scholarly journals Beta galactosidases in Arabidopsis and tomato–a mini review

2016 ◽  
Vol 44 (1) ◽  
pp. 150-158 ◽  
Author(s):  
Balakumaran Chandrasekar ◽  
Renier A.L. van der Hoorn
Keyword(s):  
Cell Wall ◽  
Signal Peptide ◽  
Expression Profiles ◽  
Plant Biology ◽  
Fruit Softening ◽  
Biological Processes ◽  
Glycosyl Hydrolases ◽  
Seed Imbibition ◽  
Galactosyl Residues

Beta galactosidases (BGALs) are glycosyl hydrolases that remove terminal β-D-galactosyl residues from β-D-galactosides. There are 17 predicted BGAL genes in the genomes of both Arabidopsis (BGAL1–17) and tomato (TBG1–17). All tested BGALs have BGAL activity but their distinct expression profiles and ancient phylogenetic separation indicates that these enzymes fulfil diverse, non-redundant roles in plant biology. The majority of these BGALs are predicted to have signal peptide and thought to act during cell wall-related biological processes. Interestingly, deletion of BGAL6 and BGAL10 in Arabidopsis causes reduced mucilage release during seed imbibition and shorter siliques respectively, whereas TBG4 depletion by RNAi decreases in fruit softening in tomato. The majority of plant BGALs remain to be characterized.

scholarly journals The Craterostigma plantagineum protein kinase CpWAK1 interacts with pectin and integrates different environmental signals in the cell wall

Planta ◽  
2021 ◽  
Vol 253 (5) ◽  
Author(s):  
Peilei Chen ◽  
Valentino Giarola ◽  
Dorothea Bartels
Keyword(s):  
Cell Wall ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Cell Wall Protein ◽  
Biological Processes ◽  
Environmental Signals ◽  
High Affinity ◽  
Craterostigma Plantagineum ◽  
Receptor Kinases

Abstract Main conclusion The cell wall protein CpWAK1 interacts with pectin, participates in decoding cell wall signals, and induces different downstream responses. Abstract Cell wall-associated protein kinases (WAKs) are transmembrane receptor kinases. In the desiccation-tolerant resurrection plant Craterostigma plantagineum, CpWAK1 has been shown to be involved in stress responses and cell expansion by forming a complex with the C. plantagineum glycine-rich protein1 (CpGRP1). This prompted us to extend the studies of WAK genes in C. plantagineum. The phylogenetic analyses of WAKs from C. plantagineum and from other species suggest that these genes have been duplicated after species divergence. Expression profiles indicate that CpWAKs are involved in various biological processes, including dehydration-induced responses and SA- and JA-related reactions to pathogens and wounding. CpWAK1 shows a high affinity for “egg-box” pectin structures. ELISA assays revealed that the binding of CpWAKs to pectins is modulated by CpGRP1 and it depends on the apoplastic pH. The formation of CpWAK multimers is the prerequisite for the CpWAK–pectin binding. Different pectin extracts lead to opposite trends of CpWAK–pectin binding in the presence of Ca2+ at pH 8. These observations demonstrate that CpWAKs can potentially discriminate and integrate cell wall signals generated by diverse stimuli, in concert with other elements, such as CpGRP1, pHapo, Ca2+[apo], and via the formation of CpWAK multimers.

scholarly journals (472) Yeast Expressed Tomato β-Galactosidases 1, 4, and 5 Have Activity against Synthetic and Plant-derived Cell Wall Substrates

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1092B-1092 ◽  
Author(s):  
Megumi Ishimaru ◽  
David L. Smith ◽  
Kenneth C. Gross
Keyword(s):  
Cell Wall ◽  
Tomato Fruit ◽  
Wall Material ◽  
Wall Structure ◽  
Fruit Softening ◽  
Pectic Polysaccharides ◽  
Wide Range ◽  
Fruit Pericarp ◽  
Galactosyl Residues

