RSC Chemical Biology最新文献_第2页

A versatile bioluminescent probe with tunable color† 颜色可调的多功能生物发光探针。

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-20 DOI: 10.1039/D4CB00101J

Zachary R. Torrey, Lila P. Halbers, Lorenzo Scipioni, Giulia Tedeschi, Michelle A. Digman and Jennifer A. Prescher

引用次数: 0

Rapid formation of Nε-(carboxymethyl)lysine (CML) from ribose depends on glyoxal production by oxidation† 核糖快速形成 Nε-(羧甲基)赖氨酸 (CML) 取决于氧化产生乙二醛

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-18 DOI: 10.1039/D4CB00183D

Hikari Sugawa, Tsuyoshi Ikeda, Yuki Tominaga, Nana Katsuta and Ryoji Nagai

{"title":"Rapid formation of Nε-(carboxymethyl)lysine (CML) from ribose depends on glyoxal production by oxidation†","authors":"Hikari Sugawa, Tsuyoshi Ikeda, Yuki Tominaga, Nana Katsuta and Ryoji Nagai","doi":"10.1039/D4CB00183D","DOIUrl":"10.1039/D4CB00183D","url":null,"abstract":" N ε-(Carboxymethyl)lysine (CML) is a major advanced glycation end-product (AGE) involved in protein dysfunction and inflammation in vivo. Its accumulation increases with age and is enhanced with the pathogenesis of diabetic complications. Therefore, the pathways involved in CML formation should be elucidated to understand the pathological conditions involved in CML. Ribose is widely used in glycation research because it shows a high reactivity with proteins to form AGEs. We previously demonstrated that ribose generates CML more rapidly than other reducing sugars, such as glucose; however, the underlying mechanism remains unclear. In this study, we focused on the pathway of CML formation from ribose. As a result, glyoxal (GO) was the most abundant product generated from ribose among the tested reducing sugars and was significantly correlated with CML formation from ribose-modified protein. The coefficient of determination (R2) for CML formation between the ribose-modified protein and Amadori products or the ribose degradation product (RDP)-modified protein was higher for the RDP-modified protein. CML formation from ribose degradation products (RDP) incubated with protein significantly correlated with CML formation from GO-modified protein (rs = 0.95, p = 0.0000000869). GO and CML formation were inhibited by diethylenetriaminepentaacetic acid (DTPA) and enhanced by iron chloride. Additionally, flavonoid compounds such as isoquercetin, which are known to inhibit CML, also inhibited GO formation from ribose and CML formation. In conclusion, ribose undergoes auto-oxidation and oxidative cleavage between C-2 and C-3 to generate GO and enhance CML accumulation.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00183d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemical inhibition of cell surface modification sensitizes bacteria to phage infection† 细胞表面修饰的化学抑制使细菌对噬菌体感染敏感

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-13 DOI: 10.1039/D4CB00070F

Marian Aba Addo, Zhiyu Zang and Joseph P. Gerdt

{"title":"Chemical inhibition of cell surface modification sensitizes bacteria to phage infection†","authors":"Marian Aba Addo, Zhiyu Zang and Joseph P. Gerdt","doi":"10.1039/D4CB00070F","DOIUrl":"10.1039/D4CB00070F","url":null,"abstract":"Many bacteriophages that infect Gram-positive bacteria rely on the bacterial cell surface polymer wall teichoic acid (WTA) as a receptor. However, some bacteria modulate their cell wall with D-alanine residues, which can disrupt phage adsorption. The prevalence and significance of WTA alanylation as an anti-phage defense is unknown. A chemical inhibitor of WTA D-alanylation could be employed to efficiently screen phage-host combinations for those that exhibit alanylation-dependent infections. Since the incorporation of D-alanine residues into the cell wall requires the activity of D-alanine:alanyl carrier protein ligase (DltA), a DltA inhibitor was employed as this tool. Herein, we found that a chemical probe inhibiting DltA activity impeded bacterial cell wall alanylation and enhanced infectivity of many phages against Bacillus subtilis, including phages Phi29, SPP1, SPO1, SP50, and Goe2. This finding reveals the breadth of immunity conferred by WTA alanylation in B. subtilis, which was previously known to impact only phages Phi29 and SPP1, but not SPO1, SP50, or Goe2. DltA inhibition selectively promoted infection by several phages that bind WTA, having no impact on the flagellotropic phage PBS1. Unexpectedly, DltA inhibition also had no effect on phage SP10, which binds to WTA. This selective chemical tool has the potential to unravel bacteriophage interactions with bacteria, leading to improved phage therapies in the future.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00070f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Access to capped RNAs by chemical ligation† 通过化学连接获取封端 RNA

