The role of the ribosomal stalk in the activity of ricin, Shiga-like toxin 1 and Shiga-like toxin 2 in Saccharomyces cerevisiae

Ricin, Shiga-like toxin 1 (Stx1) and Shiga-like toxin 2 (Stx2) are ribosome inactivating proteins (RIPs) that catalytically remove an adenine residue from the highly conserved α-sarcin/ricin loop (SRL) in the large ribosomal subunit, inhibiting the translocation step of protein synthesis. Although all RIPs act on the same substrate, they differ in the ribosome specificity among different kingdoms. Ricin is only active towards the eukaryotic ribosomes, while Stx1 and Stx2 are active towards both prokaryotic and eukaryotic ribosomes. Infection with E. coli O157:H7 containing Stx2 is more likely to lead to hemolytic uremic syndrome (HUS) and progress to more severe disease than infection with E. coli O157:H7 containing Stx1. Accumulating evidence indicates that interaction of RIPs with different ribosomal proteins may be responsible for the ribosome specificity. By expressing the enzymatic A subunits of ricin, Stx1 and Stx2 in Saccharomyces cerevisiae, this study presents evidence that the ribosomal stalk is the docking site for ricin, Stx1 and Stx2, but not PAP. The results suggest that the P proteins of the ribosomal stalk recruit the RIPs to the ribosome to build a toxin pool near the SRL, facilitating depurination of the SRL. Stx2 depurinates ribosomes more efficiently than Stx1 regardless of the defects in the ribosomal stalk both in vitro and in vivo. Addition of purified P1α/P2β proteins has the most impact on the ribosome depurination by Stx1 than Stx2 and RTA. These results suggest that Stx1 is more dependent on the ribosomal stalk than Stx2. A model is proposed to describe the interaction between Stx1A and the ribosomal stalk. The ribosome-bound and the cytoplasmic pool of stalk P proteins play important roles in the depurination of the SRL, ribosome binding and cytotoxicity of the three different toxins. The cytoplasmic pool of P proteins and stalk conformation affect each toxin differently and these differences contribute to their relative cytotoxicity.Ph.D.Includes bibliographical referencesIncludes vitaby Jiachi Chio

Characterization of the Probiotic Potential of Lactic Acid Bacteria Isolated from Kimchi, Yogurt, and Baby Feces in Hong Kong and Their Performance in Soymilk Fermentation

Background: There are several potential healthy or nutritional benefits from the use of lactic acid bacteria (LAB) in foods. This study aimed to characterize the LAB isolates from kimchi, yogurt, and baby feces in the Hong Kong area and evaluate their performance in fermented soymilk, which allowed us to assess their potential use in future experiments. Methods: General characteristics including tolerance to acid, NaCl, bile salts and phenol, antimicrobial activity to various pathogens, and adhesive ability to Caco-2 cells were evaluated using 18 LAB in this study. To further demonstrate the influence of such isolates in soymilk fermentation, we measured viability by plating and noting changes in pH, amino acid content, aglyconic isoflavones content and antioxidant capacities in vitro, such as scavenging ability, and iron chelating ability. Results: In this study, various LAB isolates belonging to Lactobacillusrhamnosus, Lactobacillus sakei, Lactiplantibacillus plantarum, andLeuconostocmesenteroides isolated in Hong Kong were evaluated. L. plantarum isolates R7, AC12, and AC14.1, and L. rhamnosus AC1 showed higher tolerance to acid, NaCl, bile salts, and phenol as compared to the other isolates tested. L. plantarum isolates AC12, AC13 and AC14.1, and L. rhamnosus AC1 harbored strong antimicrobial activity. L. plantarum isolates R7, AC12, AC13 and AC14.1, and L. paracasei isolates R6 and R8 showed higher adhesive ability than the other tested isolates. In soymilk, the viable numbers of L. paracasei R5, L. plantarum R7, L. rhamnosus AC1, L. sakei AC2, and Leu. mesenteroides AC5 were much higher than the other tested isolates after 48 h of fermentation. The pH value measuring the lactic acid level in soymilk fermented by L. plantarum AC14.1 was the lowest in comparison to those in soymilk fermented by other isolates. In addition, the levels of free amino acids and isoflavones in the aglycone forms of L. rhamnosus AC1-fermented soymilk were the highest. L. rhamnosus AC1-fermented soymilk also showed the highest antioxidant potential, including DPPH scavenging ability and iron chelating ability. Conclusions: In general, L. plantarum isolates R7 and AC14.1 and L. rhamnosus AC1 exhibited higher tolerance to challenging conditions as compared to the other isolates. Moreover, L. rhamnosus AC1 exhibited superior performance in soymilk fermentation and potential as a starter and probiotic culture

