Faculty Opinions recommendation of Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA.

Specific gene probe detection methods that utilise a non-selective culturing step were tested for the ability to recognise the presence of quiescent enteric bacteria (Escherichia coli and Enterococcus faecalis ) within illuminated freshwater and seawater microcosms. An E. coli specific uidA gene probe and a 23S rRNA oligonucleotide probe for Enterococci were compared with recoveries using membrane filtration and incubation on selective media (mTEC and mE respectively). From these microcosm experiments a greater initial detection (from 4 hours to 1 day) of E. coli and Ent. faecalis using gene probe methods was observed. Additionally, a comparison of E. coli direct viable counts (DVC) in sunlight exposed microcosms with recoveries by selective media and gene probe methods revealed a large number of viable non-culturable cells. This suggests that enumeration of E. coli by a gene probe method is limited by the replication of the bacteria during the initial non-selective enrichment step. The detection of stressed Ent. faecalis by the oligonucleotide gene probe method was significantly greater than recovery on selective mE agar, indicating an Enterococci non-growth phase.

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Macrolide-Resistant and Macrolide-Sensitive Mycoplasma pneumoniae Pneumonia in Children Treated Using Early Corticosteroids

Journal of Clinical Medicine ◽

10.3390/jcm10061309 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1309

Author(s):

Hye Young Han ◽

Ki Cheol Park ◽

Eun-Ae Yang ◽

Kyung-Yil Lee

Keyword(s):

Mycoplasma Pneumoniae ◽

Serological Test ◽

Corticosteroid Treatment ◽

23S Rrna ◽

Laboratory Parameters ◽

The Mean ◽

Domain V ◽

Positive Results ◽

Mycoplasma Pneumoniae Pneumonia

We have found that early corticosteroid therapy was effective for reducing morbidity during five Korea-wide epidemics. We evaluated the clinical and laboratory parameters of 56 children who received early corticosteroid treatment for pneumonia that was caused by macrolide-resistant Mycoplasma pneumoniae (M. pneumoniae) or macrolide-sensitive M. pneumoniae between July 2019 and February 2020. All subjects had dual positive results from a PCR assay and serological test, and received corticosteroids within 24–36 h after admission. Point mutation of residues 2063, 2064, and 2067 was identified in domain V of 23S rRNA. The mean age was 6.8 years and the male:female ratio was 1.2:1 (31:25 patients). Most of the subjects had macrolide-resistant M. pneumoniae (73%), and all mutated strains had the A2063G transition. No significant differences in clinical and laboratory parameters were observed between macrolide-resistant and macrolide-sensitive M. pneumoniae groups that were treated with early dose-adjusted corticosteroids. Higher-dose steroid treatment may be needed for patients who have fever that persists for >48 h or increased biomarkers such as lactate dehydrogenase concentration at follow-up despite a usual dose of steroid therapy.

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Mitochondrial genome evolution in pelagophyte algae

Genome Biology and Evolution ◽

10.1093/gbe/evab018 ◽

2021 ◽

Author(s):

Shannon J Sibbald ◽

Maggie Lawton ◽

John M Archibald

Keyword(s):

Mitochondrial Genome ◽

Harmful Algal Blooms ◽

Algal Blooms ◽

23S Rrna ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Unique Region ◽

Long Read ◽

Genomic Studies ◽

Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

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Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkab084 ◽

2021 ◽

Cited By ~ 1

Author(s):

J G E Laumen ◽

S S Manoharan-Basil ◽

E Verhoeven ◽

S Abdellati ◽

I De Baetselier ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Ribosomal Proteins ◽

Efflux Pump ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Evolution Of Resistance ◽

High Level ◽

Azithromycin Resistance ◽

Level Resistance

Abstract Background The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide. Objectives To characterize the genetic pathways leading to high-level azithromycin resistance. Methods A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing. Results Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low- to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA, mainly the well-known A2059G and C2611T mutations, but also at position A2058G. Conclusions This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.

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Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-021-00456-5 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Konrad Egli ◽

Anna Roditscheff ◽

Ursula Flückiger ◽

Martin Risch ◽

Lorenz Risch ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

23S Rrna ◽

Rrna Gene ◽

Limited Information ◽

Specific Pcr ◽

Appropriate Treatment ◽

23S Rrna Gene ◽

Allele Type ◽

Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

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trans-Translation inhibitors bind to a novel site on the ribosome and clear Neisseria gonorrhoeae in vivo

Nature Communications ◽

10.1038/s41467-021-22012-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zachary D. Aron ◽

Atousa Mehrani ◽

Eric D. Hoffer ◽

Kristie L. Connolly ◽

Pooja Srinivas ◽

...

