scholarly journals Novel de novo synthesized phosphate carrier compound ABA-PEG20k-Pi20 suppresses collagenase production in Enterococcus faecalis and prevents colonic anastomotic leak in an experimental model

2018 ◽  
Vol 105 (10) ◽  
pp. 1368-1376 ◽  
Author(s):  
M. Wiegerinck ◽  
S. K. Hyoju ◽  
J. Mao ◽  
A. Zaborin ◽  
C. Adriaansens ◽  
...  
Keyword(s):  
Anastomotic Leak ◽  
Experimental Model ◽  
Enterococcus Faecalis ◽  
De Novo ◽  
Phosphate Carrier

scholarly journals Transcription polymerase–catalyzed emergence of novel RNA replicons

Science ◽  
2020 ◽  
Vol 368 (6487) ◽  
pp. eaay0688 ◽  
Author(s):  
Nimit Jain ◽  
Lucas R. Blauch ◽  
Michal R. Szymanski ◽  
Rhiju Das ◽  
Sindy K. Y. Tang ◽  
...  
Keyword(s):  
Experimental Model ◽  
Hepatitis Delta Virus ◽  
De Novo ◽  
Rna Replication ◽  
Hereditary Material ◽  
Rolling Circle ◽  
Naturally Occurring ◽  
T7 Bacteriophage ◽  
Delta Virus

Transcription polymerases can exhibit an unusual mode of regenerating certain RNA templates from RNA, yielding systems that can replicate and evolve with RNA as the information carrier. Two classes of pathogenic RNAs (hepatitis delta virus in animals and viroids in plants) are copied by host transcription polymerases. Using in vitro RNA replication by the transcription polymerase of T7 bacteriophage as an experimental model, we identify hundreds of new replicating RNAs, define three mechanistic hallmarks of replication (subterminal de novo initiation, RNA shape-shifting, and interrupted rolling-circle synthesis), and describe emergence from DNA seeds as a mechanism for the origin of novel RNA replicons. These results inform models for the origins and replication of naturally occurring RNA genetic elements and suggest a means by which diverse RNA populations could be propagated as hereditary material in cellular contexts.

scholarly journals Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers common genetic features and a chromosomal hotspot for optrA acquisition

2019 ◽  
Author(s):  
Ana R. Freitas ◽  
Ana P. Tedim ◽  
Carla Novais ◽  
Luísa Peixe
Keyword(s):  
Enterococcus Faecalis ◽  
De Novo ◽  
Integration Site ◽  
Medium Size ◽  
Multiple Sources ◽  
Animal Reservoir ◽  
Phylogenetic Structure ◽  
Healthy Humans ◽  
Wide Range ◽  
Genetic Features

AbstractLinezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we still lack a comprehensive analysis of human and animal optrA-LREfs strains. We investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 28 publicly available optrA-positive E. faecalis genomes from different hosts in 7 countries. In the genome-level analysis, in house databases with 57 virulence and 391 plasmid replication genes were tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera, mainly but not exclusive from Firmicutes. The content in AMR and virulence genes was highly identical in contrast to the diversity of phages and plasmids observed. Epidemiologically unrelated clones (ST476-like and ST21-like) obtained from human clinical and animal hosts in different continents over 5 years (2012-2017) were phylogenetically related (3-122 SNPs difference). They also exhibited identical AMR and virulence profiles, highlighting a global spread of optrA-positive strains with relevant adaptive traits in livestock and that they might originate from an animal reservoir. optrA was located on the chromosome within a Tn6674-like element (n=9) or on medium-size plasmids (30-60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was identical in chromosomal (Tn6674) and plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted in the same ΔradC integration site and embedded in a 32 kb chromosomal platform common to diverse strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012-2018. This platform is conserved among hundreds of E. faecalis genomes and we here propose a conserved chromosomal hotspot for optrA integration. The finding of optrA in strains sharing identical adaptive features and genetic backgrounds across different hosts and countries suggest the occurrence of common and independent genetic events occurring in distant regions, and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact in the efficacy of linezolid for the treatment of Gram-positive infections.

