Investigating the effect of an identified mutation within a critical site of PAS domain of WalK protein in a vancomycin-intermediate resistant Staphylococcus aureus by computational approaches

Abstract Background Vancomycin-intermediate resistant Staphylococcus aureus (VISA) is becoming a common cause of nosocomial infections worldwide. VISA isolates are developed by unclear molecular mechanisms via mutations in several genes, including walKR. Although studies have verified some of these mutations, there are a few studies that pay attention to the importance of molecular modelling of mutations. Method For genomic and transcriptomic comparisons in a laboratory-derived VISA strain and its parental strain, Sanger sequencing and reverse transcriptase quantitative PCR (RT-qPCR) methods were used, respectively. After structural protein mapping of the detected mutation, mutation effects were analyzed using molecular computational approaches and crystal structures of related proteins. Results A mutation WalK-H364R was occurred in a functional zinc ion coordinating residue within the PAS domain in the VISA strain. WalK-H364R was predicted to destabilize protein and decrease WalK interactions with proteins and nucleic acids. The RT-qPCR method showed downregulation of walKR, WalKR-regulated autolysins, and agr locus. Conclusion Overall, WalK-H364R mutation within a critical metal-coordinating site was presumably related to the VISA development. We assume that the WalK-H364R mutation resulted in deleterious effects on protein, which was verified by walKR gene expression changes.. Therefore, molecular modelling provides detailed insight into the molecular mechanism of VISA development, in particular, where allelic replacement experiments are not readily available.

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Molecular Insight Into the Mutation Within Critical Zinc2+-Binding Site in the PAS Domain of WalK in Vancomycin-Intermediate Resistant Staphylococcus Aureus

10.21203/rs.3.rs-131302/v1 ◽

2020 ◽

Author(s):

Neda Baseri ◽

Shahin Najar-Peerayeh ◽

Bita Bakhshi

Keyword(s):

Staphylococcus Aureus ◽

Molecular Modeling ◽

Molecular Mechanisms ◽

Zinc Ion ◽

Pas Domain ◽

Structural Protein ◽

Protein Mapping ◽

Critical Metal ◽

Pcr Method ◽

Insight Into

Abstract Vancomycin-intermediate resistant Staphylococcus aureus (VISA), one of the common causes of nosocomial infection, is developed by mutations, including in walKR, with unclear molecular mechanisms. Although studies have verified some of these mutations, there are a few studies to pay attention to the importance of molecular modeling of mutations. Here, the Sanger sequencing for comparing gene sequences of WlKR between a VISA and its parental strain revealed mutation WalK-H364R. Structural protein mapping showed that H364R was located in a functional zinc ion coordinating residue within the cytoplasmic Per-Arnt-Sim (PAS) domain. The structural and functional effects of this mutation were analyzed using molecular computational approaches based on the recently determined crystal structures of the PAS domain of S. aureus. WalK-H364R was predicted to destabilize protein and decrease WalK interactions with proteins and nucleic acids. The qRT-PCR method showed downregulation of walKR and WalKR-regulated autolysins, which verified the molecular computational results.Overall, WalK-H364R within a critical metal-coordinating site is linked to VISA development through the walKR gene expression changes as well as the destructive effects on protein.Therefore, molecular modeling can be provided detailed insight into the molecular mechanism of VISA development, in particular, where complementation experiments are not readily available.

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Progress in understanding the role of lncRNA in programmed cell death

Cell Death Discovery ◽

10.1038/s41420-021-00407-1 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Na Jiang ◽

Xiaoyu Zhang ◽

Xuejun Gu ◽

Xiaozhuang Li ◽

Lei Shang

Keyword(s):