Prolonged High-Fat Diet Consumption throughout Adulthood in Mice Induced Neurobehavioral Deterioration via Gut-Brain Axis

Neuropsychiatric disorders have been one of the worldwide health problems contributing to profound social and economic consequences. It is reported that consumption of an excessive high-fat diet (HFD) in middle age could induce cognitive and emotional dysfunctions, whereas the mechanisms of the effects of long-term HFD intake on brain disorders have not been fully investigated. We propose a hypothesis that prolonged HFD intake throughout adulthood could lead to neurobehavioral deterioration via gut-brain axis. In this study, the adult C57BL/6J mice consuming long-term HFD (24 weeks) exhibited more anxiety-like, depression-like, and disruptive social behaviors and poorer performance in learning and memory than control mice fed with a normal diet (ND). In addition, the homeostasis of gut microbiota was impaired by long-term HFD consumption. Changes in some flora, such as Prevotellaceae_NK3B31_group and Ruminococcus, within the gut communities, were correlated to neurobehavioral alterations. Furthermore, the gut permeability was increased after prolonged HFD intake due to the decreased thickness of the mucus layer and reduced expression of tight junction proteins in the colon. The mRNA levels of genes related to synaptic-plasticity, neuronal development, microglia maturation, and activation in the hippocampus and prefrontal cortex of HFD-fed mice were lower than those in mice fed with ND. Interestingly, the transcripts of genes related to tight junction proteins, ZO-1 and Occludin involved in blood-brain-barrier (BBB), were decreased in both hippocampus and prefrontal cortex after long-term HFD consumption. Those results indicated that chronic consumption of HFD in mice resulted in gut microbiota dysbiosis, which induced decreased expression of mucus and tight junction proteins in the colon, in turn leading to local and systemic inflammation. Those changes could further contribute to the impairment of brain functions and neurobehavioral alterations, including mood, sociability, learning and memory. In short, long-term HFD intake throughout adulthood could induce behavioral phenotypes related to neuropsychiatric disorders via gut-brain axis. The observations of this study provide potential intervention strategies to reduce the risk of HFD via targeting the gut or manipulating gut microbiota

Development of a quantitative RT-PCR assay to examine the kinetics of ribosome depurination by ribosome inactivating proteins using Saccharomyces cerevisiae as a model

Ricin produced by the castor bean plant and Shiga toxins produced by pathogenic Escherichia coli (STEC) and Shigella dysenteriae are type II ribosome inactivating proteins (RIPs), containing an enzymatically active A subunit that inhibits protein synthesis by removing an adenine from the α-sarcin/ricin loop (SRL) of the 28S rRNA. There are currently no known antidotes to Shiga toxin or ricin, and the ability to screen large chemical libraries for inhibitors has been hindered by lack of quantitative assays for catalytic activity that can be adapted to a high throughput format. Here, we describe the development of a robust and quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay that can directly measure the toxins' catalytic activity on ribosomes and can be used to examine the kinetics of depurination in vivo. The qRT-PCR assay exhibited a much wider dynamic range than the previously used primer extension assay (500-fold vs. 16-fold) and increased sensitivity (60 pM vs. 0.57 nM). Using this assay, a 400-fold increase in ribosome depurination was observed in yeast expressing ricin A chain (RTA) relative to uninduced cells. Pteroic acid, a known inhibitor of enzymatic activity, inhibited ribosome depurination by RTA and Shiga toxin 2 with an IC50 of ∼100 μM, while inhibitors of ricin transport failed to inhibit catalytic activity. These results demonstrate that the qRT-PCR assay would enable refined kinetic studies with RIPs and could be a powerful screening tool to identify inhibitors of catalytic activity

