scholarly journals A soil-binding polysaccharide complex released from root hairs functions in rhizosheath formation

2021 ◽  
Author(s):  
Andrew F. Galloway ◽  
Jumana Akhtar ◽  
Emma Burak ◽  
Susan E. Marcus ◽  
Katie J. Field ◽  
...  
Keyword(s):  
Root Exudates ◽  
Root Exudate ◽  
Binding Capacity ◽  
Root Hairs ◽  
Arabinogalactan Protein ◽  
Wild Type ◽  
Binding Properties ◽  
Polysaccharide Complex ◽  
Acidic Form ◽  
Neutral Polymer

SUMMARYTo elucidate factors involved in rhizosheath formation, wild type (WT) barley (Hordeum vulgare L. cv. Pallas) and a root hairless mutant, bald root barley (brb), were investigated with a combination of physiological, biochemical and immunochemical assays. When grown in soil, WT barley roots bound ∼5-fold more soil than brb per unit root length. High molecular weight (HMW) polysaccharide exudates of brb roots had less soil-binding capacity than those of WT root exudates. Carbohydrate and glycan monoclonal antibody analyses of HMW polysaccharide exudates indicated differing glycan profiles. Relative to WT plants, root exudates of brb had reduced signals for arabinogalactan-protein (AGP), extensin and heteroxylan epitopes than brb. In contrast, the brb root exudate contained ∼25-fold more detectable xyloglucan epitope relative to WT. Epitope detection chromatography indicated that the increased detection of xyloglucan in brb exudates was due to enhanced abundance of a neutral polymer. Exudate preparations from brb had decreased amounts of an acidic form of xyloglucan associated with root-hair located glycoprotein and heteroxylan epitopes and with soil-binding properties. Therefore, in addition to physically structuring soil particles, root hairs facilitate rhizosheath formation by releasing a soil-binding polysaccharide complex.One sentence summaryThe root exudate of a root hairless mutant of barley, relative to wild type, has an altered pattern of polysaccharide epitopes and lesser amounts of an acidic soil-binding polysaccharide complex.

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals Human Rev1 relies on insert-2 to promote selective binding and accurate replication of stabilized G-quadruplex motifs

2021 ◽  
Author(s):  
Amit Ketkar ◽  
Lane Smith ◽  
Callie Johnson ◽  
Alyssa Richey ◽  
Makayla Berry ◽  
...  
Keyword(s):  
Amino Acids ◽  
Mutation Frequency ◽  
Control Sequence ◽  
Wild Type ◽  
Binding Properties ◽  
High Affinity ◽  
G4 Dna ◽  
G Quadruplex ◽  
Forward Mutagenesis

Abstract We previously reported that human Rev1 (hRev1) bound to a parallel-stranded G-quadruplex (G4) from the c-MYC promoter with high affinity. We have extended those results to include other G4 motifs, finding that hRev1 exhibited stronger affinity for parallel-stranded G4 than either anti-parallel or hybrid folds. Amino acids in the αE helix of insert-2 were identified as being important for G4 binding. Mutating E466 and Y470 to alanine selectively perturbed G4 binding affinity. The E466K mutant restored wild-type G4 binding properties. Using a forward mutagenesis assay, we discovered that loss of hRev1 increased G4 mutation frequency >200-fold compared to the control sequence. Base substitutions and deletions occurred around and within the G4 motif. Pyridostatin (PDS) exacerbated this effect, as the mutation frequency increased >700-fold over control and deletions upstream of the G4 site more than doubled. Mutagenic replication of G4 DNA (±PDS) was partially rescued by wild-type and E466K hRev1. The E466A or Y470A mutants failed to suppress the PDS-induced increase in G4 mutation frequency. These findings have implications for the role of insert-2, a motif conserved in vertebrates but not yeast or plants, in Rev1-mediated suppression of mutagenesis during G4 replication.

VRML in Cancer Research: Local Changes in Binding Properties of Wild Type and Mutated p53 Tumor Suppressor Protein

1997 ◽  
Vol 3 (9) ◽  
pp. 382-385
Author(s):  
Gerd Moeckel ◽  
Matthias Keil ◽  
Monica Hollstein ◽  
Bertold Spiegelhalder ◽  
Helmut Bartsch ◽  
...  
Keyword(s):  
Cancer Research ◽  
Tumor Suppressor ◽  
Tumor Suppressor Protein ◽  
Wild Type ◽  
Binding Properties ◽  
P53 Tumor Suppressor ◽  
P53 Tumor Suppressor Protein

Warming increases soil carbon input in a Sibiraea angustata-dominated alpine shrub ecosystem