Enterococcus faecalis Is Associated with Anastomotic Leak in Patients Undergoing Colorectal Surgery

2021 ◽  
Author(s):  
Dana I. Anderson ◽  
Robert Keskey ◽  
Max T. Ackerman ◽  
Olga Zaborina ◽  
Neil Hyman ◽  
...  
Keyword(s):  
Colorectal Surgery ◽  
Anastomotic Leak ◽  
Enterococcus Faecalis

scholarly journals Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

2020 ◽  
Vol 6 (6) ◽  
Author(s):  
Ana R. Freitas ◽  
Ana P. Tedim ◽  
Carla Novais ◽  
Val F. Lanza ◽  
Luísa Peixe
Keyword(s):  
Enterococcus Faecalis ◽  
Type Species ◽  
De Novo ◽  
Integration Site ◽  
Medium Size ◽  
Phylogenetic Structure ◽  
Content Type ◽  
Link Type ◽  
Healthy Humans ◽  
Wide Range

Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes . Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.

scholarly journals Cadmium SAD phasing at CuKα wavelength

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 84
Author(s):  
Igor E. Eliseev ◽  
Anna N. Yudenko ◽  
Valeria M. Ukrainskaya ◽  
Oleg B. Chakchir
Keyword(s):  
Experimental Model ◽  
De Novo ◽  
Common Method ◽  
Single Domain Antibody ◽  
Anomalous Diffraction ◽  
Cadmium Ions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Domain Antibody ◽  
Sad Phasing

Single-wavelength anomalous diffraction (SAD) is the most common method for de novo elucidation of macromolecular structures by X-ray crystallography. It requires an anomalous scatterer in a crystal to calculate phases. A recent study by Panneerselvam et al. emphasized the utility of cadmium ions for SAD phasing at the standard synchrotron wavelength of 1 Å. Here we show that cadmium is also useful for phasing of crystals collected in-house with CuKα radiation. Using a crystal of single-domain antibody as an experimental model, we demonstrate how cadmium SAD can be conveniently employed to solve a CuKα dataset. We then discuss the factors which make this method generally applicable.

scholarly journals Removal of peptidoglycan and inhibition of active cellular processes leads to daptomycin tolerance in Enterococcus faecalis

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254796
Author(s):  
Rachel D. Johnston ◽  
Brittni M. Woodall ◽  
Johnathan Harrison ◽  
Shawn R. Campagna ◽  
Elizabeth M. Fozo
Keyword(s):  
Enterococcus Faecalis ◽  
Fatty Acid Biosynthesis ◽  
De Novo ◽  
Intact Cell ◽  
Growth Conditions ◽  
Protein Synthesis Inhibitor ◽  
Synthesis Inhibitor ◽  
Cellular Processes ◽  
Peptidoglycan Synthesis ◽  
Cyclic Lipopeptide

Daptomycin is a cyclic lipopeptide antibiotic used in the clinic for treatment of severe enterococcal infections. Recent reports indicate that daptomycin targets active cellular processes, specifically, peptidoglycan biosynthesis. Within, we examined the efficacy of daptomycin against Enterococcus faecalis under a range of environmental growth conditions including inhibitors that target active cellular processes. Daptomycin was far less effective against cells in late stationary phase compared to cells in exponential phase, and this was independent of cellular ATP levels. Further, the addition of either the de novo protein synthesis inhibitor chloramphenicol or the fatty acid biosynthesis inhibitor cerulenin induced survival against daptomycin far better than controls. Alterations in metabolites associated with peptidoglycan synthesis correlated with protection against daptomycin. This was further supported as removal of peptidoglycan induced physiological daptomycin tolerance, a synergistic relation between daptomycin and fosfomycin, an inhibitor of the fist committed step peptidoglycan synthesis, was observed, as well as an additive effect when daptomycin was combined with ampicillin, which targets crosslinking of peptidoglycan strands. Removal of the peptidoglycan of Enterococcus faecium, Staphylococcus aureus, and Bacillus subtilis also resulted in significant protection against daptomycin in comparison to whole cells with intact cell walls. Based on these observations, we conclude that bacterial growth phase and metabolic activity, as well as the presence/absence of peptidoglycan are major contributors to the efficacy of daptomycin.

