scholarly journals Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance

2021 ◽  
Vol 12 ◽  
Author(s):  
Jaime Rosas-Díaz ◽  
Alejandra Escobar-Zepeda ◽  
Libertad Adaya ◽  
Jorge Rojas-Vargas ◽  
Diego Humberto Cuervo-Amaya ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Genomic Analysis ◽  
Marine Species ◽  
Degradation Pathway ◽  
Pathogenic Potential ◽  
Gene Copies ◽  
Intermediate Metabolites ◽  
Polycyclic Aromatic ◽  
Species Specific

Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.

scholarly journals Illuminating microbial species-specific effects on organic matter remineralization in marine sediments

2019 ◽  
Author(s):  
Nagissa Mahmoudi ◽  
Tim N. Enke ◽  
Steven R. Beaupré ◽  
Andreas P. Teske ◽  
Otto X. Cordero ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community Composition ◽  
Hydrolytic Enzymes ◽  
Genomic Analysis ◽  
Marine Microorganisms ◽  
Carbon Utilization ◽  
Carbon Isotopic ◽  
Specific Effects ◽  
Gene Copies ◽  
Species Specific

SummaryMarine microorganisms play a fundamental role in the global carbon cycle by mediating the sequestration of organic matter in ocean waters and sediments. A better understanding of how biological factors, such as microbial community composition, influence the lability and fate of organic matter is needed. Here, we explored the extent to which organic matter remineralization is influenced by species-specific metabolic capabilities. We carried out aerobic time-series incubations of Guaymas basin sediments to quantify the dynamics of carbon utilization by two different heterotrophic marine isolates. Continuous measurement of respiratory CO2 production and its carbon isotopic compositions (13C and 14C) shows species-specific differences in the rate, quantity, and type of organic matter remineralized. Each species was incubated with hydrothermally-influenced vs. unimpacted sediments, resulting in a ~3-fold difference in respiratory CO2 yield across the experiments. Genomic analysis indicated that the observed carbon utilization patterns may be attributed in part to the number of gene copies encoding for extracellular hydrolytic enzymes. Our results demonstrate that the lability and remineralization of organic matter in marine environments is not only a function of chemical composition and/or environmental conditions, but also a function of the microorganisms that are present and active.

scholarly journals The Role of Fucose-Containing Glycan Motifs Across Taxonomic Kingdoms

2021 ◽  
Vol 8 ◽  
Author(s):  
Luc Thomès ◽  
Daniel Bojar
Keyword(s):  
Molecular Mimicry ◽  
Large Species ◽  
Pathogenic Potential ◽  
Domains Of Life ◽  
Small Set ◽  
Recognition Systems ◽  
Species Specific ◽  
Taxonomic Groups ◽  
Shed Light

The extraordinary diversity of glycans leads to large differences in the glycomes of different kingdoms of life. Yet, while most monosaccharides are solely found in certain taxonomic groups, there is a small set of monosaccharides with widespread distribution across nearly all domains of life. These general monosaccharides are particularly relevant for glycan motifs, as they can readily be used by commensals and pathogens to mimic host glycans or hijack existing glycan recognition systems. Among these, the monosaccharide fucose is especially interesting, as it frequently presents itself as a terminal monosaccharide, primed for interaction with proteins. Here, we analyze fucose-containing glycan motifs across all taxonomic kingdoms. Using a hereby presented large species-specific glycan dataset and a plethora of methods for glycan-focused bioinformatics and machine learning, we identify characteristic as well as shared fucose-containing glycan motifs for various taxonomic groups, demonstrating clear differences in fucose usage. Even within domains, fucose is used differentially based on an organism’s physiology and habitat. We particularly highlight differences in fucose-containing motifs between vertebrates and invertebrates. With the example of pathogenic and non-pathogenic Escherichia coli strains, we also demonstrate the importance of fucose-containing motifs in molecular mimicry and thereby pathogenic potential. We envision that this study will shed light on an important class of glycan motifs, with potential new insights into the role of fucosylated glycans in symbiosis, pathogenicity, and immunity.

