Biochimie最新文献

{"title":"Targeting mono- and dual-species biofilms of Staphylococcus aureus and Pseudomonas aeruginosa by the recombinant anticoagulant enzyme PAPC from micromycete Aspergillus ochraceus.","authors":"Aya Rafea Nasr, Sergei K Komarevtsev, Diana R Baidamshina, Ayan B Ryskulova, Dmitriy A Makarov, Vasiliy N Stepanenko, Elena Yu Trizna, Anna S Gorshkova, Alexander A Osmolovskiy, Konstantin A Miroshnikov, Airat R Kayumov","doi":"10.1016/j.biochi.2024.11.002","DOIUrl":"10.1016/j.biochi.2024.11.002","url":null,"abstract":"<p><p>Microbial biofilms have recently emerged as a critical target for treating bacterial infections due to their crucial role in developing antibiotic resistance. The wide-spectrum activity of proteolytic enzymes makes them particularly suitable for disrupting biofilms formed by diverse bacterial species, including dual-species biofilms. In this study, we propose the Protease-Activator of Protein C (PAPC) of human blood plasma, an enzyme produced by the micromycete Aspergillus ochraceus, as a novel tool to degrade the protein scaffold of mono- or dual-species biofilms formed by Staphylococcus aureus and Pseudomonas aeruginosa. The recombinant PAPC was successfully refolded after expression in E. coli BL21 (DE3) and demonstrated activity 100-fold higher compared to the native enzyme purified from the A. ochraceus culture liquid. The enzyme significantly destroyed mono- and dual-species biofilms formed by S. aureus and P. aeruginosa. In addition, PAPC significantly enhanced the antimicrobial treatment efficacy in both mono- and dual-species biofilms: in the presence of PAPC at 100 μg/ml, the effective concentration of the ciprofloxacin and ceftriaxone was reduced at least four-fold. Thus, the enzyme represents a reasonable solution to the complications resulting from biofilm formation and antibiotic resistance, especially wound and medical devices infections.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanical and structural features of three AcSp proteins underlie the diverse material properties of aciniform silks of Neoscona spiders.","authors":"Zheng Peng, Rui Wen","doi":"10.1016/j.biochi.2024.10.017","DOIUrl":"10.1016/j.biochi.2024.10.017","url":null,"abstract":"<p><p>Spider silks are desirable multicomponent biomaterials characterized by great tensile strength, extensibility, and biocompatibility. Of all spider silk types, aciniform silk has highest toughness due to its combination of high tensile strength and elsticity. Here, we identify three major spidroin components (AcSp1A, AcSp1B, and AcSp2) from aciniform silk of orbweb weaving spider, Neoscona scylloides, and present their full-length coding gene sequences. Comparative sequence and expression level analysis show that AcSp1B has highest expression level and higher serine content than other two AcSp proteins, while the AcSp2 shows very low mRNA level. Furthermore, three recombinant minimalist AcSp proteins are produced and could be induced to form fibers by shear forces in a physiological buffer. The manual-drawn AcSp1B fiber shows strongest tensile strength among three AcSp fibers because of its higher β-sheet formed by abundant serine content. We also compare mechanical properties of aciniform silks between two Neoscona species (N. theisi and N. scylloides) and found that aciniform silks from N. theisi exhibit higher tensile strength than those of N. scylloides, which may result from altering expression levels of two AcSp1 proteins. Collectively, our results provide insights into the mechanical features of each component in aciniform silk from N. scylloides and reveal the molecular mechanism of diverse material properties of aciniform silk among species.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pro-inflammatory responses of innate immune cells to Leishmania RNA virus 2-infected L. major support the survival and proliferation of the parasites.","authors":"Asal Katebi, Matineh Nouri, Ava Behrouzi, Soheila Ajdary, Farhad Riazi-Rad","doi":"10.1016/j.biochi.2024.10.015","DOIUrl":"10.1016/j.biochi.2024.10.015","url":null,"abstract":"<p><p>Infection of Leishmania by Leishmania RNA virus (LRV) has been proposed as a pathogenic factor that induces pro-inflammatory responses through the TLR3/TLR4 signaling pathway. We investigated the effect of L. major infection by LRV2 on innate immune cell responses (human neutrophil (HL-60) and macrophage (THP-1) cell lines). The expression levels of pro- and anti-inflammatory cytokine and chemokine genes as well as genes involved in the amino acid metabolism of arginine were then investigated by RT-qPCR. Moreover, the expression of TLR genes and their downstream signaling pathways were compared in THP-1 cells infected with the two isolates. Apoptosis was also evaluated in infected THP-1 and HL-60 cells using the PI/Annexin V flow cytometry assay. In both cell lines, the expression of pro-inflammatory cytokines increased in response to LRV2+ L. major (Lm+), and the expression of chemokines shifted toward macrophage recruitment. In contrast to LRV2- L. major (Lm-), Lm + infected THP-1 cells acquired the M2-like phenotype. The presence of LRV2 increased the gene expression of TLRs and their signaling pathways, especially TLR3 and TLR4, which was proportional to the increase in pro-inflammatory cytokines. In addition, Lm + increased the expression of IL-10 and IFN-β, which contribute to the survival and growth of the parasite in the phagolysosome. Altogether, our results showed that Lm + could stimulate pro-inflammatory responses that promote parasite replication and stabilization in the host.