How an unusual chemosensory system forms arrays on the bacterial nucleoid

2020 ◽  
Vol 48 (2) ◽  
pp. 347-356
Author(s):  
Emilia M.F. Mauriello
Keyword(s):  
Signal Amplification ◽  
Bacterial Species ◽  
Supramolecular Organization ◽  
Chemosensory System ◽  
Bacterial Nucleoid ◽  
Direct Binding ◽  
Functional Features ◽  
Gliding Bacterium ◽  
Multiple Clusters ◽  
Chemosensory Systems

Chemosensory systems are signaling pathways elegantly organized in hexagonal arrays that confer unique functional features to these systems such as signal amplification. Chemosensory arrays adopt different subcellular localizations from one bacterial species to another, yet keeping their supramolecular organization unmodified. In the gliding bacterium Myxococcus xanthus, a cytoplasmic chemosensory system, Frz, forms multiple clusters on the nucleoid through the direct binding of the FrzCD receptor to DNA. A small CheW-like protein, FrzB, might be responsible for the formation of multiple (instead of just one) Frz arrays. In this review, we summarize what is known on Frz array formation on the bacterial chromosome and discuss hypotheses on how FrzB might contribute to the nucleation of multiple clusters. Finally, we will propose some possible biological explanations for this type of localization pattern.

scholarly journals In Silico Analysis: Annotations about Structural and Functional Features of DUF 2726 Family Member Proteins

2016 ◽  
pp. 53-58
Author(s):  
SM Sabbir Alam ◽  
M Ruhul Amin ◽  
M Anwar Hossain
Keyword(s):  
Nucleic Acid ◽  
Nuclear Localization ◽  
Nuclear Localization Signal ◽  
Bacterial Species ◽  
Nucleic Acid Binding ◽  
Protein Families ◽  
Binding Properties ◽  
Pfam Database ◽  
Localization Signal ◽  
Functional Features

Domains of unknown functions (DUFs) are a big set of protein families within the Pfam database that includes proteins of unknown function. In the absence of functional information, proteins are classified into different families based on conserved amino acid sequences and are potentially functionally important. In Pfam database, the numbers of families of DUFs are rapidly increasing and in current the fraction of DUF families had increased to about twenty two percent of all protein families. In this study we targeted DUF2726 member proteins which are mainly present in different bacterial species of Gamma-proteobacteria and have a particular domain organization. We analyzed the protein sequences of domain DUF2726 using different computational tools and databases. We found that this domain contains a nuclear localization signal peptide, which is conserved in Escherichia spp. and Shigella spp. It were also predicted that it has nucleic acid binding properties. Analyzing protein-protein interactions functional partners associated with DUF 2726 were revealed. Protein secondary structure, transmembrane helices structure were predicted. We have found that it has gene neighbourhood and co-occurrences with protein RepA and RepB. RepA and RepB are functionally associated with replication. RepA is a replication protein and RepB is a replication regulatory protein. Presence of a nucleic acid binding properties, a nuclear localization signal (NLS) signalling peptide, and possible interaction pattern with replication proteins, conjectures its possible role as a NLS like signalling peptide.Bangladesh J Microbiol, Volume 31, Number 1-2,June-Dec 2014, pp 53-58

scholarly journals Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes

2016 ◽  
Author(s):  
Gregorio Iraola ◽  
Hugo Naya
Keyword(s):  
Best Practices ◽  
Polyphasic Taxonomy ◽  
Bacterial Species ◽  
Genomic Data ◽  
Link Type ◽  
Prokaryotic Genomes ◽  
Functional Features ◽  
Definition Of ◽  
Ecological Coherence ◽  
Metabolic Signatures

Taxonomy of prokaryotes has remained a controversial discipline due to the extreme plasticity of microorganisms, causing inconsistencies between phenotypic and genotypic classifications. The genomics era has enhanced taxonomy but also opened new debates about the best practices for incorporating genomic data into polyphasic taxonomy protocols, which are fairly biased towards the identification of bacterial species. Here we use an extensive dataset of Archaea and Bacteria to prove that metabolic signatures coded in their genomes are informative traits that allow to accurately classify organisms coherently to higher taxonomic ranks, and to associate functional features with the definition of taxa. Our results support the ecological coherence of higher taxonomic ranks and reconciles taxonomy with traditional chemotaxonomic traits inferred from genomes. KARL, a simple and free tool useful for assisting polyphasic taxonomy or to perform functional prospections is also presented (https://github.com/giraola/KARL).

scholarly journals Tuning Functional Behavior of Humic Acids through Interactions with Stöber Silica Nanoparticles

