Adhesins encoded by the gingipain genes of Porphyromonas gingivalis are responsible for co-aggregation with Prevotella intermedia

Microbiology ◽  
2003 ◽  
Vol 149 (5) ◽  
pp. 1257-1264 ◽  
Author(s):  
Arihide Kamaguchi ◽  
Tohru Ohyama ◽  
Eiko Sakai ◽  
Reiko Nakamura ◽  
Toshihiro Watanabe ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Bacterial Species ◽  
Gel Filtration ◽  
Prevotella Intermedia ◽  
Bacterial Cells ◽  
Terminal Portion ◽  
Genes Encoding ◽  
Sepharose 4B ◽  
Genomic Dna Sequence ◽  
Aggregation Factors

Co-aggregation among bacterial cells caused by the adherence of one bacterial species to another is a potential colonization mechanism. Several putative aggregation factors for co-aggregation between Porphyromonas (Por.) gingivalis and Prevotella (Pre.) intermedia were partially purified from Por. gingivalis vesicles by gel filtration and affinity chromatography. Antisera against the aggregation factors were made. Analysis using these antisera revealed that 18 and 44 kDa proteins might be responsible for Por. gingivalis vesicle-mediated aggregation of Pre. intermedia. Using antiserum against the 18 kDa protein, the DNA region encoding it was cloned from Por. gingivalis genomic DNA. Sequence analysis revealed that the DNA region was located within the rgpA and kgp genes, encoding Arg-gingipain (Rgp) and Lys-gingipain (Kgp), respectively, and it encoded non-catalytic adhesin domain regions, namely a C-terminal portion of HGP15, the entire HGP17 sequence and an N-terminal portion of HGP27. A portion of the DNA sequence was also found in the haemagglutinin A (hagA) gene. A recombinant glutathione S-transferase (GST)–HGP17 fusion protein reacted to antiserum against the 18 kDa protein and Pre. intermedia cells could adhere to GST–HGP17-conjugated Sepharose 4B beads, indicating that the HGP17 domain protein is responsible for Por. gingivalis vesicle-mediated aggregation of Pre. intermedia.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

scholarly journals β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization

2020 ◽  
Vol 9 (1) ◽  
pp. 55
Author(s):  
María Florencia Eberhardt ◽  
José Matías Irazoqui ◽  
Ariel Fernando Amadio
Keyword(s):  
Bacterial Species ◽  
Value Added ◽  
Raw Material ◽  
Activity Levels ◽  
Treatment Technology ◽  
Catalytic Domains ◽  
Stabilization Ponds ◽  
Cazy Database ◽  
Genes Encoding ◽  
Value Added Products

Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds’ metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries’ by-products.

scholarly journals Identification of the Genes Encoding the Cytosolic Translation Release Factors from Podospora anserina and Analysis of Their Role During the Life Cycle

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1763-1775 ◽  
Author(s):  
Bénédicte Gagny ◽  
Philippe Silar
Keyword(s):  
Life Span ◽  
Translation Termination ◽  
Podospora Anserina ◽  
Terminal Region ◽  
Terminal Portion ◽  
Nonsense Mutations ◽  
Translation Fidelity ◽  
Reproductive Impairment ◽  
Genes Encoding ◽  
Nonsense Suppressor

Abstract In an attempt to decipher their role in the life history and senescence process of the filamentous fungus Podospora anserina, we have cloned the su1 and su2 genes, previously identified as implicated in cytosolic translation fidelity. We show that these genes are the equivalents of the SUP35 and SUP45 genes of Saccharomyces cerevisiae, which encode the cytosolic translation termination factors eRF3 and eRF1, respectively. Mutations in these genes that suppress nonsense mutations may lead to drastic mycelium morphology changes and sexual impairment but have little effect on life span. Deletion of su1, coding for the P. anserina eRF3, is lethal. Diminution of its expression leads to a nonsense suppressor phenotype whereas its overexpression leads to an antisuppressor phenotype. P. anserina eRF3 presents an N-terminal region structurally related to the yeast eRF3 one. Deletion of the N-terminal region of P. anserina eRF3 does not cause any vegetative alteration; especially life span is not changed. However, it promotes a reproductive impairment. Contrary to what happens in S. cerevisiae, deletion of the N terminus of the protein promotes a nonsense suppressor phenotype. Genetic analysis suggests that this domain of eRF3 acts in P. anserina as a cis-activator of the C-terminal portion and is required for proper reproduction.

scholarly journals Bacteria in the global atmosphere – Part 2: Modeling of emissions and transport between different ecosystems

2009 ◽  
Vol 9 (23) ◽  
pp. 9281-9297 ◽  
Author(s):  
S. M. Burrows ◽  
T. Butler ◽  
P. Jöckel ◽  
H. Tost ◽  
A. Kerkweg ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Residence Time ◽  
General Circulation ◽  
Bacterial Species ◽  
Circulation Model ◽  
Cloud Condensation Nucleus ◽  
Cloud Formation ◽  
Emission Region ◽  
Culturable Bacteria ◽  
Bacterial Cells

