scholarly journals Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus

2016 ◽  
Vol 198 (9) ◽  
pp. 1401-1413 ◽  
Author(s):  
José Manuel Borrero-de Acuña ◽  
Manfred Rohde ◽  
Josef Wissing ◽  
Lothar Jänsch ◽  
Max Schobert ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Pseudomonas Aeruginosa ◽  
Nitrous Oxide ◽  
Protein Interactions ◽  
Molecular Basis ◽  
Protein Network ◽  
Protein Protein Interactions ◽  
Content Type ◽  
Enzyme Complexes

ABSTRACTOxidative phosphorylation using multiple-component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacteriumPseudomonas aeruginosa. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO3−→ NO2−→ NO → N2O → N2. Genetic experiments suggested that the nitric oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy colocalization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous oxide reductase NosZ is linked via NosR. The nitrate transporter NarK2, the nitrate regulatory system NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins NosFL were also found to be attached. A number of proteins associated with energy generation, including electron-donating dehydrogenases, the complete ATP synthase, almost all enzymes of the tricarboxylic acid (TCA) cycle, and the Sec system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane, and periplasmic proteins to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment.IMPORTANCEThe processes of cellular energy generation are catalyzed by large multiprotein enzyme complexes. The molecular basis for the interaction of these complexes is poorly understood. We employed membrane interactomics and electron microscopy to determine the protein-protein interactions involved. The well-investigated enzyme complexes of denitrification of the pathogenic bacteriumPseudomonas aeruginosaserved as a model. Denitrification is one essential step of the universal N cycle and provides the bacterium with an effective alternative to oxygen respiration. This process allows the bacterium to form biofilms, which create low-oxygen habitats and which are a key in the infection mechanism. Our results provide new insights into the molecular basis of respiration, as well as opening a new window into the infection strategies of this pathogen.

scholarly journals The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Kathleen L McCann ◽  
Takamasa Teramoto ◽  
Jun Zhang ◽  
Traci M Tanaka Hall ◽  
Susan J Baserga
Keyword(s):  
Protein Interactions ◽  
Molecular Basis ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Rrna Processing ◽  
Protein Protein Interactions ◽  
Recognition Motif ◽  
Processing Defects

ANE syndrome is a ribosomopathy caused by a mutation in an RNA recognition motif of RBM28, a nucleolar protein conserved to yeast (Nop4). While patients with ANE syndrome have fewer mature ribosomes, it is unclear how this mutation disrupts ribosome assembly. Here we use yeast as a model system and show that the mutation confers growth and pre-rRNA processing defects. Recently, we found that Nop4 is a hub protein in the nucleolar large subunit (LSU) processome interactome. Here we demonstrate that the ANE syndrome mutation disrupts Nop4’s hub function by abrogating several of Nop4’s protein-protein interactions. Circular dichroism and NMR demonstrate that the ANE syndrome mutation in RRM3 of human RBM28 disrupts domain folding. We conclude that the ANE syndrome mutation generates defective protein folding which abrogates protein-protein interactions and causes faulty pre-LSU rRNA processing, thus revealing one aspect of the molecular basis of this human disease.

scholarly journals Effect of Nitroxides on Swarming Motility and Biofilm Formation, Multicellular Behaviors in Pseudomonas aeruginosa

2013 ◽  
Vol 57 (10) ◽  
pp. 4877-4881 ◽  
Author(s):  
César de la Fuente-Núñez ◽  
Fany Reffuveille ◽  
Kathryn E. Fairfull-Smith ◽  
Robert E. W. Hancock
Keyword(s):  
Nitric Oxide ◽  
Pseudomonas Aeruginosa ◽  
Biofilm Formation ◽  
Wild Type ◽  
Planktonic Cells ◽  
Swarming Motility ◽  
Content Type ◽  
Exogenous Addition ◽  
Biofilm Dispersion ◽  
Dispersal Activity

ABSTRACTThe ability of nitric oxide (NO) to induce biofilm dispersion has been well established. Here, we investigated the effect of nitroxides (sterically hindered nitric oxide analogues) on biofilm formation and swarming motility inPseudomonas aeruginosa. A transposon mutant unable to produce nitric oxide endogenously (nirS) was deficient in swarming motility relative to the wild type and the complemented strain. Moreover, expression of thenirSgene was upregulated by 9.65-fold in wild-type swarming cells compared to planktonic cells. Wild-type swarming levels were substantially restored upon the exogenous addition of nitroxide containing compounds, a finding consistent with the hypothesis that NO is necessary for swarming motility. Here, we showed that nitroxides not only mimicked the dispersal activity of NO but also prevented biofilms from forming in flow cell chambers. In addition, anirStransposon mutant was deficient in biofilm formation relative to the wild type and the complemented strain, thus implicating NO in the formation of biofilms. Intriguingly, despite its stand-alone action in inhibiting biofilm formation and promoting dispersal, a nitroxide partially restored the ability of anirSmutant to form biofilms.