Keyword(s):

Oral Dose ◽

Neisseria Gonorrhoeae ◽

Multiple Drug ◽

Specific Inhibition ◽

Drug Resistant ◽

Peptidyl Transfer ◽

Bacterial Ribosome ◽

Multiple Drug Resistant ◽

Unique Site

AbstractBacterial ribosome rescue pathways that remove ribosomes stalled on mRNAs during translation have been proposed as novel antibiotic targets because they are essential in bacteria and are not conserved in humans. We previously reported the discovery of a family of acylaminooxadiazoles that selectively inhibit trans-translation, the main ribosome rescue pathway in bacteria. Here, we report optimization of the pharmacokinetic and antibiotic properties of the acylaminooxadiazoles, producing MBX-4132, which clears multiple-drug resistant Neisseria gonorrhoeae infection in mice after a single oral dose. Single particle cryogenic-EM studies of non-stop ribosomes show that acylaminooxadiazoles bind to a unique site near the peptidyl-transfer center and significantly alter the conformation of ribosomal protein bL27, suggesting a novel mechanism for specific inhibition of trans-translation by these molecules. These results show that trans-translation is a viable therapeutic target and reveal a new conformation within the bacterial ribosome that may be critical for ribosome rescue pathways.

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Protein synthesis in the liver of rats injected with cholesteryl 14-methylhexadecanoate

Biochemical Journal ◽

10.1042/bj1290367 ◽

1972 ◽

Vol 129 (2) ◽

pp. 367-372 ◽

Cited By ~ 1

Author(s):

E. Komárková ◽

J. Hradec

Keyword(s):

Protein Synthesis ◽

Liver Tissue ◽

Regulatory Mechanism ◽

Relative Content ◽

Time Intervals ◽

Peptidyl Transfer ◽

Significant Stimulation ◽

Peptide Elongation

1. Rats were injected intraperitoneally with cholesteryl 14-methylhexadecanoate and killed after various intervals of time up to 3 days; ribosomes and cell sap were isolated from their liver tissue. These fractions were tested for their ability to participate in protein synthesis. 2. Protein synthesis in complete systems containing ribosomes, cell sap and all necessary cofactors was significantly enhanced at 12 and 72h after the injection and significantly inhibited at 24h. At early times after injection isolated ribosomes had a slightly enhanced ability to bind nRNA. Peptide-elongation processes (i.e. binding of aminoacyl-tRNA to ribosomes, peptidyl transfer and polyphenylalanine synthesis) showed significant stimulation or inhibition depending on the time after injection of the ester. 3. A correlation was found between the ability of cell sap to stimulate polyphenylalanine synthesis and the relative cholesteryl 14-methylhexadecanoate content in the postmicrosomal supernatant at different time-intervals after administration of the ester. No significant changes were found in its content in the whole liver tissue. 4. Since the injected ester has previously been shown to accumulate in some enzymic fractions, the changes in its relative content may represent a regulatory mechanism modulating the rate of protein synthesis.

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Antimicrobial Resistance Profiles and Macrolide Resistance Mechanisms of Campylobacter coli Isolated from Pigs and Chickens

Microorganisms ◽

10.3390/microorganisms9051077 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1077

Author(s):

Ji-Hyun Choi ◽

Dong Chan Moon ◽

Abraham Fikru Mechesso ◽

Hee Young Kang ◽

Su-Jeong Kim ◽

...

Keyword(s):

Nalidixic Acid ◽

Ribosomal Proteins ◽

Resistance Mechanisms ◽

23S Rrna ◽

Considerable Proportion ◽

Rrna Gene ◽

Campylobacter Coli ◽

Erythromycin Resistance ◽

Public Health Hazards ◽

Resistance Rates

We identified 1218 Campylobacter coli isolates from fecal and carcass samples of pigs (n = 643) and chickens (n = 575) between 2010 and 2018. About 99% of the isolates were resistant to at least one antimicrobial agent. The isolates exhibited high resistance rates (>75%) to ciprofloxacin, nalidixic acid, and tetracycline. Azithromycin and erythromycin resistance rates were the highest in isolates from pigs (39.7% and 39.2%, respectively) compared to those of chickens (15.8% and 16.3%, respectively). Additionally, a low-to-moderate proportion of the isolates were resistant to florfenicol, gentamicin, clindamycin, and telithromycin. Multidrug resistance (MDR) was found in 83.1% of the isolates, and profiles of MDR usually included ciprofloxacin, nalidixic acid, and tetracycline. We found point mutation (A2075G) in domain V of the 23S rRNA gene in the majority of erythromycin-resistant isolates. Multilocus sequence typing of 137 erythromycin-resistant C. coli isolates revealed 37 previously reported sequence types (STs) and 8 novel STs. M192I, A103VI, and G74A substitutions were frequently noted in the ribosomal proteins L4 or L22. Further, we identified a considerable proportion (>90%) of erythromycin-resistant isolates carrying virulence factor genes: flaA, cadF, ceuE, and VirB. The prudent use of antimicrobials and regular microbiological investigation in food animals will be vital in limiting the public health hazards of C. coli in Korea.

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Evolution of ribosomal protein network architectures

Scientific Reports ◽

10.1038/s41598-020-80194-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Youri Timsit ◽

Grégoire Sergeant-Perthuis ◽

Daniel Bennequin

Keyword(s):

Selective Pressure ◽

Experimental Studies ◽

Protein Networks ◽

Network Architectures ◽

Mathematical Study ◽

Remote Communication ◽

Aromatic Residues ◽

Peptidyl Transfer ◽

Exit Tunnel ◽

Long Range Communication

AbstractTo perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom’s r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.

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