Lignin deposits in xylem vessels of pedicel regulate water transport during seed maturation in soybean (Glycine max L. Merr.)
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PROVIDER: PRJNA563629 | ENA |
REPOSITORIES: ENA
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Project description:Seed desiccation during maturation is important process for seed post-maturation behavior and harvest. However, the desiccation mechanism in soybean seed maturation is hardly known. In this study, water content in seed, pod and pedicel decreased faster than that in peduncle and stem. Therefore, we focus on the pedicel during seed maturation. By morphological analysis, the deposits in xylem vessels were confirmed in pedicel at 61 day after flowering (DAF), when there are not the deposits in peduncle. It was clarified by microarray analysis that lignin biosynthesis related genes expressed in pedicel at 61 DAF. Indeed, GmPAL, Gm4CL, GmC3H and GmCAD, which are lignin biosynthesis related genes, increased in pedicel during seed maturation. Furthermore, lignin content in pedicel also increased toward at 61 DAF and accumulated in the xylem vessels. These results suggested that lignin deposits into xylem vessels in pedicel cause the soybean seed desiccation during seed maturation.
2021-04-01 | GSE136771 | GEO
Project description:We report the in vivo binding of transcription factor MerR in the presence and absence of mercury as measured by ChIPSeq.
2014-12-31 | GSE60461 | GEO
Project description:The MerR family of transcriptional regulators are dimeric proteins with an N-terminal helix-turn-helix DNA binding domain (DBD), followed by an antiparallel coiled-coil subunit interaction region, and usually by a C-terminal effector binding domain (EBD). This family is distinguished by the high amino acid similarity in the DBD and low similarity in the EBD, consistent with the role of this domain in each protein in sensing effector molecules. Most members of the family are activators, and act at promoters with long spacer regions and respond to the binding of inducers by distorting the promoter DNA to allow open complex formation and transcriptional activation. In MerR proteins the EBD contains a metal binding pocket formed by three cysteines. This Cys center characteristic of MerR regulators is primarily suited for metal binding and mediates activation of metal detoxification systems in bacteria. Over the last decade, it has become clear that the MerR family of regulators is more diverse than originally recognized. The availability of completed bacterial genome sequences has enabled the search for additional types of MerR-like regulators. We here present a novel MerR-like transcription factor lacking an EBD involved in iron uptake regulation (MliR) present in the marine bacterium Bizionia argentinensis (JUB59). An in silico analysis revealed that homologues of the MliR protein are widely distributed among different bacterial species. Deletion of the mliR gene led to decreased cell growth, increased cell adhesion and filamentation. RNA sequencing analysis showed that expression of several iron uptake-related mRNAs were downregulated in mliR-deletion mutant. Through NMR-based metabolomics, ICP-MS, fluorescence microscopy and biochemical analysis we evaluated metabolic and phenotypic changes associated with mliR deletion. This work provides the first evidence of a MerR-family regulator involved in iron uptake and contributes to expanding our current knowledge on iron metabolism.in bacteria.
2022-08-23 | GSE189140 | GEO
Project description:We used unsupervised hierarchical clustering to analyse expression in primary ovarian tumors and associated abdominal deposits. GeneGo pathway analysis of differentially expressed genes between primary tumors and deposits revealed 4 of the top 10 pathways related to cytoskeleton remodeling and cell adhesion. Primary ovarian tumours and matched abdominal deposits were selected for RNA extraction and hybridization on Affymetrix microarrays.
2012-06-14 | E-GEOD-38734 | biostudies-arrayexpress
Project description:Glycine max (Linn.) Merr. Raw sequence reads
| PRJNA886475 | ENA
Project description:PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.
| S-EPMC7501814 | biostudies-literature
Project description:Cell wall patterning is central to determining the shape and function of plant cells. Protoxylem and metaxylem vessel cells deposit banded and pitted cell walls, respectively, which enable their distinctive water transport capabilities, but the mechanisms that specify which cell wall pattern is laid down remain unknown. Here, we show that the pitted cell wall pattern in metaxylem vessels is specified by transcriptional control of actin polymerization. A newly isolated allele of KNOTTED-like homeobox transcription factor 7 (KNAT7) was associated with the formation of banded cell walls in metaxylem vessels. To identify the genes responsible for altering the cell wall pattern in knat7 xylem vessels, we performed an RNA-seq analysis of knat7. We used in vitro cultures of hypocotyls and cotyledons because the population of differentiating xylem cells in intact roots is tiny and these methods efficiently induce ectopic differentiation of xylem vessel elements. Formin Homology Domain-Containing Protein 11 (FH11) was upregulated in knat7 metaxylem, but expressed only in protoxylem vessels in wild-type plants. Loss of FH11 suppressed the knat7 phenotype. Conversely, ectopic overexpression of FH11 in metaxylems mimicked the knat7 phenotype. FH11 function required its plasma membrane anchoring and the actin polymerization activity. Actin polymerization by FH11 at the plasma membrane caused the dispersion of activated ROP GTPases, the determinant of pit formation. These results suggest that decontrol of actin polymerization at the plasma membrane abolishes the pitted cell wall formation and promotes the formation of banded cell walls in metaxylem vessels. This study unveils the importance of the proper control of actin polymerization on cell wall pattern specification.
2025-01-15 | GSE286145 | GEO
Project description:1. Assessment of correlation between tumor deposits and clinicopathological characteristics of colorectal cancer.
2. Detection of association between tumor deposits and stage of colorectal cancer.
3. Evaluate the relationship between tumor deposits and prognosis of colorectal cancer patient.
| 2368835 | ecrin-mdr-crc
Project description:Bentonite clay pressure vessels
| PRJEB39478 | ENA
Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification.
2012-05-06 | GSE37736 | GEO