Figure - available from: Journal of Proteins and Proteomics
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Representative fold structures of each pectinase family. GH28 (exo-PG, PDB ID: 3JUR; endo-PG, PDB ID: 2IQ7; RGH, PDB ID: 1RMG; endo-XGH, PDB ID: 4C2L), PL1 (PDB ID: 2QXZ), PL3 (PDB ID: 1EE6), PL9 (PDB ID:1RU4), CE8 (PDB ID: 1QJV), PL10 (PDB ID: 1GXM), PL2 (PDB ID: 2V8I), PL4 (PDB ID: 1NKG), PL26 (PDB ID: 5XQ3), PL11 (PDB ID: 2ZUX), PL22 (PDB ID: 3PE7), CE12 (PDB ID: 1DEO)
Source publication
Pectinolytic enzymes produced by a large variety of organisms are well characterized concerning their physiological and pathological activities during modification or degradation of the complex plant cell wall. The exponential growth in structural information of these enzymes over past decades has rendered insights into functionally relevant residu...
Citations
... The CAZymes annotation also showed that there were various GH families including GH13, GH19, GH154, GH28, GH102, GH77, GH4, GH24, and GH23 in the Z129 genome. The GH28 family plays important roles in pectin degradation (Zhao et al., 2013) and contains all pectindegrading hydrolases (Anuradha and Bhawaniprasad, 2019). The GH19 family contains endo-chitinases which hydrolyzes the chitinoside bond to produce N-acetyl-D-glucosamine (Nakagawa et al., 2013). ...
Introduction
Urea is an important non-protein nitrogen source for ruminants. In the rumen, ureolytic bacteria play critical roles in urea-nitrogen metabolism, however, a few ureolytic strains have been isolated and genomically sequenced. The purpose of this study was to isolate a novel ureolytic bacterial strain from cattle rumen and characterize its genome and function.
Methods
The ureolytic bacterium was isolated using an anaerobic medium with urea and phenol red as a screening indicator from the rumen fluid of dairy cattle. The genome of isolates was sequenced, assembled, annotated, and comparatively analyzed. The pan-genome analysis was performed using IPGA and the biochemical activity was also analyzed by test kits.
Results
A gram-positive ureolytic strain was isolated. Its genome had a length of 4.52 Mbp and predicted genes of 4223. The 16S rRNA gene and genome GTDB-Tk taxonomic annotation showed that it was a novel strain of Enterobacter hormaechei, and it was named E. hormaechei Z129. The pan-genome analysis showed that Z129 had the highest identity to E. hormaechei ATCC 49162 with a genome average nucleotide identity of 98.69% and possessed 238 unique genes. Strain Z129 was the first E. hormaechei strain isolated from the rumen as we know. The functional annotation of the Z129 genome showed genes related to urea metabolism, including urea transport (urtA-urtE), nickel ion transport (ureJ, tonB, nixA, exbB, exbD, and rcnA), urease activation (ureA-ureG) and ammonia assimilation (gdhA, glnA, glnB, glnE, glnL, glsA, gltB, and gltD) were present. Genes involved in carbohydrate metabolism were also present, including starch hydrolysis (amyE), cellulose hydrolysis (celB and bglX), xylose transport (xylF-xylH) and glycolysis (pgi, pgk, fbaA, eno, pfkA, gap, pyk, gpmL). Biochemical activity analysis showed that Z129 was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-glucosidase, β-glucosidase, and pyrrolidone arylaminase, and had the ability to use D-ribose, L-arabinose, and D-lactose. Urea-nitrogen hydrolysis rate of Z129 reached 55.37% at 48 h of incubation.
Discussion
Therefore, the isolated novel ureolytic strain E. hormaechei Z129 had diverse nitrogen and carbon metabolisms, and is a preferred model to study the urea hydrolysis mechanism in the rumen.
... CAZy GH28) has been shown to release digalacturonates [5]. For more details see a recent review on pectinolytic enzymes [6]. ...
