP, produces a truncated protein missing the Phox and Bem1p (PB1) domain, crucial for ARF-Aux/IAA dimerization. This renders the MP11ir isoform insensitive to Aux/IAA repression, suggesting an auxin-independent regulation. High levels of MP11ir transcript are observed during auxin- and trichostatin A-dependent induction of somatic embryogenesis. Both MP and MP11ir are essential for embryo regeneration in the mpS319 mutant. However, overexpression of a truncated MP protein ({Delta}ARF5) lacking the PB1 domain inhibits somatic embryogenesis, resulting in callus formation instead of somatic embryos. Overexpression of {Delta}ARF5, lack of MP protein (mp mutant), and interference with MP action by the auxin-resistant BODENLOS (BDL) protein affect the expression of the genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1), TAA1-RELATED 1 (TAR1), YUCCA3 (YUC3), YUC5 and YUC8, which are involved in auxin biosynthesis. The partial complementation of mpS319 by the expression of MP11ir may be due to the restoration of the expression of TAA1, TAR1, YUC3, YUC5, and YUC8 to the levels observed in the wild-type genotype Col-0. The presence of MP protein alone or in combination with MP11ir in mpS319 restored the expression of all analyzed genes compared to Col-0. Our results suggest that the analyzed auxin-related genes could be potential targets of MP11ir and/or MP. Consequently, {Delta}ARF5 overexpression alters auxin homeostasis and endogenous auxin levels, hindering embryogenic transition.

plant biology↗

bioRxiv2024

Mechanism of auxin-dependent gene regulation through composite auxin response elements

The plant signaling molecule auxin controls growth and development, largely through activating and repressing the expression of thousands of genes. Auxin-dependent transcriptional changes are mediated by DNA-binding Auxin Response Factors (ARF), whose AuxRE DNA binding sites are well-known. The identification of the first AuxRE showed this to be part of a composite element with a second motif. Indeed, systematic analysis showed other DNA motifs to be enriched in auxin-regulated promoters. Neither the basis for this enrichment nor the mechanisms for the activity of composite AuxREs is known. Here, we systematically mined Arabidopsis promoters for composite AuxRE elements enriched in auxin-responsive genes. We identified many and show that their presence is a reliable predictor of auxin response. Through mutating these elements and their higher-order modules, we demonstrate function in promoter activity. Lastly, we identified transcription factors (TFs) that bind AuxRE-associated motifs, showed their involvement in auxin response, and discovered that several of these TFs directly bind ARF proteins. We propose that ARF-TF complexes specifically bind compound motifs in promoters, and act as a source of diversification in auxin-dependent gene regulation.

plant biology↗

bioRxiv2024

Analysis of auxin responses in the fern Ceratopteris richardii identifies tissue ontogeny as a major determinant for response properties

The auxin signalling molecule regulates a range of plant growth and developmental processes. The core transcriptional machinery responsible for auxin-mediated responses is conserved across all land plants. Genetic, physiological and molecular exploration in bryophyte and angiosperm model species have shown both qualitative and quantitative differences in auxin responses. Given the highly divergent ontogeny of the dominant gametophyte (bryophytes) and sporophyte (angiosperms) generations, however, it is unclear whether such differences derive from distinct phylogeny or ontogeny. Here, we address this question by comparing a range of physiological, developmental and molecular responses to auxin in both generations of the model fern Ceratopteris richardii. We find that auxin response in Ceratopteris gametophytes closely resembles that of a thalloid bryophyte, whereas the sporophyte mimics auxin response in flowering plants. This resemblance manifests both at phenotypic and transcriptional level. Furthermore, we show that disrupting auxin transport can lead to ectopic sporophyte induction on the gametophyte, suggesting a role for auxin in the alternation of generations. Our study thus identifies ontogeny, rather than phylogeny, as a major determinant of auxin response properties in land plants. Summary statementStudies in angiosperms and bryophytes have left unresolved the roles of tissue ontogeny and species phylogeny in auxin response. We address that problem by characterizing auxin response in a fern.