2021 ◽  
Author(s):  
Mei Liu ◽  
Jia-Hao Wen ◽  
Ya-Mei Chen ◽  
Wen-Juan Xu ◽  
Qiong Wang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Root Exudates ◽  
Climate Warming ◽  
Root Exudate ◽  
Soil Organic C ◽  
Organic C ◽  
Root Litter ◽  
C Stocks ◽  
Alpine Shrub ◽  
Key Drivers

Abstract Aims Plant-derived carbon (C) inputs via foliar litter, root litter and root exudates are key drivers of soil organic C stocks. However, the responses of these three input pathways to climate warming have rarely been studied in alpine shrublands. Methods By employing a three-year warming experiment (increased by1.3 ℃), we investigated the effects of warming on the relative C contributions from foliar litter, root litter and root exudates from Sibiraea angustata, a dominant shrub species in an alpine shrubland on the eastern Qinghai-Tibetan Plateau. Important Findings The soil organic C inputs from foliar litter, root litter and root exudates were 77.45, 90.58 and 26.94 g C m -2, respectively. Warming only slightly increased the soil organic C inputs from foliar litter and root litter by 8.04 and 11.13 g C m -2, but significantly increased the root exudate C input by 15.40 g C m -2. Warming significantly increased the relative C contributions of root exudates to total C inputs by 4.6% but slightly decreased those of foliar litter and root litter by 2.5% and 2.1%, respectively. Our results highlight that climate warming may stimulate plant-derived C inputs into soils mainly through root exudates rather than litter in alpine shrublands on the Qinghai-Tibetan Plateau.

Membrane-binding properties of filensin, a cytoskeletal protein of the lens fiber cells

1992 ◽  
Vol 103 (3) ◽  
pp. 709-718 ◽  
Author(s):  
M. Brunkener ◽  
S.D. Georgatos
Keyword(s):  
Binding Capacity ◽  
Lens Fiber ◽  
Alkaline Ph ◽  
Trypsin Treatment ◽  
Binding Properties ◽  
Fiber Cells ◽  
Lens Membranes ◽  
Acylated Proteins ◽  
Triton X

Filensin is a 100/110 kDa membrane-associated protein found in lens fiber cells. Previous studies have shown that this protein polymerizes in vitro and binds strongly to vimentin and to another 47 kDa lens membrane protein. Using cosedimentation assays, flotation assays and immunoelectron microscopy, we have examined the properties of purified filensin and measured its binding to lens membranes. Filensin behaves as a ureaextractable, hydrophilic protein which does not partition with Triton X-114 and is not affected by 1 M hydroxylamine at alkaline pH, an agent known to release fatty-acylated proteins from the membrane. Immunoblotting of urea-extracted lens membranes with two different affinity-purified antibodies reveals that, unlike intact filensin, a COOH-terminal filensin degradation product (51 kDa) remains tightly associated with the membranes. Purified filensin binds directly to urea-stripped lens membranes, but not to protein-free vesicles reconstituted from total lens lipids. The binding of filensin is not significantly influenced by the purified 47 kDa protein. Interestingly, the filensin-binding capacity of urea-extracted membranes is increased at least two-fold after trypsin treatment, which removes entirely the 51 kDa peptide from the membranes and presumably unmasks additional filensin-acceptor sites. Consistent with this, filensin binds to trypsinized and non-trypsinized membranes with similar affinities (2 × 10(−7) and 4 × 10(−7) M, respectively). Treatment of the membranes with thrombin, which also eliminates the 51 kDa peptide, does not increase their binding capacity, apparently because filensin-acceptor sites are also destroyed during proteolysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Does the lack of root hairs alter root system architecture of Zea mays?

2021 ◽  
Author(s):  
Steffen Schlüter ◽  
Eva Lippold ◽  
Maxime Phalempin ◽  
Doris Vetterlein
Keyword(s):  
Zea Mays ◽  
Root System ◽  
Root Hair ◽  
System Architecture ◽  
Volume Fraction ◽  
Root Hairs ◽  
Root System Architecture ◽  
Root Diameter ◽  
Wild Type ◽  
Defective Mutant