... It has xylose moieties attached to the O-3 through a β-1,3-glycosidic bond. Different types of xylose side chains can be attached, apparently depending on the species [6]. The side chain can be removed by β-xylosidase (EC 3.2.1.37; ...
Pectin is a major constituent of the plant cell wall, comprising compounds with important industrial applications such as homogalacturonan, rhamnogalacturonan and xylogalacturonan. A large array of enzymes is involved in the degradation of this amorphous substrate. The Glycoside Hydrolase 28 (GH28) family includes polygalacturonases (PG), rhamnogalacturonases (RG) and xylogalacturonases (XG) that share a structure of three to four pleated β-sheets that form a rod with the catalytic site amidst a long, narrow groove. Although these enzymes have been studied for many years, there has been no systematic analysis. We have collected a comprehensive set of GH28 encoding sequences to study their evolution in fungi, directed at obtaining a functional classification, as well as at the identification of substrate specificity as functional constraint. Computational tools such as Alphafold, Consurf and MEME were used to identify the subfamilies’ characteristics. A hierarchic classification defines the major classes of endoPG, endoRG and endoXG as well as three exoPG classes. Ascomycete endoPGs are further classified in two subclasses whereas we identify four exoRG subclasses. Diversification towards exomode is explained by loops that appear inserted in a number of turns. Substrate-driven diversification can be identified by various specificity determining positions that appear to surround the binding groove.
... Pectate lyases (Pls) (E.C. 4.2.2.2) cleave the α-1,4-linked glycosidic bonds between D-galacturonic acid in the main chain of pectin via a ß-elimination mechanism (van den Brink and de Vries, 2011). This gives rise to an unsaturated C4-C5 galacturonosyl residue at the nonreducing end of the polysaccharide (Yoder et al., 1993;Herron et al., 2000;Kanungo and Prasad, 2019). Most Pls are predicted to be transcriptionally regulated by environmental factors like pH or availability of carbon sources (Yakoby et al., 2000;Miyara et al., 2008). ...
Phytopathogenic fungi are known to secrete specific proteins which act as virulence factors and promote host colonization. Some of them are enzymes with plant cell wall degradation capability, like pectate lyases (Pls). In this work, we examined the involvement of Pls in the infection process of Magnaporthe oryzae, the causal agent of rice blast disease. From three Plgenes annotated in the M. oryzae genome, only transcripts of MoPL1 considerably accumulated during the infection process with a peak at 72 h post inoculation. Both, gene deletion and a constitutive expression of MoPL1 in M. oryzae led to a significant reduction in virulence. By contrast, mutants that constitutively expressed an enzymatic inactive version of MoPl1 did not differ in virulence compared to the wild type isolate. This indicates that the enzymatic activity of MoPl1 is responsible for diminished virulence, which is presumably due to degradation products recognized as danger associated molecular patterns (DAMPs), which strengthen the plant immune response. Microscopic analysis of infection sites pointed to an increased plant defense response. Additionally, MoPl1 tagged with mRFP, and not the enzymatic inactive version, focally accumulated in attacked plant cells beneath appressoria and at sites where fungal hyphae transverse from one to another cell. These findings shed new light on the role of pectate lyases during tissue colonization in the necrotrophic stage of M. oryzae’s life cycle.
... The enzymes able modify pectin can be generically classified into hydrolases (e.g. exo-and endo-galacturonidases) who acts on the main polymer chains releasing mono-to oligosaccharides; esterases able to degrade ester unions releasing acids or acids and consequently decreasing the hydrophobicity of the entire polymer, and lyases able to release unsaturated oligosaccharides from pectin chains (Kanungo and Bag, 2019). In the case of matrices composed of only of pectin, hydrolases and lyases can act of the main chains that will disassemble the gel structure with the potential bulk release of the drug contained in the hydrophobic pockets and further drug release will depend on the environmental conditions. ...