Structural and Functional Characterization of OXA-48: Insight into Mechanism and Structural Basis of Substrate Recognition and Specificity

Class D β-lactamase OXA-48 is widely distributed among Gram-negative bacteria and is an important determinant of resistance to the last-resort carbapenems. Nevertheless, the detailed mechanism by which this β-lactamase hydrolyzes its substrates remains poorly understood. In this study, the complex structures of OXA-48 and various β-lactams were modeled and the potential active site residues that may interact with various β-lactams were identified and characterized to elucidate their roles in OXA-48 substrate recognition. Four residues, namely S70, K73, S118, and K208 were found to be essential for OXA-48 to undergo catalytic hydrolysis of various penicillins and carbapenems both in vivo and in vitro. T209 was found to be important for hydrolysis of imipenem, whereas R250 played a major role in hydrolyzing ampicillin, imipenem, and meropenem most likely by forming a H-bond or salt-bridge between the side chain of these two residues and the carboxylate oxygen ions of the substrates. Analysis of the effect of substitution of alanine in two residues, W105 and L158, revealed their roles in mediating the activity of OXA-48. Our data show that these residues most likely undergo hydrophobic interaction with the R groups and the core structure of the β-lactam ring in penicillins and the carbapenems, respectively. Unlike OXA-58, mass spectrometry suggested a loss of the C6-hydroxyethyl group during hydrolysis of meropenem by OXA-48, which has never been demonstrated in Class D carbapenemases. Findings in this study provide comprehensive knowledge of the mechanism of the substrate recognition and catalysis of OXA-type β-lactamases

Captopril Alleviates Chondrocyte Senescence in DOCA-Salt Hypertensive Rats Associated with Gut Microbiome Alteration

Gut microbiota is the key controller of healthy aging. Hypertension and osteoarthritis (OA) are two frequently co-existing age-related pathologies in older adults. Both are associated with gut microbiota dysbiosis. Hereby, we explore gut microbiome alteration in the Deoxycorticosterone acetate (DOCA)-induced hypertensive rat model. Captopril, an anti-hypertensive medicine, was chosen to attenuate joint damage. Knee joints were harvested for radiological and histological examination; meanwhile, fecal samples were collected for 16S rRNA and shotgun sequencing. The 16S rRNA data was annotated using Qiime 2 v2019.10, while metagenomic data was functionally profiled with HUMAnN 2.0 database. Differential abundance analyses were adopted to identify the significant bacterial genera and pathways from the gut microbiota. DOCA-induced hypertension induced p16INK4a+ senescent cells (SnCs) accumulation not only in the aorta and kidney (p < 0.05) but also knee joint, which contributed to articular cartilage degradation and subchondral bone disturbance. Captopril removed the p16INK4a + SnCs from different organs, partially lowered blood pressure, and mitigated cartilage damage. Meanwhile, these alterations were found to associate with the reduction of Escherichia-Shigella levels in the gut microbiome. As such, gut microbiota dysbiosis might emerge as a metabolic link in chondrocyte senescence induced by DOCA-triggered hypertension. The underlying molecular mechanism warrants further investigation

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis.

Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak. In this study, we analyzed the B.1.1.529 (Omicron) genome sequences collected from pediatric patients by whole viral genome amplicon sequencing using Illumina next generation sequencing platform, followed by phylogenetic analysis. The demographic, epidemiologic and clinical data of these pediatric patients are also reported in this study. Fever, cough, running nose, sore throat and vomiting were the more commonly reported symptoms in children infected by Omicron variant. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant. Seven mutations were identified in the target regions of the WHO listed SARS-CoV-2 primers and probes. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified. Our results indicate that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. Omicron may have different pathogenesis in pediatric population