scholarly journals Structural Comparison of Enterococcus faecalis and Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1257 ◽  
Author(s):  
Cecilia Pozzi ◽  
Stefania Ferrari ◽  
Rosaria Luciani ◽  
Giusy Tassone ◽  
Maria Costi ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Conformational Changes ◽  
Thymidylate Synthase ◽  
Bacterial Infections ◽  
De Novo ◽  
Selective Inhibitors ◽  
Reductive Methylation ◽  
Thymidine Monophosphate ◽  
Therapeutic Tools ◽  
Half Site

Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2′-deoxyuridine-5′-monophosphate (dUMP) using N5,N10-methylenetetrahydrofolate (mTHF) as a cofactor. TS is ubiquitous and a validated drug target. TS enzymes from different organisms differ in sequence and structure, but are all obligate homodimers. The structural and mechanistic differences between the human and bacterial enzymes are exploitable to obtain selective inhibitors of bacterial TSs that can enrich the currently available therapeutic tools against bacterial infections. Enterococcus faecalis is a pathogen fully dependent on TS for dTMP synthesis. In this study, we present four new crystal structures of Enterococcus faecalis and human TSs in complex with either the substrate dUMP or the inhibitor FdUMP. The results provide new clues about the half-site reactivity of Enterococcus faecalis TS and the mechanisms underlying the conformational changes occurring in the two enzymes. We also identify relevant differences in cofactor and inhibitor binding between Enterococcus faecalis and human TS that can guide the design of selective inhibitors against bacterial TSs.

scholarly journals The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSB-Based Medium in Staphylococcus aureus and Enterococcus faecalis

2021 ◽  
Keyword(s):  
Staphylococcus Aureus ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
De Novo ◽  
Purine Biosynthesis ◽  
Biosynthesis Pathway ◽  
Chronic Infections ◽  
De Novo Purine Biosynthesis ◽  
Cellular Pathways ◽  
Different Strains

Bacterial biofilms are involved in chronic infections and confer 10 to 1,000 times more resistance to antibiotics compared with planktonic growth, leading to complications and treatment failure. When transitioning from a planktonic lifestyle to biofilms, some Gram-positive bacteria are likely to modulate several cellular pathways, including central carbon metabolism, biosynthesis pathways, and production of secondary metabolites. These metabolic adaptations might play a crucial role in biofilm formation by Gram-positive pathogens such as Staphylococcus aureus and Enterococcus faecalis. Here, we performed a transcriptomic approach to identify cellular pathways that might be similarly regulated during biofilm formation in these bacteria. Different strains and biofilm-inducing media were used to identify a set of regulated genes that are common and independent of the environment or accessory genomes analyzed. Our approach highlighted that the de novo purine biosynthesis pathway was upregulated in biofilms of both species when using a tryptone soy broth-based medium but not so when a brain heart infusion-based medium was used. We did not identify other pathways commonly regulated between both pathogens. Gene deletions and usage of a drug targeting a key enzyme showed the importance of this pathway in biofilm formation of S. aureus. The importance of the de novo purine biosynthesis pathway might reflect an important need for purine during biofilm establishment, and thus could constitute a promising drug target. IMPORTANCE Biofilms are often involved in nosocomial infections and can cause serious chronic infections if not treated properly. Current anti-biofilm strategies rely on antibiotic usage, but they have a limited impact because of the biofilm intrinsic tolerance to drugs. Metabolism remodeling likely plays a central role during biofilm formation. Using comparative transcriptomics of different strains of Staphylococcus aureus and Enterococcus faecalis, we determined that almost all cellular adaptations are not shared between strains and species. Interestingly, we observed that the de novo purine biosynthesis pathway was upregulated during biofilm formation by both species in a specific medium. The requirement for purine could constitute an interesting new anti-biofilm target with a wide spectrum that could also prevent resistance evolution. These results are also relevant to a better understanding of the physiology of biofilm formation.

An Experimental Model for the Investigation of Purine Biosynthesis de novo in Rat Skeletal Muscle

1977 ◽  
Vol 5 (6) ◽  
pp. 1753-1755 ◽  
Author(s):  
T. GERARD SHEEHAN ◽  
BRENDAN M. BUCKLEY ◽  
ERIC R. TULLY
Keyword(s):  
Skeletal Muscle ◽  
Experimental Model ◽  
De Novo ◽  
Purine Biosynthesis ◽  
Rat Skeletal Muscle
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