The Role of Spring Flood and Landscape Type in the Terrestrial Export of Polycyclic Aromatic Compounds to Streamwater

2018 ◽  
Vol 52 (11) ◽  
pp. 6217-6225 ◽  
Author(s):  
Minh A. Nguyen ◽  
Lutz Ahrens ◽  
Jakob Gustavsson ◽  
Sarah Josefsson ◽  
Hjalmar Laudon ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Polycyclic Aromatic Compounds ◽  
Spring Flood ◽  
Landscape Type ◽  
Polycyclic Aromatic

scholarly journals Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium

2010 ◽  
Vol 192 (6) ◽  
pp. 1685-1699 ◽  
Author(s):  
Mark Eppinger ◽  
Patricia L. Worsham ◽  
Mikeljon P. Nikolich ◽  
David R. Riley ◽  
Yinong Sebastian ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Genomic Analysis ◽  
Epidemiological Studies ◽  
Human Infection ◽  
Nucleotide Polymorphisms ◽  
Pathogenic Potential ◽  
Protein Coding ◽  
Genomic Plasticity ◽  
Species Specific ◽  
Genetic Signatures

ABSTRACT To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.

scholarly journals The role of fucose-containing glycan motifs across taxonomic kingdoms

2021 ◽  
Author(s):  
Luc Thomès ◽  
Daniel Bojar
Keyword(s):  
Molecular Mimicry ◽  
Large Species ◽  
Pathogenic Potential ◽  
Pathogenic Escherichia Coli ◽  
Domains Of Life ◽  
Small Set ◽  
Recognition Systems ◽  
Species Specific ◽  
Taxonomic Groups

The extraordinary diversity of glycans leads to large differences in the glycomes of different kingdoms of life. Yet, while most monosaccharides are solely found in certain taxonomic groups, there is a small set of monosaccharides with widespread distribution across nearly all domains of life. These general monosaccharides are particularly relevant for glycan motifs, as they can readily be used by commensals and pathogens to mimic host glycans or hijack existing glycan recognition systems. Among these, the monosaccharide fucose is especially interesting, as it frequently presents itself as a terminal monosaccharide, primed for interaction with proteins. Here, we analyze fucose-containing glycan motifs across all taxonomic kingdoms. Using a hereby presented large species-specific glycan dataset and a plethora of methods for glycan-focused bioinformatics and machine learning, we identify characteristic as well as shared fucose-containing glycan motifs for various taxonomic groups, demonstrating clear differences in fucose usage. Even within domains, fucose is used differentially based on an organism's physiology and habitat. We particularly highlight differences in fucose-containing motifs between vertebrates and invertebrates. With the example of pathogenic and non-pathogenic Escherichia coli strains, we also demonstrate the importance of fucose-containing motifs in molecular mimicry and thereby pathogenic potential. Finally, we also confirm and extend the role of fucosyltransferase-coding genes (FUT) in several important biological processes that include development, immunity, and diseases, especially cancer. We envision that this study will shed light on an important class of glycan motifs, with potential new insights into the role of fucosylated glycans in symbiosis, pathogenicity, and immunity.

scholarly journals Methylxanthines (caffeine, pentoxifylline and theophylline) decrease the mutagenic effect of daunomycin, doxorubicin and mitoxantrone.

2005 ◽  
Vol 52 (4) ◽  
pp. 923-926 ◽  
Author(s):  
Jacek Piosik ◽  
Anna Gwizdek-Wiśniewska ◽  
Katarzyna Ulanowska ◽  
Jakub Ochociński ◽  
Agata Czyz ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Mutagenic Effect ◽  
Spectrophotometric Titration ◽  
Stacking Interactions ◽  
Electron Systems ◽  
Cytotoxic Effects ◽  
Aromatic Molecules ◽  
Mixed Aggregates ◽  
Polycyclic Aromatic