scholarly journals UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Theodosios Theodosiou ◽  
Nikolaos Papanikolaou ◽  
Maria Savvaki ◽  
Giulia Bonetto ◽  
Stella Maxouri ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Computational Prediction ◽  
Biomedical Literature ◽  
Protein Network ◽  
Protein Protein Interactions ◽  
High Coverage ◽  
Depth Study ◽  
Experimental Approaches ◽  
Wet Lab ◽  
User Friendly

Abstract The in-depth study of protein–protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present UniReD, a user-friendly, computational prediction tool which analyses biomedical literature in order to extract known protein associations and suggest undocumented ones. As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding a high coverage. We believe that UniReD can become an important and intuitive resource for experimental biologists in their quest for finding novel associations within a protein network and a useful tool to complement experimental approaches (e.g. mass spectrometry) by producing sorted lists of candidate proteins for further experimental validation. UniReD is available at http://bioinformatics.med.uoc.gr/unired/

scholarly journals Pseudomonas aeruginosa Triggers Macrophage Autophagy To Escape Intracellular Killing by Activation of the NLRP3 Inflammasome

2015 ◽  
Vol 84 (1) ◽  
pp. 56-66 ◽  
Author(s):  
Qiuchan Deng ◽  
Yi Wang ◽  
Yuanqing Zhang ◽  
Meiyu Li ◽  
Dandan Li ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Pseudomonas Aeruginosa ◽  
Immune Cells ◽  
Nlrp3 Inflammasome ◽  
Critical Event ◽  
Oxygen Species ◽  
Intracellular Killing ◽  
Bacterial Killing ◽  
Content Type ◽  
Human Macrophages

Assembly of the inflammasome has recently been identified to be a critical event in the initiation of inflammation. However, its role in bacterial killing remains unclear. Our study demonstrates thatPseudomonas aeruginosainfection induces the assembly of the NLRP3 inflammasome and the sequential secretion of caspase1 and interleukin-1β (IL-1β) in human macrophages. More importantly, activation of the NLRP3 inflammasome reduces the killing ofP. aeruginosain human macrophages, without affecting the generation of antimicrobial peptides, reactive oxygen species, and nitric oxide. In addition, our results demonstrate thatP. aeruginosainfection increases the amount of the LC3-II protein and triggers the formation of autophagosomes in human macrophages. TheP. aeruginosa-induced autophagy was enhanced by overexpression of NLRP3, ASC, or caspase1 but was reduced by knockdown of these core molecules of the NLRP3 inflammasome. Treatment with IL-1β enhanced autophagy in human macrophages. More importantly, IL-1β decreased the macrophage-mediated killing ofP. aeruginosa, whereas knockdown of ATG7 or Beclin1 restored the IL-1β-mediated suppression of bacterial killing. Collectively, our study explores a novel mechanism employed byP. aeruginosato escape from phagocyte killing and may provide a better understanding of the interaction betweenP. aeruginosaand host immune cells, including macrophages.

Citrulline‐nitric oxide cycle protein‐protein interactions

2007 ◽  
Vol 21 (5) ◽  
Author(s):  
Brenda R Flam ◽  
Naziya Samreen ◽  
Joel A. Strom ◽  
Larry P. Solomonson ◽  
Duane C. Eichler
Keyword(s):  
Nitric Oxide ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Nitric Oxide Cycle

scholarly journals Network Protein Interaction in Parkinson's Disease and Periodontitis Interplay: A Bioinformatic Analysis

2020 ◽  
Author(s):  
João Botelho ◽  
Paulo Mascarenhas ◽  
José João Mendes ◽  
Vanessa Machado
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Bioinformatic Analysis ◽  
Comprehensive Analysis ◽  
Protein Network ◽  
Protein Protein Interactions ◽  
Network Interaction ◽  
Genes Encoding

Recent studies supported a clinical association between Parkinson’s Disease (PD) and periodontitis. Hence, investigating possible protein interactions between these two conditions is of interest. In this study, we conducted a protein-protein network interaction analysis with recognized genes encoding proteins for PD and periodontitis. Genes of interest were collected via GWAS database. Then, we conducted a protein interaction analysis using STRING database, with a highest confidence cut-off of 0.9. Our protein network casted a comprehensive analysis of potential protein-protein interactions between PD and periodontitis. This analysis may underpin valuable information for new candidate molecular mechanisms between PD and periodontitis and may serve new potential targets for research purposes. These results should be carefully interpreted giving the limitations of this approach.

scholarly journals A Genome-WideHelicobacter pyloriMorphology Screen Uncovers a Membrane-Spanning Helical Cell Shape Complex

2019 ◽  
Vol 201 (14) ◽  
Author(s):  
Desirée C. Yang ◽  
Kris M. Blair ◽  
Jennifer A. Taylor ◽  
Timothy W. Petersen ◽  
Tate Sessler ◽  
...  
Keyword(s):  
Cell Wall ◽  
Helicobacter Pylori ◽  
Light Scattering ◽  
Protein Interactions ◽  
Cell Morphology ◽  
Cell Shape ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Content Type ◽  
H Pylori