Abstract. Bacteria are constantly being transported through the atmosphere, which may have implications for human health, agriculture, cloud formation, and the dispersal of bacterial species. We simulate the global transport of bacteria, represented as 1 μm and 3 μm diameter spherical solid particle tracers in a general circulation model. We investigate factors influencing residence time and distribution of the particles, including emission region, cloud condensation nucleus activity and removal by ice-phase precipitation. The global distribution depends strongly on the assumptions made about uptake into cloud droplets and ice. The transport is also affected, to a lesser extent, by the emission region, particulate diameter, and season. We find that the seasonal variation in atmospheric residence time is insufficient to explain by itself the observed seasonal variation in concentrations of particulate airborne culturable bacteria, indicating that this variability is mainly driven by seasonal variations in culturability and/or emission strength. We examine the potential for exchange of bacteria between ecosystems and obtain rough estimates of the flux from each ecosystem by using a maximum likelihood estimation technique, together with a new compilation of available observations described in a companion paper. Globally, we estimate the total emissions of bacteria-containing particles to the atmosphere to be 7.6×1023–3.5×1024 a−1, originating mainly from grasslands, shrubs and crops. We estimate the mass of emitted bacteria- to be 40–1800 Gg a−1, depending on the mass fraction of bacterial cells in the particles. In order to improve understanding of this topic, more measurements of the bacterial content of the air and of the rate of surface-atmosphere exchange of bacteria will be necessary. Future observations in wetlands, hot deserts, tundra, remote glacial and coastal regions and over oceans will be of particular interest.

scholarly journals Microbial Photoinactivation by Visible Light Results in Limited Loss of Membrane Integrity

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 341
Author(s):  
Katharina Hoenes ◽  
Richard Bauer ◽  
Barbara Spellerberg ◽  
Martin Hessling
Keyword(s):  
Visible Light ◽  
Pseudomonas Fluorescens ◽  
Bacterial Cell ◽  
Bacterial Species ◽  
Membrane Integrity ◽  
Cell Lysis ◽  
Microbial Inactivation ◽  
Bacterial Cells ◽  
Resistance Development ◽  
Transmission Electron

Interest in visible light irradiation as a microbial inactivation method has widely increased due to multiple possible applications. Resistance development is considered unlikely, because of the multi-target mechanism, based on the induction of reactive oxygen species by wavelength specific photosensitizers. However, the affected targets are still not completely identified. We investigated membrane integrity with the fluorescence staining kit LIVE/DEAD® BacLight™ on a Gram positive and a Gram negative bacterial species, irradiating Staphylococcus carnosus and Pseudomonas fluorescens with 405 nm and 450 nm. To exclude the generation of viable but nonculturable (VBNC) bacterial cells, we applied an ATP test, measuring the loss of vitality. Pronounced uptake of propidium iodide was only observed in Pseudomonas fluorescens at 405 nm. Transmission electron micrographs revealed no obvious differences between irradiated samples and controls, especially no indication of an increased bacterial cell lysis could be observed. Based on our results and previous literature, we suggest that visible light photoinactivation does not lead to rapid bacterial cell lysis or disruption. However, functional loss of membrane integrity due to depolarization or inactivation of membrane proteins may occur. Decomposition of the bacterial envelope following cell death might be responsible for observations of intracellular component leakage.

Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes

1993 ◽  
Vol 13 (7) ◽  
pp. 4214-4222
Author(s):  
Y Chen ◽  
J Weeks ◽  
M A Mortin ◽  
A L Greenleaf
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Sequence ◽  
Pcr Amplification ◽  
Single Strand Conformation Polymorphism ◽  
Chain Elongation ◽  
Developmental Defect ◽  
Genes Encoding ◽  
Transcript Elongation

We have mapped a number of mutations at the DNA sequence level in genes encoding the largest (RpII215) and second-largest (RpII140) subunits of Drosophila melanogaster RNA polymerase II. Using polymerase chain reaction (PCR) amplification and single-strand conformation polymorphism (SSCP) analysis, we detected 12 mutations from 14 mutant alleles (86%) as mobility shifts in nondenaturing gel electrophoresis, thus localizing the mutations to the corresponding PCR fragments of about 350 bp. We then determined the mutations at the DNA sequence level by directly subcloning the PCR fragments and sequencing them. The five mapped RpII140 mutations clustered in a C-terminal portion of the second-largest subunit, indicating the functional importance of this region of the subunit. The RpII215 mutations were distributed more broadly, although six of eight clustered in a central region of the subunit. One notable mutation that we localized to this region was the alpha-amanitin-resistant mutation RpII215C4, which also affects RNA chain elongation in vitro. RpII215C4 mapped to a position near the sites of corresponding mutations in mouse and in Caenorhabditis elegans genes, reinforcing the idea that this region is involved in amatoxin binding and transcript elongation. We also mapped mutations in both RpII215 and RpII140 that cause a developmental defect known as the Ubx effect. The clustering of these mutations in each gene suggests that they define functional domains in each subunit whose alteration induces the mutant phenotype.