Previously performed experiments showed that methylxanthines, especially caffeine, may protect cells against cytostatic or cytotoxic effects of several aromatic compounds. One of the proposed mechanisms of this protection is based on stacking interactions between pi electron systems of polycyclic aromatic molecules. In this work, we demonstrate that caffeine and other methylxanthines--pentoxifylline and theophylline--significantly decrease mutagenicity of the anticancer aromatic drugs daunomycin, doxorubicin and mitoxantrone. The spectrophotometric titration of these aromatic compounds by methylxanthines indicated formation of mixed aggregates. The concentrations of free active forms of the drugs decreased when the concentrations of methylxanthines increased in the mixture. Therefore, likely methylxanthines may play a role of scavengers of the free active forms of daunomycin, doxorubicin and mitoxantrone.

Transmission Electron Microscopy of Evaporated Perylene Thin Films

1990 ◽  
Vol 48 (2) ◽  
pp. 336-337
Author(s):  
C. Ewins ◽  
J.R. Fryer
Keyword(s):  
Electron Microscopy ◽  
Thin Films ◽  
Transmission Electron Microscopy ◽  
Molecular Electronics ◽  
High Vacuum ◽  
Amorphous Layer ◽  
Electric Heater ◽  
Transmission Electron ◽  
Polycyclic Aromatic

The preparation of thin films of organic molecules is currently receiving much attention because of the need to produce good quality thin films for molecular electronics. We have produced thin films of the polycyclic aromatic, perylene C10H12 by evaporation under high vacuum onto a potassium chloride (KCl) substrate. The role of substrate temperature in determining the morphology and crystallography of the films was then investigated by transmission electron microscopy (TEM).The substrate studied was the (001) face of a freshly cleaved crystal of KCl. The temperature of the KCl was controlled by an electric heater or a cold finger. The KCl was heated to 200°C under a vacuum of 10-6 torr and allowed to cool to the desired temperature. The perylene was then evaporated over a period of one minute from a molybdenum boat at a distance of 10cm from the KCl. The perylene thin film was then backed with an amorphous layer of carbon and floated onto copper microscope grids.

Questions on the role of biofilms for the adaptation of microorganisms to unfavorable environmental factors by the example of P. aeruginosa

2020 ◽  
Vol 99 (4) ◽  
pp. 379-383
Author(s):  
Vasily N. Afonyushkin ◽  
N. A. Donchenko ◽  
Ju. N. Kozlova ◽  
N. A. Davidova ◽  
V. Yu. Koptev ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Environmental Factors ◽  
Barrier Function ◽  
Infectious Agent ◽  
Antagonistic Activity ◽  
The Body ◽  
Main Function ◽  
Pathogenic Potential ◽  
The Face

Pseudomonas aeruginosa is a widely represented species of bacteria possessing of a pathogenic potential. This infectious agent is causing wound infections, fibrotic cystitis, fibrosing pneumonia, bacterial sepsis, etc. The microorganism is highly resistant to antiseptics, disinfectants, immune system responses of the body. The responses of a quorum sense of this kind of bacteria ensure the inclusion of many pathogenicity factors. The analysis of the scientific literature made it possible to formulate four questions concerning the role of biofilms for the adaptation of P. aeruginosa to adverse environmental factors: Is another person appears to be predominantly of a source an etiological agent or the source of P. aeruginosa infection in the environment? Does the formation of biofilms influence on the antibiotic resistance? How the antagonistic activity of microorganisms is realized in biofilm form? What is the main function of biofilms in the functioning of bacteria? A hypothesis has been put forward the effect of biofilms on the increase of antibiotic resistance of bacteria and, in particular, P. aeruginosa to be secondary in charcter. It is more likely a biofilmboth to fulfill the function of storing nutrients and provide topical competition in the face of food scarcity. In connection with the incompatibility of the molecular radii of most antibiotics and pores in biofilm, biofilm is doubtful to be capable of performing a barrier function for protecting against antibiotics. However, with respect to antibodies and immunocompetent cells, the barrier function is beyond doubt. The biofilm is more likely to fulfill the function of storing nutrients and providing topical competition in conditions of scarcity of food resources.

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