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-13 DOI: 10.1039/D4CB00165F

Karolina Bartosik and Ronald Micura

{"title":"Access to capped RNAs by chemical ligation†","authors":"Karolina Bartosik and Ronald Micura","doi":"10.1039/D4CB00165F","DOIUrl":"10.1039/D4CB00165F","url":null,"abstract":"A distinctive feature of eukaryotic mRNAs is the presence of a cap structure at the 5′ end. The typical cap consists of 7-methylguanosine linked to the first transcribed nucleotide through a 5′,5′-triphosphate bridge. It plays a key role in many processes in eukaryotic cells, including splicing, intracellular transport, initiation of translation and turnover. Synthetic capped oligonucleotides have served as useful tools for elucidating these physiological processes. In addition, cap mimics with artificial modifications are of interest for the design of mRNA-based therapeutics and vaccines. While the short cap mimics can be obtained by chemical synthesis, the preparation of capped analogs of mRNA length is still challenging and requires templated enzymatic ligation of synthetic RNA fragments. To increase the availability of capped mRNA analogs, we present here a practical and non-templated approach based on the use of click ligation resulting in RNAs bearing a single triazole linkage within the oligo-phosphate backbone. Capped RNA fragments with up to 81 nucleotides in length have thus been obtained in nanomolar yields and are in demand for biochemical, spectroscopic or structural studies.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00165f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function† 前生物肽对自三磷酸化核糖酶功能的微弱影响

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-12 DOI: 10.1039/D4CB00129J

Joshua T. Arriola, Shayan Poordian, Estefanía Martínez Valdivia, Tommy Le, Luke J. Leman, Joan G. Schellinger and Ulrich F. Müller

{"title":"Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function†","authors":"Joshua T. Arriola, Shayan Poordian, Estefanía Martínez Valdivia, Tommy Le, Luke J. Leman, Joan G. Schellinger and Ulrich F. Müller","doi":"10.1039/D4CB00129J","DOIUrl":"10.1039/D4CB00129J","url":null,"abstract":"Catalytic RNAs (ribozymes) were central to early stages of life on earth. The first ribozymes probably emerged in the presence of prebiotically generated peptides because amino acids can be generated under abiotic conditions, and amino acids can oligomerize into peptides under prebiotically plausible conditions. Here we tested whether the presence of prebiotically plausible peptides could have aided the emergence of ribozymes, by an in vitro selection of self-triphosphorylation ribozymes from random sequence in the presence of ten different octapeptides. These peptides were composed of ten different, prebiotically plausible amino acids, each as mixture of D- and L-stereoisomers. After five rounds of selection and high throughput sequencing analysis, ten ribozymes that appeared most promising for peptide benefits were tested biochemically for possible benefits from each of the ten peptides. The strongest peptide benefit enhanced ribozyme activity by 2.6-fold, similar to the effect from an increase in the pH by one-half unit. Four arbitrarily chosen ribozymes from a previous selection without peptides showed no significant change in their activity in the presence of the ten peptides. Therefore, the used prebiotically plausible peptides – peptides without evolutionarily optimized sequence, without cationic or aromatic side chains – did not provide a strong benefit for the emergence of ribozyme activity. This finding stands in contrast to previously identified polycationic peptides, conjugates between peptides and polyaromatic hydrocarbons, and modern mRNA encoded proteins, all of which can strongly increase ribozyme function. The results are discussed in the context of origins of life.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00129j?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improved synthesis of the unnatural base NaM, and evaluation of its orthogonality in in vitro transcription and translation† 非天然碱基 NaM 的改进合成及其在体外转录和翻译中的正交性评估

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-11 DOI: 10.1039/D4CB00121D

Anthony V. Le and Matthew C. T. Hartman

{"title":"Improved synthesis of the unnatural base NaM, and evaluation of its orthogonality in in vitro transcription and translation†","authors":"Anthony V. Le and Matthew C. T. Hartman","doi":"10.1039/D4CB00121D","DOIUrl":"10.1039/D4CB00121D","url":null,"abstract":"Unnatural base pairs (UBP) promise to diversify cellular function through expansion of the genetic code. Some of the most successful UBPs are the hydrophobic base pairs 5SICS:NaM and TPT3:NaM developed by Romesberg. Much of the research on these UBPs has emphasized strategies to enable their efficient replication, transcription and translation in living organisms. These experiments have achieved spectacular success in certain cases; however, the complexity of working in vivo places strong constraints on the types of experiments that can be done to optimize and improve the system. Testing UBPs in vitro, on the other hand, offers advantages including minimization of scale, the ability to precisely control the concentration of reagents, and simpler purification of products. Here we investigate the orthogonality of NaM-containing base pairs in transcription and translation, looking at background readthrough of NaM codons by the native machinery. We also describe an improved synthesis of NaM triphosphate (NaM-TP) and a new assay for testing the purity of UBP containing RNAs.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00121d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Outstanding Reviewers for RSC Chemical Biology in 2023 2023 年 RSC 化学生物学杰出审稿人

