scholarly journals Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1101
Author(s):  
Muyiwa S. Adegbaju ◽  
Olanrewaju B. Morenikeji ◽  
Eli J. Borrego ◽  
André O. Hudson ◽  
Bolaji N. Thomas
Keyword(s):  
Plant Species ◽  
Chemical Properties ◽  
Starch Degradation ◽  
Carbohydrate Binding ◽  
Interacting Proteins ◽  
Amino Acid Residues ◽  
Phosphate Content ◽  
Deleterious Mutations ◽  
Carbohydrate Binding Modules ◽  
High Phosphate

The alpha-glucan water dikinase (GWD) enzyme catalyzes starch phosphorylation, an integral step in transitory starch degradation. The high phosphate content in stored starch has great industrial value, due to its physio–chemical properties making it more versatile, although the phosphate content of stored starch varies depending on the botanical source. In this study, we used various computational approaches to gain insights into the evolution of the GWD protein in 48 plant species with possible roles in enzyme function and alteration of phosphate content in their stored starch. Our analyses identified deleterious mutations, particularly in the highly conserved 5 aromatic amino acid residues in the dual tandem carbohydrate binding modules (CBM-45) of GWD protein in C. zofingiensis, G. hirsutum, A. protothecoides, P. miliaceum, and C. reinhardtii. These findings will inform experimental designs for simultaneous repression of genes coding for GWD and the predicted interacting proteins to elucidate the role this enzyme plays in starch degradation. Our results reveal significant diversity in the evolution of GWD enzyme across plant species, which may be evolutionarily advantageous according to the varying needs for phosphorylated stored starch between plants and environments.

scholarly journals Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3175
Author(s):  
Mariana Barbosa ◽  
Hélvio Simões ◽  
Duarte Miguel F. Prazeres
Keyword(s):  
Fusion Proteins ◽  
Fluorescent Protein ◽  
Protein A ◽  
Chemical Properties ◽  
Main Idea ◽  
Bioactive Molecules ◽  
Scaffolding Protein ◽  
Carbohydrate Binding ◽  
Biological Interactions ◽  
Carbohydrate Binding Modules

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

scholarly journals Mutational Insights into the Roles of Amino Acid Residues in Ligand Binding for Two Closely Related Family 16 Carbohydrate Binding Modules

2010 ◽  
Vol 285 (45) ◽  
pp. 34665-34676 ◽  
Author(s):  
Xiaoyun Su ◽  
Vinayak Agarwal ◽  
Dylan Dodd ◽  
Brian Bae ◽  
Roderick I. Mackie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Carbohydrate Binding ◽  
Amino Acid Residues ◽  
Related Family ◽  
Carbohydrate Binding Modules

scholarly journals Molecular cloning and characterization of a novel β-1,3-xylanase possessing two putative carbohydrate-binding modules from a marine bacterium Vibrio sp. strain AX-4

2005 ◽  
Vol 388 (3) ◽  
pp. 949-957 ◽  
Author(s):  
Masashi KIYOHARA ◽  
Keishi SAKAGUCHI ◽  
Kuniko YAMAGUCHI ◽  
Toshiyoshi ARAKI ◽  
Takashi NAKAMURA ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Marine Bacterium ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
Carbohydrate Binding Modules ◽  
Hydrolysis Of ◽  
Hydrolase Family

