scholarly journals Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains

2021 ◽  
Vol 9 (3) ◽  
Author(s):  
Andrew Hutchin ◽  
Charlotte Cordery ◽  
Martin A. Walsh ◽  
Jeremy S. Webb ◽  
Ivo Tews
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Phylogenetic Analysis ◽  
Ligand Binding ◽  
Physiological Responses ◽  
Functional Differentiation ◽  
Modular Structure ◽  
Environmental Cues ◽  
Multidomain Proteins ◽  
Life Conditions ◽  
Wide Range

To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to effect movement.

scholarly journals Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Syed A. K. Shifat Ahmed ◽  
Michelle Rudden ◽  
Sabrina M. Elias ◽  
Thomas J. Smyth ◽  
Roger Marchant ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Genomic Islands ◽  
Clinical Strain ◽  
Whole Genome ◽  
Synonymous Mutations ◽  
Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

scholarly journals Re-Evaluation of the Podosphaera tridactyla Species Complex in Australia

2021 ◽  
Vol 7 (3) ◽  
pp. 171
Author(s):  
Reannon L. Smith ◽  
Tom W. May ◽  
Jatinder Kaur ◽  
Tim I. Sawbridge ◽  
Ross C. Mann ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Species Complex ◽  
Taxonomic Revision ◽  
Stone Fruit ◽  
Prunus Species ◽  
Wide Range ◽  
Unidentified Species ◽  
The Rose ◽  
Generation Sequencing

The Podosphaera tridactyla species complex is highly variable morphologically and causes powdery mildew on a wide range of Prunus species, including stone fruit. A taxonomic revision of the Po. tridactyla species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host matK chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental Prunus species accessioned as Po. tridactyla or Oidium sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using matK phylogenetic analysis, which identified that four had been misidentified as Prunus but were actually Malusprunifolia. Podosphaera species were identified using ITS+28S phylogenetic analysis, recognising three Podosphaera species on stone fruit and related ornamental Prunus hosts in Australia. These were Po.pannosa, the rose powdery mildew, and two species in the Po. tridactyla species complex: Po. ampla, which was the predominant species, and a previously unidentified species from peach, which we describe here as Po. cunningtonii.

scholarly journals The inflammatory response induced by Pseudomonas aeruginosa in macrophages enhances apoptotic cell removal

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adriana Valeria Jäger ◽  
Paula Arias ◽  
Maria Virginia Tribulatti ◽  
Marcela Adriana Brocco ◽  
Maria Victoria Pepe ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Pseudomonas Aeruginosa ◽  
Inflammatory Response ◽  
Apoptotic Cell ◽  
Bacterial Pathogen ◽  
Environmental Cues ◽  
Apoptotic Cells ◽  
Phagocytic Function ◽  
Inflammatory Stimulus ◽  
Inflammatory Conditions

AbstractPathogens phagocytosis and the uptake of apoptotic cells (efferocytosis) are essential macrophages tasks, classically considered as mutually exclusive. Macrophages have been observed to polarize into either pro-inflammatory/microbicidal or anti-inflammatory/efferocytic phenotypes. However, macrophage functions have shown to be more complex. Furthermore, little is known about the regulation of efferocytosis under inflammatory conditions. In this study, we elucidate the modulation of the macrophage efferocytic function during an inflammatory stimulus. We find that bone marrow-derived macrophages (BMDM) are very efficient in engulfing both the bacterial pathogen Pseudomonas aeruginosa and apoptotic cells. BMDM showed a high bactericidal capacity unaffected by the concomitant presence of apoptotic material. Plasticity in macrophage programming, in response to changing environmental cues, may modulate efferocytic capability. In this work, we further show that, after phagocyting and processing Pseudomonas aeruginosa, macrophages highly increase their efferocytic capacity without affecting their phagocytic function. Moreover, we demonstrate that Pseudomonas aeruginosa enhances efferocytosis of these phagocytes through the IL-6 signaling pathway. Our results show that the inflammatory response generated by the bacterial processing enhances these macrophages’ capacity to control inflammation through an increased efferocytosis.

Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems

2021 ◽  
Author(s):  
Ana Carolina de Oliveira Luz ◽  
Wilson José da Silva Junior ◽  
José Bandeira do Nascimento Junior ◽  
Julia Mariana Assis da Silva ◽  
Valdir de Queiroz Balbino ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Phylogenetic Analysis ◽  
Genetic Characteristics ◽  
Clinical Strains

Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 637-647 ◽  
Author(s):  
M A. Rouf Mian ◽  
Malay C Saha ◽  
Andrew A Hopkins ◽  
Zeng-Yu Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Tall Fescue ◽  
Related Species ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Cool Season ◽  
Phylogenetic Relations ◽  
Wide Range

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

scholarly journals Specific Control of Pseudomonas aeruginosa Surface-Associated Behaviors by Two c-di-GMP Diguanylate Cyclases

mBio ◽  
2010 ◽  
Vol 1 (4) ◽  
Author(s):  
Judith H. Merritt ◽  
Dae-Gon Ha ◽  
Kimberly N. Cowles ◽  
Wenyun Lu ◽  
Diana K. Morales ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Biofilm Formation ◽  
Extracellular Polysaccharide ◽  
Diguanylate Cyclase ◽  
Flagellar Motility ◽  
Critical Question ◽  
Cyclic Diguanylate ◽  
Critical Signal ◽  
Content Type ◽  
Wide Range

ABSTRACT The signaling nucleotide cyclic diguanylate (c-di-GMP) regulates the transition between motile and sessile growth in a wide range of bacteria. Understanding how microbes control c-di-GMP metabolism to activate specific pathways is complicated by the apparent multifold redundancy of enzymes that synthesize and degrade this dinucleotide, and several models have been proposed to explain how bacteria coordinate the actions of these many enzymes. Here we report the identification of a diguanylate cyclase (DGC), RoeA, of Pseudomonas aeruginosa that promotes the production of extracellular polysaccharide (EPS) and contributes to biofilm formation, that is, the transition from planktonic to surface-dwelling cells. Our studies reveal that RoeA and the previously described DGC SadC make distinct contributions to biofilm formation, controlling polysaccharide production and flagellar motility, respectively. Measurement of total cellular levels of c-di-GMP in ∆roeA and ∆sadC mutants in two different genetic backgrounds revealed no correlation between levels of c-di-GMP and the observed phenotypic output with regard to swarming motility and EPS production. Our data strongly argue against a model wherein changes in total levels of c-di-GMP can account for the specific surface-related phenotypes of P. aeruginosa. IMPORTANCE A critical question in the study of cyclic diguanylate (c-di-GMP) signaling is how the bacterial cell integrates contributions of multiple c-di-GMP-metabolizing enzymes to mediate its cognate functional outputs. One leading model suggests that the effects of c-di-GMP must, in part, be localized subcellularly. The data presented here show that the phenotypes controlled by two different diguanylate cyclase (DGC) enzymes have discrete outputs despite the same total level of c-di-GMP. These data support and extend the model in which localized c-di-GMP signaling likely contributes to coordination of the action of the multiple proteins involved in the synthesis, degradation, and/or binding of this critical signal.

Interaction between 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) and β-lactoglobulin

2016 ◽  
Vol 94 (8) ◽  
pp. 680-686
Author(s):  
Huiqing Li ◽  
Jing Wei ◽  
Youming Dong ◽  
Zhiyue Yu
Keyword(s):  
Ligand Binding ◽  
Sodium Salt ◽  
Stable Complex ◽  
Sodium Dodecylbenzene Sulfonate ◽  
Ph Change ◽  
Hydrophobic Domain ◽  
Acid Sodium Salt ◽  
Wide Range ◽  
Β Lactoglobulin ◽  
Small Ligands

The major bovine milk protein β-lactoglobulin (β-LG), a member of the lipocalin superfamily, can bind a wide range of ligands and act as a transporter. In the present study, the combination of the hydrophobic molecule 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) with β-LG was analyzed using fluorescence spectroscopy and AutoDock modeling to discern the major binding sites of the protein and to determine the capacity of other small ligands to bind with β-LG by utilizing TNS as a reference. The experimental data indicate that in a neutral pH environment, TNS is located in the hydrophobic domain of the protein, 2.5 nm away from the Trp19 residues of β-LG. The binding constant of the small molecule to β-LG is (3.30 ± 0.32) × 106 (mol L–1)−1. An interaction model between the ligand and β-LG was developed, and AutoDock modeling also demonstrates that the ligand is located in the central hydrophobic calyx of β-LG within the regions covered by the Förster radius of the Trp19–ligand pair. Although the interaction between the ligand and β-LG is affected by increasing ion strength, pH change, and heat treatment, the complex is maintained until the secondary structure of β-LG is destroyed. Additionally, the ligand binding stabilizes the folding of β-LG. The binding constants of sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) to β-LG were obtained using competitive ligand binding measurements. With a sensitive fluorescence signal and stable complex, the ligand could be utilized as a reference to detect the binding of other small ligands to β-LG.

scholarly journals Evaluation of antimycobacterial rhamnolipid production from non-cytotoxic strains of Pseudomonas aeruginosa isolated from rhizospheric soil of medicinal plants