<p>Root hairs are one root trait among many which enables plants to adapt to environmental conditions. How different traits are coordinated and whether some are mutually exclusive is currently poorly understood. Comparing a root hair defective mutant with its corresponding wild-type we explored if and how the mutant exhibited root growth adaption strategies and as to how far this depended on the substrate.</p><p>Zea mays root hair defective mutant (rth3) and the corresponding wild-type siblings were grown on two substrates with contrasting texture and hence nutrient mobility. Root system architecture was investigated over time using repeated X-ray computed tomography.</p><p>There was no plastic adaption of root system architecture to the lack of root hairs, which resulted in lower uptake in particular in the substrate with low P mobility. The function of the root hairs for anchoring did not result in different depth profiles of the root length density between genotypes. Both maize genotypes showed a marked response to substrate. This was well reflected in the spatiotemporal development of rhizosphere volume fraction but especially in the strong response of root diameter to substrate, irrespective of genotype.</p><p>The most salient root plasticity trait was root diameter in response to substrate, whereas coping mechanisms for missing root hairs were less evident. Further experiments are required to elucidate whether observed differences can be explained by mechanical properties beyond mechanical impedance, root or microbiome ethylene production or differences in diffusion processes within the root or the rhizosphere.</p>

Enhanced DNA binding capacity on up‐regulated epidermal wild‐type p53 in vitiligo by H 2 O 2 ‐mediated oxidation: a possible repair mechanism for DNA damage

2009 ◽  
Vol 23 (11) ◽  
pp. 3790-3807 ◽  
Author(s):  
Mohamed M. A. E. L. Salem ◽  
Mohammad Shalbaf ◽  
Nicholas C. J. Gibbons ◽  
Bhaven Chavan ◽  
J. M. Thornton ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Binding ◽  
Binding Capacity ◽  
Wild Type ◽  
Repair Mechanism ◽  
Wild Type P53 ◽  
Mediated Oxidation

In vitro studies on the behaviour of second-stage juveniles of Heterodera schachtii (Nematoda: Heteroderidae) in response to host plant root exudates

Parasitology ◽  
1991 ◽  
Vol 103 (1) ◽  
pp. 149-155 ◽  
Author(s):  
F. Grundler ◽  
L. Schnibbe ◽  
U. Wyss
Keyword(s):  
Root Exudates ◽  
Root Exudate ◽  
Plant Root ◽  
Time Lapse ◽  
Heterodera Schachtii ◽  
Second Stage ◽  
Video Recordings ◽  
Aseptic Conditions ◽  
Agarose Layer

The behaviour of Heterodera schachtii second-stage juveniles in response to mustard (Sinapis alba) rooxudates was observed and analysed under aseptic conditions in a standardized bioassay. Aggregation of juveniles on an agarose layer occurred within less than 30 min in the area where root exudates had been applied and persisted for several hours. Analysis of time-lapse video recordings showed that the aggregation did not result from a directed orientation of the juvenile towards the root exudate. This was supported by an orientation assay using single juveniles. Aggregated juveniles showed pre-infection exploratory behaviour, including stylet thrusting and head-end bending, while staying at rest for several minutes.

scholarly journals Rootstock-Scion Interaction Affects the Composition and Pathogen Inhibitory Activity of Tobacco (Nicotiana tabacum L.) Root Exudates

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1652
Author(s):  
Cheng-Sheng Zhang ◽  
Yanfen Zheng ◽  
Lijuan Peng ◽  
Jianmin Cao
Keyword(s):  
Nicotiana Tabacum ◽  
Root Exudates ◽  
Root Exudate ◽  
Phytophthora Nicotianae ◽  
Susceptible Cultivar ◽  
Black Shank ◽  
Nicotiana Tabacum L ◽  
Disease Induction ◽  
Resistant Rootstock ◽  
Ethylhexyl Phthalate

The composition and allelopathy to Phytophthora nicotianae (the causal agent of tobacco black shank disease) of root exudates from a resistant tobacco (Nicotiana tabacum L.) cultivar Gexin 3, a susceptible cultivar Xiaohuangjin 1025 and their reciprocal grafts were investigated. Grafting with disease-resistant rootstock could improve resistance to black shank; this is closely related to the allelopathy of root exudates. The root exudates from the resistant cultivar inhibited the growth of P. nicotianae, while those from the susceptible cultivar promoted the growth; the grafting varieties had intermediate properties. The root exudate composition differed among cultivars. Gexin 3 was rich in esters and fatty acids, while Xiaohuangjin 1025 contained more hydrocarbons and phenolic acids. The composition of root exudates of grafted cultivars as well as their allelopathy to P. nicotianae were altered, and tended to be close to the composition of cultivar used as rootstock. Eugenol, 4-tert-butylphenol, mono (2-ethylhexyl) phthalate, 4-hydroxybenzoic acid, 2,6-di-tert-butylphenol, dipropyl phthalate, and methyl myristate were identified as the main compounds contributing to inhibitory properties of root exudates. Sorbitol was suggested to play a role in disease induction. Overall, rootstock–scion interaction affected the composition of tobacco root exudates, which may be attributed to the different disease resistance among grafted plants, rootstock and scion.

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