plant biology↗

bioRxiv2021

AHK5 mediates ETR1-initiated multistep phosphorelay in Arabidopsis

Plants, like other sessile organisms, need to sense many different signals, and in response to them, modify their developmental programs to be able to survive in a highly changing environment. The multistep phosphorelay (MSP) in plants is a good candidate for a response mechanism that integrates multiple signal types both environmental and intrinsic in origin. Recently, ethylene was shown to control MSP activity via the histidine kinase (HK) activity of ETHYLENE RESPONSE 1 (ETR1)1,2, but the underlying molecular mechanism still remains unclear. Here we show that although ETR1 is an active HK, its receiver domain (ETR1RD) is structurally and functionally unable to accept the phosphate from the phosphorylated His in the ETR1 HK domain (ETR1HK) to initiate the phosphorelay to ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTERs (AHPs), the next link downstream members in MSP signaling. Instead, ETR1 interacts with another HK ARABIDOPSIS HISTIDINE KINASE 5 (AHK5) and transfers the phosphate from ETR1HK through the receiver domain of AHK5 (AHK5RD), and subsequently to AHP1, AHP2 and AHP3, independently of the HK activity of AHK5. We show that AHK5 is necessary for ethylene-initiated, but not cytokinin-initiated, MSP signaling in planta and that it thus mediates hormonal control of root growth.

plant biology↗

bioRxiv2021

The PLETHORA/PIN-FORMED/AUXIN network mediates terminal prehaustorium formation in the parasitic plant Striga hermonthica

The parasitic plant Striga hermonthica invades the host root through the formation of a haustorium and has detrimental impacts on cereal crops. The haustorium is derived directly from the differentiation of the Striga radicle. Currently, how Striga root cell lineages are patterned and the molecular mechanisms leading to radicle differentiation shortly after germination remain unclear. In this study, we determined the developmental-morphodynamic programs that regulate terminal haustorium formation in S. hermonthica at spatiotemporal and cellular resolutions. We showed that in S. hermonthica roots, meristematic cells first undergo multiplanar divisions, which decrease during growth and correlate with reduced expression of the stem cell regulator PLETHORA1. We also found that PIN-FORMED (PIN) proteins undergo a shift in polarity. Using the layout of the root structure and the polarity of outer-membrane PIN proteins, we constructed a mathematical model of auxin transport that explains the auxin distribution patterns observed during S. hermonthica root growth. Our results reveal a fundamental molecular and cellular framework governing the switch of S. hermonthica roots from the vegetative to the invasive state by inducing meristem differentiation through auxin excretion to the environment and explain how asymmetric PIN polarity controls auxin distribution to maintain meristem activity and sustain root growth.

plant biology↗

bioRxiv2020

Novel insights into the mode of action of 1,4-dioxane using a systems screening approach

1,4-Dioxane (1,4-DX) is an environmental contaminant found in drinking water throughout the United States (US). While it is a suspected liver carcinogen, there is no federal or state maximum contaminant level for 1,4-DX in drinking water. Very little is known about the mechanisms by which this chemical elicits liver carcinogenicity. In the present study, female BDF-1 mice were exposed to 1,4-DX (0, 50, 500 and 5,000 mg/L) in their drinking water for one or four weeks, to explore the toxic effects. Histopathological studies and a multi-omics approach (transcriptomics and metabolomics) were performed to investigate potential mechanisms of toxicity. Immunohistochemical analysis of the liver revealed increased H2AX{gamma}-positive hepatocytes (a marker of DNA double strand breaks), and an expansion of precholangiocytes (reflecting both DNA damage and repair mechanisms) after exposure. Liver transcriptomics revealed 1,4-DX-induced perturbations in signaling pathways predicted to impact the oxidative stress response, detoxification, and DNA damage. Liver, kidney, feces and urine metabolomic profiling revealed no effect of 1,4-DX exposure, and bile acid quantification in liver and feces similarly showed no effect of exposure. We speculate that the results may be reflective of DNA damage being counterbalanced by the repair response, with the net result being a null overall effect on the systemic biochemistry of the exposed mice. Our results show a novel approach for the investigation of environmental chemicals that do not elicit cell death but have activated the repair systems in response to 1,4-DX exposure.