scholarly journals Butyrivibrio hungateiMB2003 Competes Effectively for Soluble Sugars Released byButyrivibrio proteoclasticusB316Tduring Growth on Xylan or Pectin

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Nikola Palevich ◽  
William J. Kelly ◽  
Siva Ganesh ◽  
Jasna Rakonjac ◽  
Graeme T. Attwood
Keyword(s):  
Bacterial Species ◽  
Soluble Sugars ◽  
Plant Fiber ◽  
Content Type ◽  
Plant Polysaccharide ◽  
Rumen Microbes ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Enzymatic Machinery

ABSTRACTRumen bacterial species belonging to the genusButyrivibrioare important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four species are recognized; they have very similar substrate utilization profiles, but little is known about how these microorganisms are able to coexist in the rumen. To investigate this question,Butyrivibrio hungateiMB2003 andButyrivibrio proteoclasticusB316Twere grown alone or in coculture on xylan or pectin, and their growth, release of sugars, fermentation end products, and transcriptomes were examined. In monocultures, B316Twas able to grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Cocultures of B316Tgrown with MB2003 revealed that MB2003 showed growth almost equivalent to that of B316Twhen either xylan or pectin was supplied as the substrate. The effect of coculture on the transcriptomes of B316Tand MB2003 was assessed; B316Ttranscription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding proteins for carbohydrate degradation, central metabolism, oligosaccharide transport, and substrate assimilation, in order to compete with B316Tfor the released sugars. These results suggest that B316Thas a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen.IMPORTANCEFeeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation.Butyrivibriospecies are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species ofButyrivibriohave developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber.

Antimicrobial Activity of Gaseous Allyl Isothiocyanate

1997 ◽  
Vol 60 (8) ◽  
pp. 943-947 ◽  
Author(s):  
PASCAL J. DELAQUIS ◽  
PETER L. SHOLBERG
Keyword(s):  
Bacterial Species ◽  
Allyl Isothiocyanate ◽  
Model System ◽  
Penicillium Expansum ◽  
Escherichia Coli O157 ◽  
Fluorescent Pseudomonad ◽  
Bacterial Cells ◽  
E Coli ◽  
Simple Model System ◽  
Germination And Growth

A simple model system was constructed to evaluate the microbistatic and microbicidal properties of gaseous allyl isothiocyanate (AIT) against bacterial cells and fungal conidia deposited on agar surfaces. Salmonella typhimurium, Listeria monocytogenes Scott A, and Escherichia coli O157:H7 were inhibited when exposed to 1,000 μg AIT per liter. Pseudomonas corrugata, a Cytophaga species, and a fluorescent pseudomonad failed to grow in the presence of 500 μg AIT per liter. Germination and growth of Penicillium expansum, Aspergillus flavus, and Botrytis cinerea conidia was inhibited in the presence of 100 μg AIT per liter. Bactericidal and sporicidal activities varied with strain and increased with time of exposure, AIT concentration, and temperature. E. coli O157:H7 was the most resistant bacterial species tested.

scholarly journals Diversity of Free-Living and Attached Bacteria in Offshore Western Mediterranean Waters as Depicted by Analysis of Genes Encoding 16S rRNA

1999 ◽  
Vol 65 (2) ◽  
pp. 514-522 ◽  
Author(s):  
Silvia G. Acinas ◽  
Josefa Antón ◽  
Francisco Rodríguez-Valera
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Western Mediterranean ◽  
Bacterial Cells ◽  
Free Living ◽  
Attached Bacteria ◽  
Genes Encoding ◽  
Community Fingerprinting ◽  
Close Relatives ◽  
Alteromonas Macleodii

ABSTRACT In a previous study (S. G. Acinas, F. Rodrı́guez-Valera, and C. Pedrós-Alió, FEMS Microbiol. Ecol. 24:27–40, 1997), community fingerprinting by 16S rDNA restriction analysis applied to Mediterranean offshore waters showed that the free-living pelagic bacterial community was very different from the bacterial cells aggregated or attached to particles of more than about 8 μm. Here we have studied both assemblages at three depths (5, 50, and 400 m) by cloning and sequencing the 16S rDNA obtained from the same samples, and we have also studied the samples by scanning electron microscopy to detect morphology patterns. As expected, the sequences retrieved from the assemblages were very different. The subsample of attached bacteria contained very little diversity, with close relatives of a well-known species of marine bacteria, Alteromonas macleodii, representing the vast majority of the clones at every depth. On the other hand, the free-living assemblage was highly diverse and varied with depth. At 400 m, close relatives of cultivated γProteobacteria predominated, but as shown by other authors, near the surface most clones were related to phylotypes described only by sequence, in which the α Proteobacteria of the SAR11 cluster predominated. The new technique of rDNA internal spacer analysis has been utilized, confirming these results. Clones representative of the A. macleodii cluster have been completely sequenced, producing a picture that fits well with the idea that they could represent a genus with at least two species and with a characteristic depth distribution.

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