Polymers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 982 ◽  
Author(s):  
Giulio Pota ◽  
Virginia Venezia ◽  
Giuseppe Vitiello ◽  
Paola Di Donato ◽  
Valentina Mollo ◽  
...  
Keyword(s):  
Humic Acids ◽  
Sol Gel ◽  
Antioxidant Properties ◽  
Inorganic Nanoparticles ◽  
Amide Bond ◽  
Hybrid Nanoparticles ◽  
Supramolecular Organization ◽  
Paramagnetic Resonance ◽  
Physical Entrapment ◽  
Functional Features

Humic acids (HA) exhibit fascinating multifunctional features, yet degradation phenomena as well as poor stability in aqueous environments strongly limit their use. Inorganic nanoparticles are emerging as a powerful interface for the development of robust HA bio-hybrid materials with enhanced chemical stability and tunable properties. Hybrid organic-inorganic SiO2/HA nanostructures were synthesized via an in-situ sol-gel route, exploiting both physical entrapment and chemical coupling. The latter was achieved through amide bond formation between carboxyl groups of HA and the amino group of 3-aminopropyltriethoxysilane (APTS), as confirmed by Fourier-Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopy. Monodisperse hybrid nanoparticles about 90 nm in diameter were obtained in both cases, yet Electron Paramagnetic Resonance (EPR) spectroscopy highlighted the different supramolecular organization of HA. The altered HA conformation was reflected in different antioxidant properties of the conjugated nanoparticles that, however, resulted in being higher than for pure HA. Our findings proved the key role of both components in defining the morphology of the final system, as well as the efficacy of the ceramic component in templating the HA supramolecular organization and consequently tuning their functional features, thus defining a green strategy for bio-waste valorization.

scholarly journals A novel approach to the functional classification of retinal ganglion cells

2021 ◽  
Author(s):  
Gerrit Hilgen ◽  
Evgenia Kartsaki ◽  
Viktoriia Kartysh ◽  
Bruno Cessac ◽  
Evelyne Sernagor
Keyword(s):  
Large Scale ◽  
Ganglion Cells ◽  
Brain Regions ◽  
Designer Drugs ◽  
Retinal Ganglion ◽  
Novel Approach ◽  
Functional Features ◽  
Novel Strategy ◽  
Post Hoc ◽  
Multiple Clusters

Retinal neurons come in remarkable diversity based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal electrophysiology. Our novel strategy allows grouping of cells sharing gene expression and understanding how these cell classes respond to basic and complex visual scenes. Our approach consists of increasing the firing level of RGCs co-expressing a certain gene (Scnn1a or Grik4) using excitatory DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) and then correlate the location of these cells with post hoc immunostaining, to unequivocally characterize anatomical and functional features of these two groups. We grouped these isolated RGC responses into multiple clusters based on the similarity of the spike trains. With our approach, and accompanied by immunohistochemistry, we were able to extend the pre-existing list of Grik4 expressing RGC types to a total of 8 RGC types and, for the first time, we provide a phenotypical description of 14 Scnn1a-expressing RGCs. The insights and methods gained here can guide RGC classification but also neuronal classification challenges in other brain regions.

scholarly journals Three PilZ domain proteins, PlpA, PixA and PixB, have distinct functions in regulation of motility and development in Myxococcus xanthus

2021 ◽  
Author(s):  
Sofya Kuzmich ◽  
Dorota Skotnicka ◽  
Dobromir Szadkowski ◽  
Philipp Klos ◽  
María Pérez‐Burgos ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Myxococcus Xanthus ◽  
Type Iv Pili ◽  
Gliding Motility ◽  
Intact Protein ◽  
Dependent Manner ◽  
Chemosensory System ◽  
Type Iv ◽  
Acetyltransferase Domain

In bacteria, the nucleotide-based second messenger bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) binds to effectors to generate outputs in response to changes in the environment. In Myxococcus xanthus, c-di-GMP regulates type IV pili-dependent motility and the starvation-induced developmental program that results in formation of spore-filled fruiting bodies; however, little is known about the effectors that bind c-di-GMP. Here, we systematically inactivated all 24 genes encoding PilZ domain-containing proteins, which are among the most common c-di-GMP effectors. We confirm that the stand-alone PilZ-domain protein PlpA is important for regulation of motility independently of the Frz chemosensory system, and that Pkn1, which is composed of a Ser/Thr kinase domain and a PilZ domain, is specifically important for development. Moreover, we identify two PilZ-domain proteins that have distinct functions in regulating motility and development. PixB, which is composed of two PilZ domains and an acetyltransferase domain, binds c-di-GMP in vitro and regulates type IV pili-dependent and gliding motility in a Frz-dependent manner as well as development. The acetyltransferase domain is required and sufficient for function during growth while all three domains and c-di-GMP binding are essential for PixB function during development. PixA is a response regulator composed of a PilZ domain and a receiver domain, binds c-di-GMP in vitro, and regulates motility independently of the Frz system likely by setting up the polarity of the two motility systems. Our results support a model whereby PlpA, PixA and PixB act in independent pathways and have distinct functions in regulation of motility. Importance c-di-GMP signaling controls bacterial motility in many bacterial species by binding to downstream effector proteins. Here, we identify two PilZ domain-containing proteins in Myxococcus xanthus that bind c-di-GMP. We show that PixB, which contains two PilZ domains and an acetyltransferase domain, acts in a manner that depends on the Frz chemosensory system to regulate motility via the acetyltransferase domain while the intact protein and c-di-GMP binding are essential for PixB to support development. By contrast, PixA acts acts in Frz-independent mannerto regulate motility. Together with previous observations, we conclude that PilZ-domain proteins and c-di-GMP act in multiple independent pathways to regulate motility and development in M. xanthus.