Fruit softening occurs by several mechanisms, including modifications of cell wall structure by wall degrading enzymes. The most prominent change in tomato fruit pericarp wall composition is the loss of galactosyl residues throughout development and especially during ripening. In order to understand the role of galactosyl turnover in fruit softening, we successfully produced three recombinant tomato β-galactosidase/exo-galactanase (TBG) fusion proteins in yeast. TBG1, 4 and 5 enzyme properties and substrate specificities were assessed. Optimum pH of TBG1, 4 and 5 was 5.0, 4.0, and 4.5 and optimum temperature was 40∼50, 40, and 40 °C, respectively. The K ms for TBG1, 4 and 5 were 7.99, 0.09, and 2.42 mm, respectively, using p-nitrophenyl-β-D-galactopyranoside as substrate. Using synthetic and plant-derived substrates, TBG1 and 5 released galactosyl residues from 1 → 4 linkages. TBG4 released galactosyl residues from a wide range of plant-derived oligosaccharides and polysaccharides. Using tomato fruit cell wall material, TBG1, TBG4 and TBG5 released galactosyl residues from a variety of fruit stages and cell wall fractions. TBG4 released the most galactosyl residues from the ASP fraction and especially the ASP fraction from fruit at the turning stage. Interestingly, even though walls from Turning fruit stage contain less total galactosyl residues than at the Mature Green stage, TBG4 released 3–4 fold more galactose from the CSP and ASP fractions from Turning fruit. These results suggest that changes in structure of wall pectic polysaccharides leading up to the Turning stage may cause the wall to become more susceptible to hydrolysis by the TBG4 product.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

The expansin EXP1 gene in the elongation zone is induced during soybean embryonic axis germination and differentially expressed in response to ABA and PEG treatments

2020 ◽  
pp. 1-9
Author(s):  
Nidia H. Montechiarini ◽  
Luciana Delgado ◽  
Eligio N. Morandi ◽  
Néstor J. Carrillo ◽  
Carlos O. Gosparini
Keyword(s):  
Cell Wall ◽  
Seed Germination ◽  
Water Availability ◽  
Expression Profiles ◽  
Soybean Seed ◽  
Embryonic Axis ◽  
Growth Potential ◽  
Elongation Zone ◽  
Degenerate Primers ◽  
Embryonic Axes

Abstract During soybean seed germination, the expansive growth potential of the embryonic axes is driven by water uptake while cell wall loosening occurs in cells from the elongation zone (EZ). Expansins are regarded as primary promoters of cell wall remodelling in all plant expansion processes, with the expression profiles of the soybean expansins supporting their cell or tissue specificity. Therefore, we used embryonic axes isolated from whole seed and focused on the EZ to study seed germination. Using a suite of degenerate primers, we amplified an abundantly expressed expansin gene at the EZ during soybean embryonic axis germination, which was identified as EXP1 by in silico analyses. Expression studies showed that EXP1 was induced under germination conditions in distilled water and down-regulated by abscisic acid (ABA), which inhibits soybean germination by physiologically restraining expansion. Moreover, we also identified a time window of ABA responsiveness within the first 6 h of incubation in water, after which ABA lost control of both EXP1 expression and embryonic axis germination, thus confirming the early role of EXP1 in the EZ during this process. By contrast, EXP1 levels in the EZ increased even when germination was impaired by osmotically limiting the water availability required to develop the embryonic axes’ growth potential. We propose that these higher EXP1 levels are involved in the fast germination of soybean embryonic axes as soon as water availability is re-established. Taken together, our results show strong EXP1 expression in the EZ and postulate EXP1 as a target candidate for soybean seed germination control.

scholarly journals Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Localization ◽  
Expression Profiles ◽  
Cell Types ◽  
Molecular Signature ◽  
Receptor Protein ◽  
Specific Gene ◽  
Specific Cell ◽  
Biological Processes ◽  
Endometrial Cells

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

scholarly journals Identification of Key Candidate Genes Involved in the Progression of Idiopathic Pulmonary Fibrosis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1123
Author(s):  
Yu Cui ◽  
Jie Ji ◽  
Jiwei Hou ◽  
Yi Tan ◽  
Xiaodong Han
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Novel Treatments ◽  
Kegg Pathway Analysis ◽  
Cell Components ◽  
Upregulated Genes