Cell Death ◽

Programmed Cell Death ◽

Molecular Mechanisms ◽

Membrane Receptors ◽

Gene Expressions ◽

Apoptosis Pathway ◽

Stem Cell Pluripotency ◽

Extrinsic Apoptosis ◽

Related Proteins ◽

Cycle Regulation

AbstractLong non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but not translated into proteins. LncRNAs regulate gene expressions at multiple levels, such as chromatin, transcription, and post-transcription. Further, lncRNAs participate in various biological processes such as cell differentiation, cell cycle regulation, and maintenance of stem cell pluripotency. We have previously reported that lncRNAs are closely related to programmed cell death (PCD), which includes apoptosis, autophagy, necroptosis, and ferroptosis. Overexpression of lncRNA can suppress the extrinsic apoptosis pathway by downregulating of membrane receptors and protect tumor cells by inhibiting the expression of necroptosis-related proteins. Some lncRNAs can also act as competitive endogenous RNA to prevent oxidation, thereby inhibiting ferroptosis, while some are known to activate autophagy. The relationship between lncRNA and PCD has promising implications in clinical research, and reports have highlighted this relationship in various cancers such as non-small cell lung cancer and gastric cancer. This review systematically summarizes the advances in the understanding of the molecular mechanisms through which lncRNAs impact PCD.

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Albendazole reduces hepatic inflammation and endoplasmic reticulum-stress in a mouse model of chronic Echinococcus multilocularis infection

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009192 ◽

2022 ◽

Vol 16 (1) ◽

pp. e0009192

Author(s):

Michael Weingartner ◽

Simon Stücheli ◽

Fadi Jebbawi ◽

Bruno Gottstein ◽

Guido Beldi ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Endoplasmic Reticulum Stress ◽

Echinococcus Multilocularis ◽

Molecular Mechanisms ◽

Disease Recurrence ◽

Unfolded Protein ◽

Programmed Death ◽

Protein Response ◽

Host Parasite ◽

Related Proteins

Background Echinococcus multilocularis causes alveolar echinococcosis (AE), a rising zoonotic disease in the northern hemisphere. Treatment of this fatal disease is limited to chemotherapy using benzimidazoles and surgical intervention, with frequent disease recurrence in cases without radical surgery. Elucidating the molecular mechanisms underlying E. multilocularis infections and host-parasite interactions ultimately aids developing novel therapeutic options. This study explored an involvement of unfolded protein response (UPR) and endoplasmic reticulum-stress (ERS) during E. multilocularis infection in mice. Methods E. multilocularis- and mock-infected C57BL/6 mice were subdivided into vehicle, albendazole (ABZ) and anti-programmed death ligand 1 (αPD-L1) treated groups. To mimic a chronic infection, treatments of mice started six weeks post i.p. infection and continued for another eight weeks. Liver tissue was then collected to examine inflammatory cytokines and the expression of UPR- and ERS-related genes. Results E. multilocularis infection led to an upregulation of UPR- and ERS-related proteins in the liver, including ATF6, CHOP, GRP78, ERp72, H6PD and calreticulin, whilst PERK and its target eIF2α were not affected, and IRE1α and ATF4 were downregulated. ABZ treatment in E. multilocularis infected mice reversed, or at least tended to reverse, these protein expression changes to levels seen in mock-infected mice. Furthermore, ABZ treatment reversed the elevated levels of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α and interferon (IFN)-γ in the liver of infected mice. Similar to ABZ, αPD-L1 immune-treatment tended to reverse the increased CHOP and decreased ATF4 and IRE1α expression levels. Conclusions and significance AE caused chronic inflammation, UPR activation and ERS in mice. The E. multilocularis-induced inflammation and consecutive ERS was ameliorated by ABZ and αPD-L1 treatment, indicating their effectiveness to inhibit parasite proliferation and downregulate its activity status. Neither ABZ nor αPD-L1 themselves affected UPR in control mice. Further research is needed to elucidate the link between inflammation, UPR and ERS, and if these pathways offer potential for improved therapies of patients with AE.

