scholarly journals Genomic and Phenotypic Biology of Novel Strains of Dickeya zeae Isolated From Pineapple and Taro in Hawaii: Insights Into Genome Plasticity, Pathogenicity, and Virulence Determinants

2021 ◽  
Vol 12 ◽  
Author(s):  
Gamze Boluk ◽  
Dario Arizala ◽  
Shefali Dobhal ◽  
Jingxin Zhang ◽  
John Hu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Plant Pathogen ◽  
Plant Cell Wall ◽  
Extracellular Enzymes ◽  
Ananas Comosus ◽  
Secretion Systems ◽  
Genome Database ◽  
Wide Range ◽  
Complete Genomes ◽  
Pineapple Leaves

Dickeya zeae, a bacterial plant pathogen of the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro, and ornamentals and significantly reduces crop production. D. zeae causes the soft rot of taro (Colocasia esculenta) and the heart rot of pineapple (Ananas comosus). In this study, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing to sequence two high-quality complete genomes of novel strains of D. zeae: PL65 (size: 4.74997 MB; depth: 701x; GC: 53.6%) and A5410 (size: 4.7792 MB; depth: 558x; GC: 53.5%) isolated from economically important Hawaiian crops, taro, and pineapple, respectively. Additional complete genomes of D. zeae representing three additional hosts (philodendron, rice, and banana) and other species used for a taxonomic comparison were retrieved from the NCBI GenBank genome database. Genomic analyses indicated the truncated type III and IV secretion systems (T3SS and T4SS) in the taro strain, which only harbored one and two genes of T3SS and T4SS, respectively, and showed high heterogeneity in the type VI secretion system (T6SS). Unlike strain EC1, which was isolated from rice and recently reclassified as D. oryzae, neither the genome PL65 nor A5410 harbors the zeamine biosynthesis gene cluster, which plays a key role in virulence of other Dickeya species. The percentages of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between the two genomes were 94.47 and 57.00, respectively. In this study, we compared the major virulence factors [plant cell wall-degrading extracellular enzymes and protease (Prt)] produced by D. zeae strains and evaluated the virulence on taro corms and pineapple leaves. Both strains produced Prts, pectate lyases (Pels), and cellulases but no significant quantitative differences were observed (p > 0.05) between the strains. All the strains produced symptoms on taro corms and pineapple leaves, but the strain PL65 produced symptoms more rapidly than others. Our study highlights the genetic constituents of pathogenicity determinants and genomic heterogeneity that will help to understand the virulence mechanisms and aggressiveness of this plant pathogen.

scholarly journals Genomic and phenotypic biology of novel strains of Dickeya zeae isolated from pineapple and taro in Hawaii: insights into genome plasticity, pathogenicity, and virulence determinants

2021 ◽  
Author(s):  
Gamze Boluk ◽  
Dario Arizala ◽  
Shefali Dobhal ◽  
Jingxin Zhang ◽  
John Hu ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Crop Production ◽  
Plant Cell Wall ◽  
Extracellular Enzymes ◽  
Ananas Comosus ◽  
Virulence Determinants ◽  
Secretion Systems ◽  
Genome Database ◽  
Wide Range ◽  
Complete Genomes

ABSTRACTDickeya zeae, a bacterial plant pathogen in the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro and ornamentals and significantly reduces crop production; D. zeae causes soft rot of taro (Colocasia esculenta) and heart rot of pineapple (Ananas comosus). In this study, we used Pacific Biosciences to sequence two high quality complete genomes of novel strains of D. zeae: PL65 (size - 4.74997 MB; depth - 701; GC - 53.3%) and A5410 (size - 4.7792 MB; depth - 558; GC - 53.6%) isolated from economically important Hawaiian crops, taro and pineapple, respectively. Additional complete genomes of D. zeae representing two additional hosts (rice and banana), and other species for taxonomic comparison, were retrieved from the NCBI GenBank genome database. The genomic analyses indicated truncated type III and IV secretion systems (T3SS and T4SS) in the taro strain, which only harbors 1 and 2 genes of T3SS and T4SS, respectively, and showed high heterogeneity in the type VI secretion system. Unlike the EC1 strain, neither the PL65 nor the A5410 genome harbors the zeamine biosynthesis gene cluster, which plays a key role in bacterial virulence. The ANI and dDDH percentages between the two genomes were 94.47 and 57.00, respectively. In this study, we compared major virulence factors (plant cell wall-degrading extracellular enzymes and protease) produced by D. zeae strains and virulence ability on taro corms and pineapple. Both strains produced protease, pectate lyases and cellulases but no significant quantitative differences were observed (p>0.05) among the strains. All the strains produced symptoms on taro corms and pineapple leaves. Strain PL65 developed symptoms faster than the others. Our study highlights genetic constituents of pathogenicity determinants and genomic heterogeneity that will help understand the virulence mechanisms and aggressiveness of this plant pathogen.