ABSTRACTEvident in its name, the gastric pathogenHelicobacter pylorihas a helical cell morphology which facilitates efficient colonization of the human stomach. An improved light-focusing strategy allowed us to robustly distinguish even subtle perturbations ofH. pyloricell morphology by deviations in light-scattering properties measured by flow cytometry. Profiling of an arrayed genome-wide deletion library identified 28 genes that influence different aspects of cell shape, including properties of the helix, cell length or width, cell filament formation, cell shape heterogeneity, and cell branching. Included in this mutant collection were two that failed to form any helical cells, a soluble lytic transglycosylase and a previously uncharacterized putative multipass inner membrane protein HPG27_0728, renamed Csd7. A combination of cell fractionation, mutational, and immunoprecipitation experiments show that Csd7 and Csd2 collaborate to stabilize the Csd1 peptidoglycan (PG) endopeptidase. Thus, bothcsd2andcsd7mutants show the same enhancement of PG tetra-pentapeptide cross-linking ascsd1mutants. Csd7 also links Csd1 with the bactofilin CcmA via protein-protein interactions. Although Csd1 is stable inccmAmutants, these mutants show altered PG tetra-pentapeptide cross-linking, suggesting that Csd7 may directly or indirectly activate as well as stabilize Csd1. These data begin to illuminate a highly orchestrated program to regulate PG modifications that promote helical shape, which includes nine nonessential nonredundant genes required for helical shape and 26 additional genes that further modifyH. pylori’s cell morphology.IMPORTANCEThe stomach ulcer and cancer-causing pathogenHelicobacter pylorihas a helical cell shape which facilitates stomach infection. Using light scattering to measure perturbations of cell morphology, we identified 28 genes that influence different aspects of cell shape. A mutant in a previously uncharacterized protein renamed Csd7 failed to form any helical cells. Biochemical analyses showed that Csd7 collaborates with other proteins to stabilize the cell wall-degrading enzyme Csd1. Csd7 also links Csd1 with a putative filament-forming protein via protein-protein interactions. These data suggest that helical cell shape arises from a highly orchestrated program to regulate cell wall modifications. Targeting of this helical cell shape-promoting program could offer new ways to block infectivity of this important human pathogen.

scholarly journals Regulatory Role of PopN and Its Interacting Partners in Type III Secretion of Pseudomonas aeruginosa

2007 ◽  
Vol 189 (7) ◽  
pp. 2599-2609 ◽  
Author(s):  
Hongjing Yang ◽  
Zhiying Shan ◽  
Jaewha Kim ◽  
Weihui Wu ◽  
Wei Lian ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Protein Interactions ◽  
Type Iii Secretion ◽  
Calcium Binding ◽  
High Capacity ◽  
Calcium Signal ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Type Iii

ABSTRACT The type III secretion system (T3SS) of Pseudomonas aeruginosa plays a significant role in pathogenesis. We have previously identified type III secretion factor (TSF), which is required for effective secretion of the type III effector molecules, in addition to the low calcium signal. TSF includes many low-affinity high-capacity calcium binding proteins, such as serum albumin and casein. A search for the TSF binding targets on the bacterial outer membrane resulted in identification of PopN, a component of the T3SS that is readily detectable on the bacterial cell surface. PopN specifically interacts with Pcr1, and both popN and pcr1 mutants have a constitutive type III secretion phenotype, suggesting that the two proteins form a complex that functions as a T3SS repressor. Further analysis of the popN operon genes resulted in identification of protein-protein interactions between Pcr1 and Pcr4 and between Pcr4 and Pcr3, as well as between PopN and Pcr2 in the presence of PscB. Unlike popN and pcr1 mutants, pcr3 and pcr4 mutants are totally defective in type III secretion, while a pcr2 mutant exhibits reduced type III secretion. Interestingly, PopN, Pcr1, Pcr2, and Pcr4 are all secreted in a type III secretion machinery-dependent manner, while Pcr3 is not. These findings imply that these components have important regulatory roles in controlling type III secretion.

Dynamic behavior of biomaterials uncovered by cryo-electron microscopy.

2020 ◽  
Vol 23 ◽  
Author(s):  
Yimin Zhao ◽  
Yizhen Zhao ◽  
Bingquan Peng ◽  
Lei Zhang
Keyword(s):  
Electron Microscopy ◽  
Protein Interactions ◽  
Rapid Development ◽  
Conformational Space ◽  
Biological Macromolecules ◽  
Protein Protein Interactions ◽  
Static Structure ◽  
Cryo Electron Microscopy ◽  
Biological Complexes ◽  
Functional Mechanisms

: Structural biology develops rapidly as time goes on. Based only on static structure analysis of biomaterials is not enough to satisfy the studies of their functional mechanisms, with a huge obstacle for the dynamic process of biological complexes. The rapid development of cryo-electron microscopy(cryo-EM) technology makes that it is possible to observe the near-atomic resolution structures and dynamic nature of biological macromolecules, in the fields of dynamic characteristics of proteins, protein-protein interactions, molecular recognition, and structure-based design. In this review, we systematically elaborate the contribution of cryo-EM technology in the field of biomaterials such as ribosome motion, membrane protein structure and conformational space, dynamic transmission within the plasma membrane and clinical applications. We also put forwards a new standpoint in the development of cryo-EM technology.

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