Idiopathic pulmonary fibrosis (IPF) is a lethal, agnogenic interstitial lung disease with limited therapeutic options. To investigate vital genes involved in the development of IPF, we integrated and compared four expression profiles (GSE110147, GSE53845, GSE24206, and GSE10667), including 87 IPF samples and 40 normal samples. By reanalyzing these datasets, we managed to identify 62 upregulated genes and 20 downregulated genes in IPF samples compared with normal samples. Differentially expressed genes (DEGs) were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to illustrate relevant pathways of IPF, biological processes, molecular function, and cell components. The DEGs were then subjected to protein–protein interaction (PPI) for network analysis, serving to find 11 key candidate genes (ANXA3, STX11, THBS2, MMP1, MMP9, MMP7, MMP10, SPP1, COL1A1, ITGB8, IGF1). The result of RT-qPCR and immunohistochemical staining verified our finding as well. In summary, we identified 11 key candidate genes related to the process of IPF, which may contribute to novel treatments of IPF.

scholarly journals Gene Expression Profiles at Moxibustioned Site (ST36): A Microarray Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Hai-Yan Yin ◽  
Yong Tang ◽  
Sheng-Feng Lu ◽  
Ling Luo ◽  
Jia-Ping Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Expression Profiles ◽  
Alternative Therapy ◽  
Gene Expression Profiles ◽  
Biological Processes ◽  
Physiological Conditions ◽  
Pathological Conditions ◽  
Molecular Events ◽  
Zusanli Acupoint

As a major alternative therapy in Traditional Chinese Medicine, it has been demonstrated that moxibustion could generate a series of molecular events in blood, spleen, and brain, and so forth. However, what would happen at the moxibustioned site remained unclear. To answer this question, we performed a microarray analysis with skin tissue taken from the moxibustioned site also Zusanli acupoint (ST36) where 15-minute moxibustion stimulation was administrated. The results exhibited 145 upregulated and 72 downregulated genes which responded immediately under physiological conditions, and 255 upregulated and 243 downregulated genes under pathological conditions. Interestingly, most of the pathways and biological processes of the differentially expressed genes (DEGs) under pathological conditions get involved in immunity, while those under physiological conditions are involved in metabolism.

scholarly journals Insights into the Mode of Action of Chitosan as an Antibacterial Compound

2008 ◽  
Vol 74 (12) ◽  
pp. 3764-3773 ◽  
Author(s):  
Dina Raafat ◽  
Kristine von Bargen ◽  
Albert Haas ◽  
Hans-Georg Sahl
Keyword(s):  
Antimicrobial Activity ◽  
Cell Wall ◽  
Cell Membrane ◽  
Mode Of Action ◽  
Membrane Lipids ◽  
Expression Profiles ◽  
Transcriptional Response ◽  
Response Analysis ◽  
Sequence Of Events ◽  
Wide Range

ABSTRACT Chitosan is a polysaccharide biopolymer that combines a unique set of versatile physicochemical and biological characteristics which allow for a wide range of applications. Although its antimicrobial activity is well documented, its mode of action has hitherto remained only vaguely defined. In this work we investigated the antimicrobial mode of action of chitosan using a combination of approaches, including in vitro assays, killing kinetics, cellular leakage measurements, membrane potential estimations, and electron microscopy, in addition to transcriptional response analysis. Chitosan, whose antimicrobial activity was influenced by several factors, exhibited a dose-dependent growth-inhibitory effect. A simultaneous permeabilization of the cell membrane to small cellular components, coupled to a significant membrane depolarization, was detected. A concomitant interference with cell wall biosynthesis was not observed. Chitosan treatment of Staphylococcus simulans 22 cells did not give rise to cell wall lysis; the cell membrane also remained intact. Analysis of transcriptional response data revealed that chitosan treatment leads to multiple changes in the expression profiles of Staphylococcus aureus SG511 genes involved in the regulation of stress and autolysis, as well as genes associated with energy metabolism. Finally, a possible mechanism for chitosan's activity is postulated. Although we contend that there might not be a single classical target that would explain chitosan's antimicrobial action, we speculate that binding of chitosan to teichoic acids, coupled with a potential extraction of membrane lipids (predominantly lipoteichoic acid) results in a sequence of events, ultimately leading to bacterial death.

Fruit softening correlates with enzymatic and compositional changes in fruit cell wall during ripening in ‘Bluecrop’ highbush blueberries

2019 ◽  
Vol 245 ◽  
pp. 163-170 ◽  
Author(s):  
Sinath Chea ◽  
Duk Jun Yu ◽  
Junhyung Park ◽  
Hee Duk Oh ◽  
Sun Woo Chung ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Softening ◽  
Compositional Changes ◽  
Highbush Blueberries
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