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Secreted Frizzled Related Proteins in Cardiovascular and Metabolic Diseases

Frontiers in Endocrinology ◽

10.3389/fendo.2021.712217 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hua Guan ◽

Jin Zhang ◽

Jing Luan ◽

Hao Xu ◽

Zhenghao Huang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Metabolic Diseases ◽

Structural Characteristics ◽

Wnt Signaling Pathway ◽

Secreted Protein ◽

Related Protein ◽

Disease Biomarkers ◽

Protein Levels ◽

Related Proteins

Abnormal gene expression and secreted protein levels are accompanied by extensive pathological changes. Secreted frizzled related protein (SFRP) family members are antagonistic inhibitors of the Wnt signaling pathway, and they were recently found to be involved in the pathogenesis of a variety of metabolic diseases, which has led to extensive interest in SFRPs. Previous reports highlighted the importance of SFRPs in lipid metabolism, obesity, type 2 diabetes mellitus and cardiovascular diseases. In this review, we provide a detailed introduction of SFRPs, including their structural characteristics, receptors, inhibitors, signaling pathways and metabolic disease impacts. In addition to summarizing the pathologies and potential molecular mechanisms associated with SFRPs, this review further suggests the potential future use of SFRPs as disease biomarkers therapeutic targets.

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Mechanisms of Action And Clinical Implications of MicroRNAs in the Drug Resistance of Gastric Cancer

Frontiers in Oncology ◽

10.3389/fonc.2021.768918 ◽

2021 ◽

Vol 11 ◽

Author(s):

Ying Liu ◽

Xiang Ao ◽

Guoqiang Ji ◽

Yuan Zhang ◽

Wanpeng Yu ◽

...

Keyword(s):

Gastric Cancer ◽

Drug Resistance ◽

Molecular Mechanisms ◽

Malignant Tumors ◽

Life Quality ◽

Therapeutic Targets ◽

Chemotherapeutic Agents ◽

Response To Chemotherapy ◽

Novel Biomarkers ◽

Related Proteins

Gastric cancer (GC) is one of the most common malignant tumors of digestive systems worldwide, with high recurrence and mortality. Chemotherapy is still the standard treatment option for GC and can effectively improve the survival and life quality of GC patients. However, with the emergence of drug resistance, the clinical application of chemotherapeutic agents has been seriously restricted in GC patients. Although the mechanisms of drug resistance have been broadly investigated, they are still largely unknown. MicroRNAs (miRNAs) are a large group of small non-coding RNAs (ncRNAs) widely involved in the occurrence and progression of many cancer types, including GC. An increasing amount of evidence suggests that miRNAs may play crucial roles in the development of drug resistance by regulating some drug resistance-related proteins as well as gene expression. Some also exhibit great potential as novel biomarkers for predicting drug response to chemotherapy and therapeutic targets for GC patients. In this review, we systematically summarize recent advances in miRNAs and focus on their molecular mechanisms in the development of drug resistance in GC progression. We also highlight the potential of drug resistance-related miRNAs as biomarkers and therapeutic targets for GC patients.

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Beneficial Impact and Molecular Mechanism of Bacillus Coagulans on Piglets Intestine

10.20944/preprints201805.0084.v1 ◽

2018 ◽

Author(s):

Tao Wu ◽

Yang Lv ◽

Xueni Li ◽

Lin Zhang ◽

Yutao Shi ◽

...

Keyword(s):