Extracellular hydrolytic enzymes in the fungal genus Verticillium: adaptations for pathogenesis

1999 ◽  
Vol 45 (10) ◽  
pp. 856-864 ◽  
Author(s):  
Michael J Bidochka ◽  
Susan Burke ◽  
Luna Ng
Keyword(s):  
Plant Pathogen ◽  
Plant Pathogens ◽  
Plant Cell Wall ◽  
Extracellular Enzymes ◽  
Hydrolytic Enzymes ◽  
Pathogenic Fungi ◽  
Verticillium Lecanii ◽  
Opportunistic Pathogens ◽  
Broad Array ◽  
Fungal Genus

The insect and plant pathogens within the fungal genus Verticillium showed enzymatic adaptation (production and regulation) directed to the degradation of some of the polymers found in the integument of their respective hosts. For example, the facultative plant pathogens (V. albo-atrum and V. dahliae) produced greater levels of cellulase and xylanase than the facultative insect pathogen (V. lecanii). Verticillium lecanii produced extracellular subtilisin-like protease when grown in insect cuticle medium but not in plant cell wall medium, while the plant pathogen V. albo-atrum showed a diminished regulatory component in the production of this enzyme. The opportunistic pathogens (V. fungicola and V. coccosporum) and the saprobic species (V. rexianum) were less specific in the production and regulation of several proteases as well as cellulases and xylanases. A dendrogram based on cluster analysis compiled from fungal API-ZYM profiles showed commonalties in a broad array of extracellular enzymes within a host-pathogen group (i.e. insect or plant pathogen). The opportunistic pathogens were dispersed throughout the dendrogram, suggestive of the diversity in type and expression of extracellular enzymes.Key words: extracellular enzymes, pathogenic fungi.

scholarly journals A Two-Component Regulatory System, pehR-pehS, Controls Endopolygalacturonase Production and Virulence in the Plant Pathogen Erwinia carotovora subsp. carotovora

2000 ◽  
Vol 13 (4) ◽  
pp. 447-455 ◽  
Author(s):  
Diana Flego ◽  
Reet Marits ◽  
Anders R. B. Eriksson ◽  
Viia Kõiv ◽  
Maj-Brit Karlsson ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Transcriptional Activation ◽  
Plant Cell Wall ◽  
Extracellular Enzymes ◽  
Regulatory System ◽  
Erwinia Carotovora ◽  
Virulence Determinants ◽  
Cell Wall Degrading Enzymes ◽  
Two Component ◽  
Specific Regulation

Genes coding for the main virulence determinants of the plant pathogen Erwinia carotovora subsp. carotovora, the plant cell wall-degrading enzymes, are under the coordinate control of global regulator systems including both positive and negative factors. In addition to this global control, some virulence determinants are subject to specific regulation. We have previously shown that mutations in the pehR locus result in reduced virulence and impaired production of one of these enzymes, an endopolygalacturonase (PehA). In contrast, these pehR strains produce essentially wild-type levels of other extracellular enzymes including pectate lyases and cellulases. In this work, we characterized the pehR locus and showed that the DNA sequence is composed of two genes, designated pehR and pehS, present in an operon. Mutations in either pehR or pehS caused a Peh-negative phenotype and resulted in reduced virulence on tobacco seedlings. Complementation experiments indicated that both genes are required for transcriptional activation of the endopolygalacturonase gene, pehA, as well as restoration of virulence. Structural characterization of the pehR-pehS operon demonstrated that the corresponding polypeptides are highly similar to the two-component transcriptional regulators PhoP-PhoQ of both Escherichia coli and Salmonella typhimurium. Functional similarity of PehR-PehS with PhoP-PhoQ of E. coli and S. typhimurium was demonstrated by genetic complementation.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of Gan1D, a GH1 6-phospho-β-galactosidase fromGeobacillus stearothermophilusT1