We cloned a novel β-1,3-xylanase gene, consisting of a 1728-bp open reading frame encoding 576 amino acid residues, from a marine bacterium, Vibrio sp. strain AX-4. Sequence analysis revealed that the β-1,3-xylanase is a modular enzyme composed of a putative catalytic module belonging to glycoside hydrolase family 26 and two putative carbohydrate-binding modules belonging to family 31. The recombinant enzyme hydrolysed β-1,3-xylan to yield xylo-oligosaccharides with different numbers of xylose units, mainly xylobiose, xylotriose and xylotetraose. However, the enzyme did not hydrolyse β-1,4-xylan, β-1,4-mannan, β-1,4-glucan, β-1,3-xylobiose or p-nitrophenyl-β-xyloside. When β-1,3-xylo-oligosaccharides were used as the substrate, the kcat value of the enzyme for xylopentaose was found to be 40 times higher than that for xylotetraose, and xylotriose was extremely resistant to hydrolysis by the enzyme. A PSI-BLAST search revealed two possible catalytic Glu residues (Glu-138 as an acid/base catalyst and Glu-234 as a nucleophile), both of which are generally conserved in glycoside hydrolase superfamily A. Replacement of these two conserved Glu residues with Asp and Gln resulted in a significant decrease and complete loss of enzyme activity respectively, without a change in their CD spectra, suggesting that these Glu residues are the catalytic residues of β-1,3-xylanase. The present study also clearly shows that the non-catalytic putative carbohydrate-binding modules play an important role in the hydrolysis of insoluble β-1,3-xylan, but not that of soluble glycol-β-1,3-xylan. Furthermore, repeating a putative carbohydrate-binding module strongly enhanced the hydrolysis of the insoluble substrate.

scholarly journals Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

2021 ◽  
pp. 100638
Author(s):  
Marie Sofie Møller ◽  
Souad El Bouaballati ◽  
Bernard Henrissat ◽  
Birte Svensson
Keyword(s):  
Functional Diversity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

scholarly journals Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Hsing Liu ◽  
Yu-Chen Lin ◽  
Chen-Shuan Chung ◽  
Kevin Liu ◽  
Ya-Hui Chang ◽  
...  
Keyword(s):  
Markov Models ◽  
Protein Domains ◽  
Degradation Pathway ◽  
The Other ◽  
Carbohydrate Binding ◽  
Gram Stain ◽  
Active Protein ◽  
Metabolic Potential ◽  
Independent Validation ◽  
Carbohydrate Binding Modules

AbstractBowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97, p < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10−4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10−5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

scholarly journals Family 6 carbohydrate-binding modules display multiple β1,3-linked glucan-specific binding interfaces

2009 ◽  
Vol 300 (1) ◽  
pp. 48-57 ◽  
Author(s):  
Márcia A.S. Correia ◽  
Virgínia M.R. Pires ◽  
Harry J. Gilbert ◽  
David N. Bolam ◽  
Vânia O. Fernandes ◽  
...  
Keyword(s):  
Specific Binding ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Binding Interfaces

scholarly journals Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution

BioTechniques ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 435-443 ◽  
Author(s):  
Shi-You Ding ◽  
Qi Xu ◽  
Mursheda K. Ali ◽  
John O. Baker ◽  
Edward A. Bayer ◽  
...  
Keyword(s):  
Molecular Level ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Complex Carbohydrates ◽  
Derivatives Of

scholarly journals Effect of Media Containing Processed Fiber, Fertilization, and Fumigation on Appearance and Growth in Containerized Woody Perennial Plants

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 658c-658
Author(s):  
Sanliang Gu ◽  
Leslie H. Fuchigami ◽  
Victor Sahakian
Keyword(s):  
Plant Species ◽  
Woody Plant ◽  
Chemical Properties ◽  
Physical And Chemical Properties ◽  
Perennial Species ◽  
Rooted Cuttings ◽  
Woody Perennial ◽  
The Media ◽  
Physical And Chemical ◽  
And Chemical Properties

Applicability of processed fiber (methane digested cow manure) as a substitute for peatmoss for production of various containerized perennial woody plant species with various fertilization and fumigation practices was investigated in this study. Liner plants of five species and rooted cuttings of 41 species were potted in various media containing processed fiber as the replacement of peatmoss with or without fertilization and fumigation, with commercial mix as control. Plants varied in their responses to the media, fertilization, and/or fumigation. Most plant species performed well in the media containing processed fiber. The physical and chemical properties of processed fiber, either alone or mixed with other media components, were satisfactory for producing woody perennial species even with less fertilization and no fumigation.

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