Molecular Mechanism ◽

Molecular Mechanisms ◽

Caspase 3 ◽

Bacillus Coagulans ◽

Basal Diet ◽

Control Group ◽

Villus Height ◽

Intestinal Integrity ◽

Beneficial Impact ◽

Related Proteins

This research was to investigate beneficial impact and molecular mechanism of B. coagulans on piglets intestine. Twenty-four 21 days old weaned piglets were allotted to three treatments: control group (basal diet), B6 group (basal diet + 2×106 CFU/g B. coagulans), B7 group (basal diet + 2×107 CFU/g B. coagulans). The results showed that compared with control group, B6 and B7 group significantly decreased diarrhea rate and the concent of CHOL, GGT and DAO in plasma; decreased villus height and increase crypt depth in jejunum and ileum; increased the activities of SOD and CAT and decreased the concent of MDA and H2O2 in intestine. These data suggested that supplementing B. coagulans had beneficial impacts on promoting nutrients metabolism, maintaining intestinal integrity and alleviating oxidative stress and diarrhea. Futher research of molecular mechanisms showed that, these beneficial impacts were regulated by changing expression levels of related proteins (including HSP70, Caspase-3, Bax, Villin and Occludin), and genes (including RPL4, IFN-α, IFN-β, IFN-γ, MX1, MX2, OAS1, IL-1β, IL-4, CXCL-9, CCL-2, AQP3, SGLT-1, LPL, INSR and b0,+AT), and altering community composition of gut microbiota (particularly family Clostridiaceae, Enterobacteriaceae, and Veillonellaceae and genus Prevotella, Turicibacter, and Lactobacillus).

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Human urine alters methicillin-resistant Staphylococcus aureus virulence and transcriptome

Applied and Environmental Microbiology ◽

10.1128/aem.00744-21 ◽

2021 ◽

Author(s):

Santosh Paudel ◽

Kamal Bagale ◽

Swapnil Patel ◽

Nicholas J. Kooyers ◽

Ritwij Kulkarni

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Human Urine ◽

Molecular Mechanisms ◽

Methicillin Resistant ◽

Life Threatening ◽

Tract Infections

Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) is an emerging cause of hospital-associated urinary tract infections (UTI), especially in catheterized individuals. Despite being rare, MRSA UTI are prone to potentially life-threatening exacerbations such as bacteremia that can be refractory to routine antibiotic therapy. To delineate the molecular mechanisms governing MRSA urinary pathogenesis, we exposed three S. aureus clinical isolates, including two MRSA strains to human urine for 2h and analyzed virulence characteristics and changes in gene expression. The in vitro virulence assays showed that human urine rapidly alters adherence to human bladder epithelial cells and fibronectin, hemolysis of sheep RBCs, and surface hydrophobicity in a staphylococcal strain-specific manner. In addition, RNA-Seq analysis of uropathogenic strain MRSA-1369 revealed that 2h-long exposure to human urine alters MRSA transcriptome, by modifying expression of genes encoding enzymes catalyzing metabolic pathways, virulence factors, and transcriptional regulators. In summary, our results provide important insights into how human urine specifically and rapidly alters MRSA physiology and facilitates MRSA survival in the nutrient-limiting and hostile urinary microenvironment. Importance: Methicillin-resistant Staphylococcus aureus (MRSA) is an uncommon cause of urinary tract infections (UTI) in the general population. However, it is important to understand MRSA pathophysiology in the urinary tract because isolation of MRSA in urine samples often precedes potentially life-threatening MRSA bacteremia. In this report, we describe how exposure to human urine alters MRSA global gene expression and virulence. We hypothesize that these alterations may aid MRSA in acclimating to the nutrient-limiting, immunologically hostile conditions within the urinary tract leading to MRSA-UTI.

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Human Defensins: A Novel Approach in the Fight against Skin Colonizing Staphylococcus aureus

Antibiotics ◽

10.3390/antibiotics9040198 ◽

2020 ◽

Vol 9 (4) ◽

pp. 198 ◽

Cited By ~ 9

Author(s):

Olga Scudiero ◽

Mariarita Brancaccio ◽

Cristina Mennitti ◽

Sonia Laneri ◽

Barbara Lombardo ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Innate Immunity ◽