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis and evaluation of water-soluble antioxidants derived from l-carnosine and syringaldehyde (or vanillin).","authors":"Collins Antwi-Boasiako, Blessed Agbemade, Jacqueline H Ko, Veronica Barone, Rebecca L Uzarski, Choon Young Lee","doi":"10.1016/j.biochi.2024.10.002","DOIUrl":"10.1016/j.biochi.2024.10.002","url":null,"abstract":"<p><p>Polyphenols are well known for their health-related benefits, including antioxidant activities, but most of them are hydrophobic, decreasing their bioavailability. This study reports water-soluble trimeric antioxidants synthesized with l-carnosine and the hydrophobic ortho-methoxy-substituted phenolic unit, syringaldehyde or vanillin. In the DPPH assay, carnosine-syringaldehyde (7.5 μM) and carnosine-vanillin (19 μM) derivatives showed much lower IC50 values than ascorbic acid (27.5 μM) and sodium ascorbate (30.5 μM) standards. According to the AAPH assay, carnosine-syringaldehyde and carnosine-vanillin protect DNA at concentrations as low as 6.5 μM and 26 μM, respectively, while both sodium ascorbate and ascorbic acid protected until 52 μM. Another notable property of these antioxidants is that they can protect DNA well against hydroxyl radicals, produced via the Fenton reaction: carnosine-syringaldehyde showed DNA protection at all tested concentrations (833-1.6 μM), but the protection was slightly weaker between 26 and 1.6 μM. Carnosine-vanillin showed strong protection in the 833-104 μM range and some protection between 52 and 3.2 μM. Conversely, both sodium ascorbate and ascorbic acid did not protect DNA at any tested concentrations. In the pro-oxidant potential assessments, the synthesized antioxidants did not show any pro-oxidant effects at all tested concentrations. In comparison, sodium ascorbate at 833-13 μM and ascorbic acid at 833-52 μM both exhibited severe pro-oxidant effects. Our study highlights the significance of ortho-methoxy groups in antioxidants. Their electron-donating properties enhance antioxidant activities, while their steric bulk hinders the binding of transition metal ions to the phenolic hydroxyl group, thereby preventing pro-oxidant effects. The hydrophobicity of ortho-methoxy substituted phenols can be mitigated by attaching them to a highly water-soluble scaffold containing functional groups that can facilitate charge formation in the end products, such as carnosine.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Highly specific aptamer trap for extremophilic RNA polymerases.","authors":"Ivan Petushkov, Andrey Feklistov, Andrey Kulbachinskiy","doi":"10.1016/j.biochi.2024.05.014","DOIUrl":"https://doi.org/10.1016/j.biochi.2024.05.014","url":null,"abstract":"<p><p>During transcription initiation, the holoenzyme of bacterial RNA polymerase (RNAP) specifically recognizes promoters using a dedicated σ factor. During transcription elongation, the core enzyme of RNAP interacts with nucleic acids mainly nonspecifically, by stably locking the DNA template and RNA transcript inside the main cleft. Here, we present a synthetic DNA aptamer that is specifically recognized by both core and holoenzyme RNAPs from extremophilic bacteria of the Deinococcus-Thermus lineage. The aptamer binds RNAP with subnanomolar affinities, forming extremely stable complexes even at high ionic strength conditions, blocks RNAP interactions with the DNA template and inhibits RNAP activity during transcription elongation. We propose that the aptamer binds at a conserved site within the downstream DNA-binding cleft of RNAP and traps it in an inactive conformation. The aptamer can potentially be used for structural studies to reveal RNAP conformational states, affinity binding of RNAP and associated factors, and screening of transcriptional inhibitors.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inside front cover-EDB","authors":"","doi":"10.1016/S0300-9084(23)00260-2","DOIUrl":"https://doi.org/10.1016/S0300-9084(23)00260-2","url":null,"abstract":"","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":"214 ","pages":"Page IFC"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49670825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing telomeric-like G4 structures with full or partial 2′-deoxy-5-hydroxyuridine substitutions","authors":"Zoltán Szeltner ,&nbsp;Györgyi Ferenc ,&nbsp;Tünde Juhász ,&nbsp;Zoltán Kupihár ,&nbsp;Zoltán Váradi ,&nbsp;Dávid Szüts ,&nbsp;Lajos Kovács","doi":"10.1016/j.biochi.2023.01.009","DOIUrl":"https://doi.org/10.1016/j.biochi.2023.01.009","url":null,"abstract":"<div><p><span><span>Guanine<span> quadruplexes (G4s) are stable four-stranded secondary DNA structures held together by noncanonical G-G base tetrads. We synthesised the </span></span>nucleoside analogue 2′-deoxy-5-hydroxyuridine (H) and inserted its phosphoramidite into telomeric repeat-type model </span>oligonucleotides<span><span><span><span>. Full and partial substitutions were made, replacing all guanines in all the three tetrads of a three-tier G4 structure, or only in the putative upper, central, or lower tetrads. We characterised these modified structures using CD, UV absorbance spectroscopy, native gel studies, and a capture oligo-based G4 disruption kinetic assay. The strand separation activity of BLM helicase on these substituted structures was also investigated. Two of the partially H-substituted constructs adopted G4-like structures, but displayed lower thermal stabilities compared to unsubstituted G4. The construct modified in its central tetrad remained mostly denatured, but the possibility of a special structure for the fully replaced variant remained open. H substitutions did not interfere with the G4-resolving activity of BLM helicase, but its efficiency was highly influenced by construct topology and even more by the G4 ligand PhenDC3. Our results suggest that the H modification can be incorporated into G quadruplexes, but only at certain positions to maintain G4 stability. The destabilizing effect observed for 2′-deoxy-5-hydroxyuridine indicates that the </span>cytosine </span>deamination product 5-hydroxyuracil and its nucleoside counterpart in </span>RNA (5-hydroxyuridine), might also be destabilizing in cellular DNA and RNA quadruplexes. The kinetic assay employed in this study can be generally employed for a fast comparison of the stabilities of various G4s either in their free or ligand-bound states.</span></p></div>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":"214 ","pages":"Pages 33-44"},"PeriodicalIF":0.0,"publicationDate":"2023-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49670757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}