2014 ◽  
Vol 70 (2) ◽  
pp. 225-231 ◽  
Author(s):  
Shifra Lansky ◽  
Arie Zehavi ◽  
Roie Dann ◽  
Hay Dvir ◽  
Hassan Belrhali ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Extracellular Enzymes ◽  
Biochemical Characterization ◽  
Crystal Structure Analysis ◽  
Crystallographic Analysis ◽  
Glycoside Hydrolases ◽  
Cell Wall Polysaccharides ◽  
Data Set ◽  
Cell Parameters ◽  
Wide Range

Geobacillus stearothermophilusT1 is a Gram-positive thermophilic soil bacterium that contains an extensive system for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. The bacterium uses a number of extracellular enzymes that break down the high-molecular-weight polysaccharides into short oligosaccharides, which enter the cell and are further hydrolyzed into sugar monomers by dedicated intracellular glycoside hydrolases. The interest in the biochemical characterization and structural analysis of these proteins originates mainly from the wide range of their potential biotechnological applications. Studying the different hemicellulolytic utilization systems inG. stearothermophilusT1, a new galactan-utilization gene cluster was recently identified, which encodes a number of proteins, one of which is a GH1 putative 6-phospho-β-galactosidase (Gan1D). Gan1D has recently been cloned, overexpressed, purified and crystallized as part of its comprehensive structure–function study. The best crystals obtained for this enzyme belonged to the triclinic space groupP1, with average crystallographic unit-cell parameters ofa = 67.0,b= 78.1,c= 92.1 Å, α = 102.4, β = 93.5, γ = 91.7°. A full diffraction data set to 1.33 Å resolution has been collected for the wild-type enzyme, as measured from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for the detailed three-dimensional crystal structure analysis of Gan1D.

scholarly journals Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mingju Hao ◽  
Wanshan Ma ◽  
Xiutao Dong ◽  
Xiaofeng Li ◽  
Fang Cheng ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Analysis ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Genomic Islands ◽  
Genome Database ◽  
Genomic Features ◽  
Wide Range ◽  
Complete Genomes

Abstract Background The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities. Although hundreds of complete genomes of clinical P. aeruginosa isolates have been sequenced, only a few complete genomes of mucoid strains are available, limiting a comprehensive understanding of this important group of opportunistic pathogens. Herein, the complete genome of a clinically isolated mucoid strain P. aeruginosa JNQH-PA57 was sequenced and assembled using Illumina and Oxford nanopore sequencing technologies. Genomic features, phylogenetic relationships, and comparative genomics of this pathogen were comprehensively analyzed using various bioinformatics tools. A series of phenotypic and molecular-genetic tests were conducted to investigate the mechanisms of carbapenem resistance in this strain. Results Several genomic features of MDR P. aeruginosa JNQH-PA57 were identified based on the whole-genome sequencing. We found that the accessory genome of JNQH-PA57 including several prophages, genomic islands, as well as a PAPI-1 family integrative and conjugative element (ICE), mainly contributed to the larger genome of this strain (6,747,067 bp) compared to other popular P. aeruginosa strains (with an average genome size of 6,445,223 bp) listed in Pseudomonas Genome Database. Colony morphology analysis and biofilm crystal staining assay respectively demonstrated an enhanced alginate production and a thicker biofilm formation capability of JNQH-PA57. A deleted mutation at nt 424 presented in mucA gene, resulted in the upregulated expression of a sigma-factor AlgU and a GDP mannose dehydrogenase AlgD, which might explain the mucoid phenotype of this strain. As for the carbapenem resistance mechanisms, our results revealed that the interplay between impaired OprD porin, chromosomal β-lactamase OXA-488 expression, MexAB-OprM and MexXY-OprM efflux pumps overexpression, synergistically with the alginates-overproducing protective biofilm, conferred the high carbapenem resistance to P. aeruginosa JNQH-PA57. Conclusion Based on the genome analysis, we could demonstrate that the upregulated expression of algU and algD, which due to the truncation variant of MucA, might account for the mucoid phenotype of JNQH-PA57. Moreover, the resistance to carbapenem in P. aeruginosa JNQH-PA57 is multifactorial. The dataset presented in this study provided an essential genetic basis for the comprehensive cognition of the physiology, pathogenicity, and carbapenem resistance mechanisms of this clinical mucoid strain.