pharmacology and toxicology↗

bioRxiv2019

Initiation and regulation of vascular tissue identity in the Arabidopsis embryo

Development of plant vascular tissues involves tissue specification, growth, pattern formation and cell type differentiation. While later steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We have used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we find that vascular identity is established in the 16-cell embryo. After a transient precursor state however, there is no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We find that while AUXIN RESPONSE FACTOR5/MONOPTEROS/ (ARF5/MP)-dependent auxin response is required, it is not sufficient for tissue establishment. We therefore used a large-scale enhanced Yeast One Hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, modulates vascular gene expression, along with its homolog GBF1. Furthermore, GBFs bind to MP and modulate its activity. Our work uncovers components of a gene regulatory network that controls the initiation of vascular tissue identity, one of which involves the interaction of MP and GBF2 proteins.

plant biology↗

bioRxiv2019

Synergic action of Vitamin D3 and 17β-estradiol on behavioral impairments induced by unpredictable mild stress in the adult ovariectomized female rats

The aim of the present study was study changes in antidepressant-like responses to Vitamin D3 (VD3) supplementation in three different doses (1.0, 2.5, and 5.0 mg/kg, s.c.) in long-term ovariectomized (OVX) rats treated with low dose of 17{beta}-E2 (0.5 g/rat, s.c.) during chronic unpredictable mild stress (CUMS). Sucrose preference (SPT), forced swimming (FST), and open-field (OFT) tests were administered to measure depression-like behavior. Brain-derived neurotrophic factor (BDNF), and serotonine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels in the hippocampus were measured by ELISA, western blotting analysis, and by using high performance liquid chromatography (HPLC), respectively.\n\nThe findings demonstrated that VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17{beta}-E2 increased sucrose consumption in the SPT and decreased depression-like in the FST of the long-term OVX rats exposed to CUMS. VD3 (5.0 mg/kg) resulted in significant elevated levels of hippocampal BDNF protein expression, as well as to the normalization of 5-HT and 5-HIAA levels in long-term OVX rats plus 17{beta}-E2 compared to the OVX rats plus solvent or 17{beta}-E2 submitted to CUMS. There were no significant effects of VD3 (1.0 and 2.5 mg/kg) treatment on both BDNF protein levels and 5-HT turnover in the hippocampus of the long-term OVX rats treated with 17{beta}-E2 exposed to CUMS compared to the long-term OVX with CUMS rats plus solvent.\n\nIn conclusion, VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17{beta}-E2 had a synergic antianhedonic- and antidepressant-like effects in the adult female rats following long-term ovariectomy submitted to CUMS. This is the first study in long-term OVX female rats showing beneficial effects of VD3 on depression-like behavior that are depended on the presence/absence of stressful factors.

animal behavior and cognition↗

bioRxiv2019

Molecular pathway analysis indicates a distinct metabolic and immune phenotype in women with right-sided colon cancer

Colon cancer is the third most commonly diagnosed cancer in the United States. Recent reports have shown that the location of the primary tumor is of clinical importance. Patients with right-sided cancers (RCCs) (tumors arising between the cecum and proximal transverse colon) have poorer clinical outcomes than those with left-sided colon cancers (LCCs) (tumors arising between the distal transverse colon and sigmoid colon, excluding the rectum). Interestingly, women have a lower incidence of colon cancer than men do. However, women have a higher propensity for RCC than men. Identification of gene expression differences between RCC and LCC is considered a potential means of prognostication. Furthermore, studying colon cancer sidedness could reveal important predictive markers for response to various treatments. This study provides a comprehensive bioinformatic analysis of various genes and molecular pathways that correlated with sex and anatomical location of colon cancer using four publicly available annotated datasets housed in the National Center for Biotechnology Informations Gene Expression Omnibus (GEO). We identified differentially expressed genes in tumor tissues from women with RCC, which showed attenuated energy and nutrient metabolism when compared to women with LCC. Specifically, we showed that the downregulation of 5 AMP-activated protein kinase alpha subunit (AMPK) and downregulated anti-tumor immune response in women with RCC. This difference was not seen when comparing tumor tissues from men with RCC to men with LCC. Therefore, women with RCC may have a specific metabolic and immune phenotype which accounts for differences in prognosis and treatment response.

cell biology↗

bioRxiv2018

Capturing auxin response factors syntax using DNA binding models

Auxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We find that the genome binding of two ARFs (ARF2 and ARF5/Monopteros/MP) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrate why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrate their power with biochemical experiments on the regulatory regions of the IAA19 model gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin up-regulated genes, thus deciphering the ARFbs syntax functional for regulation. This provides a general method to exploit the potential of genome-wide DNA binding assays and decode gene regulation.

plant biology↗