scholarly journals Identification and Functional Characterization of Arylamine N-Acetyltransferases in Eubacteria: Evidence for Highly Selective Acetylation of 5-Aminosalicylic Acid

2001 ◽  
Vol 183 (11) ◽  
pp. 3417-3427 ◽  
Author(s):  
Claudine Deloménie ◽  
Sylvaine Fouix ◽  
Sandrine Longuemaux ◽  
Naı̈ma Brahimi ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Shigella Flexneri ◽  
Bacterial Species ◽  
Klebsiella Oxytoca ◽  
Functional Characterization ◽  
Catalytic Efficiency ◽  
Aminosalicylic Acid ◽  
Acetyltransferase Activity ◽  
Serovar Typhimurium ◽  
Functional Features

ABSTRACT Arylamine N-acetyltransferase activity has been described in various bacterial species. BacterialN-acetyltransferases, including those from bacteria of the gut flora, may be involved in the metabolism of xenobiotics, thereby exerting physiopathological effects. We characterized these enzymes further by steady-state kinetics, time-dependent inhibition, and DNA hybridization in 40 species, mostly from the human intestinal microflora. We report for the first timeN-acetyltransferase activity in 11 species ofProteobacteriaceae from seven genera: Citrobacter amalonaticus, Citrobacter farmeri, Citrobacter freundii, Klebsiella ozaenae, Klebsiella oxytoca, Klebsiella rhinoscleromatis, Morganella morganii, Serratia marcescens, Shigella flexneri, Plesiomonas shigelloides, and Vibrio cholerae. We estimated apparent kinetic parameters and found that 5-aminosalicylic acid, a compound efficient in the treatment of inflammatory bowel diseases, was acetylated with a catalytic efficiency 27 to 645 times higher than that for its isomer, 4-aminosalicylic acid. In contrast,para-aminobenzoic acid, a folate precursor in bacteria, was poorly acetylated. Of the wild-type strains studied, Pseudomonas aeruginosa was the best acetylator in terms of both substrate spectrum and catalytic efficiency. DNA hybridization with aSalmonella enterica serovar Typhimurium-derived probe suggested the presence of this enzyme in eight proteobacterial and four gram-positive species. Molecular aspects together with the kinetic data suggest distinct functional features for this class of microbial enzymes.

Structural analysis of the photosynthetic membrane from Ectothiorhodospira halochloris

1983 ◽  
Vol 41 ◽  
pp. 740-741
Author(s):  
H. Engelhardt ◽  
R. Guckenberger ◽  
W. Baumeister
Keyword(s):  
Lattice Structure ◽  
Bacterial Species ◽  
Hexagonal Lattice ◽  
Reaction Centre ◽  
Photosynthetic Membrane ◽  
Rhodopseudomonas Viridis ◽  
Photosynthetic Membranes ◽  
Ectothiorhodospira Halochloris ◽  
Main Components

Bacterial photosynthetic membranes contain, apart from lipids and electron transport components, reaction centre (RC) and light harvesting (LH) polypeptides as the main components. The RC-LH complexes in Rhodopseudomonas viridis membranes are known since quite seme time to form a hexagonal lattice structure in vivo; hence this membrane attracted the particular attention of electron microscopists. Contrary to previous claims in the literature we found, however, that 2-D periodically organized photosynthetic membranes are not a unique feature of Rhodopseudomonas viridis. At least five bacterial species, all bacteriophyll b - containing, possess membranes with the RC-LH complexes regularly arrayed. All these membranes appear to have a similar lattice structure and fine-morphology. The lattice spacings of the Ectothiorhodospira haloohloris, Ectothiorhodospira abdelmalekii and Rhodopseudomonas viridis membranes are close to 13 nm, those of Thiocapsa pfennigii and Rhodopseudomonas sulfoviridis are slightly smaller (∼12.5 nm).

Specific Labeling of Protein Domains with Antibody Fragments

1981 ◽  
Vol 39 ◽  
pp. 416-417
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler
Keyword(s):  
Image Processing ◽  
Specific Protein ◽  
Antibody Fragments ◽  
Supramolecular Organization ◽  
Two Dimensional ◽  
Ordered Structures ◽  
Virus Capsids ◽  
Processing Techniques

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.

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