Aspergillus sydowii Strain SCAU066 and Aspergillus versicolor Isolate BAB-6580: Potential Source of Xylanolytic, Cellulolytic and Amylolytic Enzymes

2020 ◽  
Vol 14 (2) ◽  
pp. 15
Author(s):  
Zaidah Zainal ariffin
Keyword(s):  
Extracellular Enzymes ◽  
Biologically Active ◽  
Aspergillus Versicolor ◽  
Aspergillus Sydowii ◽  
Aspergillus Tamarii ◽  
Alternative Source ◽  
Amylolytic Enzymes ◽  
Potato Dextrose Broth ◽  
Wide Range ◽  
Pharmaceutical Industries

Fungi is known to produce a wide range of biologically active metabolites and enzymes. Enzymes produced by fungi are utilized in food and pharmaceutical industries because of their rich enzymatic profile. Filamentous fungi are particularly interesting due to their high production of extracellular enzymes which has a large industrial potential. The aim of this study is to isolate potential soil fungi species that are able to produce functional enzymes for industries. Five Aspergillus species were successfully isolated from antibiotic overexposed soil (GPS coordinate of N3.093219 E101.40269) by standard microbiological method. The isolated fungi were identified via morphological observations and molecular tools; polymerase chain reactions, ITS 1 (5’- TCC GTA GGT GAA CCT GCG G3’) forward primer and ITS 4 (5’-TCC TCC GCT TAT TGA TAT GC-3’) reverse primer. The isolated fungi were identified as Aspergillus sydowii strain SCAU066, Aspergillus tamarii isolate TN-7, Aspergillus candidus strain KUFA 0062, Aspergillus versicolor isolate BAB-6580, and Aspergillus protuberus strain KAS 6024. Supernatant obtained via submerged fermentation of the isolated fungi in potato dextrose broth (PDB) and extracted via centrifugation was loaded onto specific media to screen for the production of xylanolytic, cellulolytic and amylolytic enzymes. The present findings indicate that Aspergillus sydowii strain SCAU066 and Aspergillus versicolor isolate BAB-6580 have great potential as an alternative source of xylanolytic, cellulolytic and amylolytic enzymes.

Synthesis and Biological Evaluation of Novel 4,5,6,7-Tetrahydrobenzo[D]-Thiazol-2- Yl Derivatives Derived from Dimedone with Anti-Tumor, C-Met, Tyrosine Kinase and Pim-1 Inhibitions

2019 ◽  
Vol 19 (12) ◽  
pp. 1438-1453 ◽  
Author(s):  
Rafat M. Mohareb ◽  
Amr S. Abouzied ◽  
Nermeen S. Abbas
Keyword(s):  
Tyrosine Kinase ◽  
Tumor Cell ◽  
Cell Lines ◽  
Single Molecule ◽  
Anticancer Agents ◽  
Biological Evaluation ◽  
New Drugs ◽  
Tumor Cell Lines ◽  
Thiazole Derivatives ◽  
Wide Range

Background: Dimedone and thiazole moieties are privileged scaffolds (acting as primary pharmacophores) in many compounds that are useful to treat several diseases, mainly tropical infectious diseases. Thiazole derivatives are a very important class of compounds due to their wide range of pharmaceutical and therapeutic activities. On the other hand, dimedone is used to synthesize many therapeutically active compounds. Therefore, the combination of both moieties through a single molecule to produce heterocyclic compounds will produce excellent anticancer agents. Objective: The present work reports the synthesis of 47 new substances belonging to two classes of compounds: Dimedone and thiazoles, with the purpose of developing new drugs that present high specificity for tumor cells and low toxicity to the organism. To achieve this goal, our strategy was to synthesize a series of 4,5,6,7-tetrahydrobenzo[d]-thiazol-2-yl derivatives using the reaction of the 2-bromodimedone with cyanothioacetamide. Methods: The reaction of 2-bromodimedone with cyanothioacetamide gave the 4,5,6,7-tetrahydrobenzo[d]- thiazol-2-yl derivative 4. The reactivity of compound 4 towards some chemical reagents was observed to produce different heterocyclic derivatives. Results: A cytotoxic screening was performed to evaluate the performance of the new derivatives in six tumor cell lines. Thirteen compounds were shown to be promising toward the tumor cell lines which were further evaluated toward five tyrosine kinases. Conclusion: The results of antitumor screening showed that many of the tested compounds were of high inhibition towards the tested cell lines. Compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 21b, 21c, 20d and 21d were the most potent compounds toward c-Met kinase and PC-3 cell line. The most promising compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 20c, 20d, 21b, 21c and 21d were further investigated against tyrosine kinase (c-Kit, Flt-3, VEGFR-2, EGFR, and PDGFR). Compounds 6c, 11b, 11d, 14b, 15c, and 20d were selected to examine their Pim-1 kinase inhibition activity the results revealed that compounds 11b, 11d and 15c had high activities.