Enzymes exhibit a tremendous potential due to the catalytic activity in response to physiological conditions and specific microenvironments. Exploiting these properties in combination with the versatility of biopolymers, a fascinating field for the rational development of a new class of “smart” delivery systems for therapeutic molecules is proposed. Many strategies have been recently developed to produce matrices with the desirable properties of molecular release, and enzymes could be playing a relevant role in modify the chemical composition of the polymers, the porosity and surface area of the matrices and modulate the kinetic of controlled release. Enzyme based computational systems have appeared as a relevant complementary tool to design novel smart bioactive matrices for programmable drug delivery. The present review is reporting the recent advances and projections of smart biopolymeric matrices activated by enzymes for sustained release of therapeutic molecules, highlighting various applications in the area of advanced drug delivery.
Carbohydrate-binding proteins known as “Lectins” play a crucial
role in host-pathogen interactions. Most of the viral surface proteins have lectin activity. In fact, they make the first line of communication with the host cells. Recent reports indicating the haemagglutination property and structural evidences of coronaviral protein bound with Sialic acid (Sia) draw our attention to exploring the presence of lectins in the Betacoronavirus genus from reference genomes. We have considered the seventeen reference genomes of different species and subspecies under the Betacoronavirus genus to identify lectin fold/domain(s) types. We have employed three strategies for characterizing lectin fold/domain(s). The strategies include the sequence-based search against the conserved domain database (CDD) and profile HMMER and Structurebased search against Protein Data Bank (PDB) and unified platform of lectins UniLectin3D database. Interestingly, both the identified proteins, namely Hemagglutinin-esterase (HE) and Spike (S) protein, were localized on viral membranes and played a pivotal role in host-pathogen interactions. These protein structures are fabricated by most pliable b-strands forming varied architectures and topologies, such as b-sandwich, jelly-roll fold, b-barrel, b-prism, b-trefoil, b-propeller and b-hairpins. The identified lectin fold/domain(s) were compared with the characterized ones and were docked with Sia using HADDOCK, and the binding affinity was calculated using the PRODIGY server. Molecular docking studies reveal that all the identified lectin fold/domains agree with the Canyon hypothesis.
Furthermore, it could be observed that coronaviruses are constantly evolving by shedding their extra baggage. The latter variants were found to have only the lectin domain but not the esterase domain.
Special features of the protopectin complex structure of plant tissue suggest the necessity of performing point destruction of certain glycoside bonds in the structure of rhamnogalacturonan polymer chains for industrial production of pectin. These chains include homogalacturonan sites and branching zones. As the homogalacturonan fragments of the protopectin complex carry the main functional load, glycoside bonds between residues of rhamnose and galacturonic acid are targeted bonds. For their directional destruction, it is most expedient to use enzymes of lyase and hydrolase action. The aim of this review is to systemize notions of molecular specific features of enzymes of lyase and hydrolase action that catalyze the process of enzymatic destruction of the rhamnogalacturonan main chain. The paper examines systematics of lyase and hydrolase enzymes by mechanism of destruction of glycoside bonds and by molecular structure. It is shown that the classification data intercross, as a result, each family can include one or several enzyme groups. The review shows the main structural difference of enzymes of lyase and hydrolase action that consists in the obligatory presence of Ca ²⁺ cations in the composition of lyase enzymes. These cations take part in stabilization of conformation of the enzyme molecule and in the catalytic process per se blocking the residue of galacturonic acid. Ca ²⁺ cations are absent in the composition of targeted hydrolase enzymes. Molecular specific features of lyase enzymes determine sensitivity of their catalytic activity to the presence of Ca ²⁺ cations in the system. Exceeding certain concentration can lead to the antagonistic effect. There is no unambiguous idea of this regarding hydrolase enzymes. The review demonstrates the necessity of studying approaches to assessment of expediency of preliminary partial removal of cations from the substrate.