Molecular Mechanisms ◽

Biological Activities ◽

Interleukin 1 ◽

Interleukin 17 ◽

Skin Infections ◽

Skin Disorders ◽

Novel Approach ◽

Pharmacological Potential

Staphylococcus aureus is a microorganism capable of causing numerous diseases of the human skin. The incidence of S. aureus skin infections reflects the conflict between the host skin′s immune defenses and the S. aureus’ virulence elements. Antimicrobial peptides (AMPs) are small protein molecules involved in numerous biological activities, playing a very important role in the innate immunity. They constitute the defense of the host′s skin, which prevents harmful microorganisms from entering the epithelial barrier, including S. aureus. However, S. aureus uses ambiguous mechanisms against host defenses by promoting colonization and skin infections. Our review aims to provide a reference collection on host-pathogen interactions in skin disorders, including S. aureus infections and its resistance to methicillin (MRSA). In addition to these, we discuss the involvement of defensins and other innate immunity mediators (i.e., toll receptors, interleukin-1, and interleukin-17), involved in the defense of the host against the skin disorders caused by S. aureus, and then focus on the evasion mechanisms developed by the pathogenic microorganism under analysis. This review provides the “state of the art” on molecular mechanisms underlying S. aureus skin infection and the pharmacological potential of AMPs as a new therapeutic strategy, in order to define alternative directions in the fight against cutaneous disease.

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Iron homeostasis: new tales from the crypt

Blood ◽

10.1182/blood.v96.13.4020 ◽

2000 ◽

Vol 96 (13) ◽

pp. 4020-4027 ◽

Cited By ~ 106

Author(s):

Cindy N. Roy ◽

Caroline A. Enns

Keyword(s):

Iron Uptake ◽

Iron Transport ◽

Iron Homeostasis ◽

Molecular Mechanisms ◽

Hereditary Hemochromatosis ◽

The Body ◽

Regulatory Proteins ◽

Iron Regulatory Proteins ◽

Duodenal Epithelium ◽

Related Proteins

Abstract The enterocyte is a highly specialized cell of the duodenal epithelium that coordinates iron uptake and transport into the body. Until recently, the molecular mechanisms underlying iron absorption and iron homeostasis have remained a mystery. This review focuses on the proteins and regulatory mechanisms known to be present in the enterocyte precursor cell and in the mature enterocyte. The recent cloning of a basolateral iron transporter and investigations into its regulation provide new insights into possible mechanisms for iron transport and homeostasis. The roles of proteins such as iron regulatory proteins, the hereditary hemochromatosis protein (HFE)–transferrin receptor complex, and hephaestin in regulating this transporter and in regulating iron transport across the intestinal epithelium are discussed. A speculative, but testable, model for the maintenance of iron homeostasis, which incorporates the changes in the iron-related proteins associated with the life cycle of the enterocyte as it journeys from the crypt to the tip of the villous is proposed.

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Exotoxins of Staphylococcus aureus

Clinical Microbiology Reviews ◽

10.1128/cmr.13.1.16 ◽

2000 ◽

Vol 13 (1) ◽

pp. 16-34 ◽

Cited By ~ 341

Author(s):

Martin M. Dinges ◽

Paul M. Orwin ◽

Patrick M. Schlievert

Keyword(s):

Staphylococcus Aureus ◽

Toxic Shock Syndrome ◽

Molecular Basis ◽

Molecular Mechanisms ◽

Food Poisoning ◽

Structure And Function ◽

Toxic Shock ◽

The Family ◽

Toxic Shock Syndrome Toxin ◽

And Function

SUMMARY This article reviews the literature regarding the structure and function of two types of exotoxins expressed by Staphylococcus aureus, pyrogenic toxin superantigens (PTSAgs) and hemolysins. The molecular basis of PTSAg toxicity is presented in the context of two diseases known to be caused by these exotoxins: toxic shock syndrome and staphylococcal food poisoning. The family of staphylococcal PTSAgs presently includes toxic shock syndrome toxin-1 (TSST-1) and most of the staphylococcal enterotoxins (SEs) (SEA, SEB, SEC, SED, SEE, SEG, and SEH). As the name implies, the PTSAgs are multifunctional proteins that invariably exhibit lethal activity, pyrogenicity, superantigenicity, and the capacity to induce lethal hypersensitivity to endotoxin. Other properties exhibited by one or more staphylococcal PTSAgs include emetic activity (SEs) and penetration across mucosal barriers (TSST-1). A detailed review of the molecular mechanisms underlying the toxicity of the staphylococcal hemolysins is also presented.

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