scholarly journals Degradation Products of Polychlorinated Biphenyls and Their In Vitro Transformation by Ligninolytic Fungi

Toxics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 81
Author(s):  
Kamila Šrédlová ◽  
Kateřina Šírová ◽  
Tatiana Stella ◽  
Tomáš Cajthaml
Keyword(s):  
Polychlorinated Biphenyls ◽  
Extracellular Enzymes ◽  
Degradation Products ◽  
Transformation Products ◽  
Irpex Lacteus ◽  
Chlorobenzoic Acid ◽  
Ligninolytic Fungi ◽  
Wide Range ◽  
Pcb Metabolites

Metabolites of polychlorinated biphenyls (PCBs)—hydroxylated PCBs (OH‑PCBs), chlorobenzyl alcohols (CB‑OHs), and chlorobenzaldehydes (CB‑CHOs)—were incubated in vitro with the extracellular liquid of Pleurotus ostreatus, which contains mainly laccase and low manganese-dependent peroxidase (MnP) activity. The enzymes were able to decrease the amount of most of the tested OH‑PCBs by > 80% within 1 h; the removal of more recalcitrant OH‑PCBs was greatly enhanced by the addition of the laccase mediator syringaldehyde. Conversely, glutathione substantially hindered the reaction, suggesting that it acted as a laccase inhibitor. Hydroxylated dibenzofuran and chlorobenzoic acid were identified as transformation products of OH‑PCBs. The extracellular enzymes also oxidized the CB‑OHs to the corresponding CB‑CHOs on the order of hours to days; however, the mediated and nonmediated setups exhibited only slight differences, and the participating enzymes could not be determined. When CB‑CHOs were used as the substrates, only partial transformation was observed. In an additional experiment, the extracellular liquid of Irpex lacteus, which contains predominantly MnP, was able to efficiently transform CB‑CHOs with the aid of glutathione; mono‑ and di-chloroacetophenones were detected as transformation products. These results demonstrate that extracellular enzymes of ligninolytic fungi can act on a wide range of PCB metabolites, emphasizing their potential for bioremediation.

scholarly journals Xylanolytic Bacillus species for xylooligosaccharides production: a critical review

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Rozina Rashid ◽  
Muhammad Sohail
Keyword(s):  
Large Scale ◽  
Extracellular Enzymes ◽  
Membrane Separation ◽  
Well Being ◽  
Bacillus Species ◽  
Scale Production ◽  
Food Ingredients ◽  
Large Scale Production ◽  
Wide Range ◽  
Biological Impacts

AbstractThe capacity of different Bacillus species to produce large amounts of extracellular enzymes and ability to ferment various substrates at a wide range of pH and temperature has placed them among the most promising hosts for the industrial production of many improved and novel products. The global interest in prebiotics, for example, xylooligosaccharides (XOs) is ever increasing, rousing the quest for various forms with expanded productivity. This article provides an overview of xylanase producing bacilli, with more emphasis on their capacity to be used in the production of the XOs, followed by the purification strategies, characteristics and application of XOs from bacilli. The large-scale production of XOs is carried out from a number of xylan-rich lignocellulosic materials by chemical or enzymatic hydrolysis followed by purification through chromatography, vacuum evaporation, solvent extraction or membrane separation methods. Utilization of XOs in the production of functional products as food ingredients brings well-being to individuals by improving defense system and eliminating pathogens. In addition to the effects related to health, a variety of other biological impacts have also been discussed.

EXTRACELLULAR ENZYMES FROM STRAINS OF SORANGIUM

1965 ◽  
Vol 11 (1) ◽  
pp. 109-118 ◽  
Author(s):  
D. C. Gillespie ◽  
F. D. Cook
Keyword(s):  
Bacterial Cell ◽  
Cell Walls ◽  
Extracellular Enzymes ◽  
Soil Organisms ◽  
Wide Range ◽  
Bacterial Cell Walls

Soil organisms belonging to the myxobacter group and predatory on molds, yeasts, nematodes, and streptomycetes as well as on a wide range of bacteria elaborate at least two extracellular enzymes: a protease and a lysin. The protease hydrolyzes casein and haemoglobin and is inactive against bacterial cell walls while the lysin hydrolyzes bacterial cell walls but is inactive on proteins. These enzymes have been separated on hydroxylapatite columns and some of their properties are described. The predatory action of many of the isolates may be explained by the secretion and subsequent action of these two enzymes.

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