2016 ◽  
Vol 4 (2) ◽  
pp. 112 ◽  
Author(s):  
Alok K Mishra ◽  
Rikesh K Dubey ◽  
Shivraj M Yabaji ◽  
Swati Jaiswal
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Medicinal Plants ◽  
Biochemical Characterization ◽  
Rhizospheric Soil ◽  
Rhamnolipid Production ◽  
Medicinal Value ◽  
Wide Range ◽  
Rrna Sequencing ◽  
Inhibitory Potential ◽  
Potent Inhibitory Activity

Rhamnolipids (RLs) are the bacterial derived biosurfactants and known for a wide range of industrial and therapeutic applications. They exhibit potent anti-bacterial activity against various gram positive, gram negative and acid fast bacteria including Mycobacterium tuberculosis. Since, Pseudomonas is one of the largest known genuses containing a variety of rhamnolipid producing strains. Therefore, in this study, we selectively isolated the Pseudomonas aeruginosa strains from the rhizospheric soil of the Indian plants of medicinal value, e.g. Azadirachta Indica and Ficus spp., and evaluated them for their natural ability to produce antibacterial rhamnolipids. The bacteria were identified on the basis of 16s rRNA sequencing and biochemical characterization. Among 33 of P. aeruginosa isolates from different soil samples, four isolates showed potent inhibitory activity against methicillin resistant Staphylococcus aureus (MRSA) and fast grower mycobacterial spp. The inhibitory potential of the isolates was found to be correlated with their ability to produce RLs in the medium. The industrial viability of the strains was assessed on the basis of cytotoxicity determining alternative allele, exoS/exoU and cell mediated cytotoxicity against murine macrophages J774.1. The newly isolated strains harbor exoS allele and exhibits lower cell mediated cytotoxicity on macrophage cell line as compared to the clinical strains PA-BAA-427 and PA-27853 used as a control in this study.Evaluation of antimycobacterial rhamnolipid production from non-cytotoxic strains of Pseudomonas aeruginosa isolated from rhizospheric soil of medicinal plants

scholarly journals Alarm substance from adult zebrafish alters early embryonic development in offspring

2010 ◽  
Vol 6 (4) ◽  
pp. 525-528 ◽  
Author(s):  
S. Mourabit ◽  
S. D. Rundle ◽  
J. I. Spicer ◽  
K. A. Sloman
Keyword(s):  
Embryonic Development ◽  
Inclusive Fitness ◽  
Heart Function ◽  
Physiological Responses ◽  
Early Embryonic Development ◽  
Alarm Substance ◽  
Adult Zebrafish ◽  
Skin Injury ◽  
Wide Range ◽  
Alarm Substances

Alarm substances elicit behavioural responses in a wide range of animals but effects on early embryonic development are virtually unknown. Here we investigated whether skin injury-induced alarm substances caused physiological responses in embryos produced by two Danio species ( Danio rerio and Danio albolineatus ). Both species showed more rapid physiological development in the presence of alarm substance, although there were subtle differences between them: D. rerio had advanced muscle contraction and heart function, whereas D. albolineatus had advanced heart function only. Hence, alarm cues from injured or dying fish may be of benefit to their offspring, inducing physiological responses and potentially increasing their inclusive fitness.

scholarly journals The Interned Soldiers of UРR Army at the Camp Stshalkovo in Poland (the Second Half of 1921 – the Beginning of 1922): the Moral and Life Conditions

2017 ◽  
pp. 182-195
Author(s):  
I. Sribnyak
Keyword(s):  
Armed Forces ◽  
Educational Work ◽  
Material Resources ◽  
Life Conditions ◽  
Wide Range ◽  
Red Army ◽  
Group A ◽  
Moral Condition ◽  
The Government ◽  
Destructive Processes

The article analyzes the moral condition and conditions of staying of interned Ukrainian soldiers in the camp of Stshalkovo (Poland) in the second half of 1921 – early 1922. Based on the use of a wide range of archival sources, the author concludes that the camp everyday life of the wartime period was marked by significant difficulties due to its extraordinary crowding and presence in the camp of interned and captured soldiers of other formations (Balahovtsy and Red Army soldiers). The lack of any material resources, the lack of adequate and high-quality food, the lack of fuel for heating booths, anti-Ukrainian agitation, led to the fact that a part of Ukrainian soldiers lost national moral values. In order to prevent the demoralization of Ukrainian warfare, the command of the group tried to intensify cultural and educational work in the camp, but due to lack of premises and lack of resources, it slowly collapsed. Some of the interned ones did not withstand the burden of hopeless and burdensome camping munitions, and left the camp in search of better living conditions. Obviously, this was a dangerous trend, and the command of the interned troops in various ways tried to prevent it from further spreading. The leader of the group A. Pиzitsky was particularly opposed to the destructive processes in the camp. His measures were fully understood and supported by the higher military leadership of the Armed Forces and the Government of the UPR.

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