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-06 DOI: 10.1039/D4CB90038C

引用次数: 0

Bibacillin 1: a two-component lantibiotic from Bacillus thuringiensis† 比巴西林 1：来自苏云金芽孢杆菌的双组分杀菌剂

IF 4.2

RSC Chemical Biology Pub Date : 2024-09-04 DOI: 10.1039/D4CB00192C

Ryan Moreira, Yi Yang, Youran Luo, Michael S. Gilmore and Wilfred A. van der Donk

{"title":"Bibacillin 1: a two-component lantibiotic from Bacillus thuringiensis†","authors":"Ryan Moreira, Yi Yang, Youran Luo, Michael S. Gilmore and Wilfred A. van der Donk","doi":"10.1039/D4CB00192C","DOIUrl":"10.1039/D4CB00192C","url":null,"abstract":"Here we describe bibacillin 1 – a two-component lantibiotic from Bacillus thuringiensis. The peptides that comprise bibacillin 1 are modified by a class II lanthipeptide synthetase Bib1M producing two peptides with non-overlapping ring patterns that are reminiscent of cerecidin and the short component of the enterococcal cytolysin (CylLS′′), a virulence factor associated with human disease. Stereochemical analysis demonstrated that each component contains LL-methyllanthionine and DL-lanthionine. The mature bibacillin 1 peptides showed cooperative bactericidal activity against Gram-positive bacteria, including members of the ESKAPE pathogens, and weak hemolytic activity. Optimal ratio studies suggest that bibacillin 1 works best when the components are present in a 1 : 1 ratio, but near optimal activity was observed at ratios strongly favouring one component over the other, suggesting that the two peptides may have different but complementary targets. Mechanism of action studies suggest a lipid II-independent killing action distinguishing bibacillin 1 from two other two-component lantibiotics haloduracin and lacticin 3147. One of the two components of bibacillin 1 showed cross reactivity with the cytolysin regulatory system. These result support the involvement of bibacillin 1 in quorum sensing and raise questions about the impact of CylLS′′-like natural products on lanthipeptide expression in diverse bacterial communities.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00192c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Capture of RNA G-quadruplex structures using an l-RNA aptamer† 使用 l-RNA 合体捕获 RNA G-四重结构。

IF 4.2

RSC Chemical Biology Pub Date : 2024-08-29 DOI: 10.1039/D4CB00161C

Sin Yu Lam, Mubarak Ishaq Umar, Haizhou Zhao, Jieyu Zhao and Chun Kit Kwok

{"title":"Capture of RNA G-quadruplex structures using an l-RNA aptamer†","authors":"Sin Yu Lam, Mubarak Ishaq Umar, Haizhou Zhao, Jieyu Zhao and Chun Kit Kwok","doi":"10.1039/D4CB00161C","DOIUrl":"10.1039/D4CB00161C","url":null,"abstract":"G-quadruplexes (dG4 and rG4) are nucleic acid secondary structures formed by the self-assembly of certain G-rich sequences, and they have distinctive chemical properties and play crucial roles in fundamental biological processes. Small molecule G4 ligands were shown to be crucial in characterizing G4s and understanding their functions. Nevertheless, concerns regarding the specificity of these synthetic ligands for further investigation of G4s, especially for rG4 isolation purposes, have been raised. In comparison to G4 ligands, we propose a novel magnetic bead-based pulldown assay that enables the selective capture of general rG4s using functionalized L-Apt.4-1c from both simple buffer and complex media, including total RNA and the cell lysate. We found that our L-RNA aptamer can pulldown general rG4s with a higher efficiency and specificity than the G4 small molecule ligand BioTASQ v.1 in the presence of non-target competitors, including dG4 and non-G4 structures. Our findings reveal that biotinylated L-aptamers can serve as effective molecular tools for the affinity-based enrichment of rG4 of interest using this new assay, which was also verified by quantitative reverse transcription-polymerase chain reaction (RT-qPCR) on endogenous transcripts. This work provides new and important insights into rG4 isolation using a functionalized L-aptamer, which can potentially be applied in a transcript-specific or transcriptome-wide manner in the future.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11359968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa† 控制铜绿假单胞菌生物膜扩散调节因子 RbdA 的磷酸二酯酶活性。

IF 4.2

RSC Chemical Biology Pub Date : 2024-08-27 DOI: 10.1039/D4CB00113C

Charlotte Cordery, Jack Craddock, Martin Malý, Kieran Basavaraja, Jeremy S. Webb, Martin A. Walsh and Ivo Tews

{"title":"Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa†","authors":"Charlotte Cordery, Jack Craddock, Martin Malý, Kieran Basavaraja, Jeremy S. Webb, Martin A. Walsh and Ivo Tews","doi":"10.1039/D4CB00113C","DOIUrl":"10.1039/D4CB00113C","url":null,"abstract":"The switch between planktonic and biofilm lifestyle correlates with intracellular concentration of the second messenger bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). While bacteria possess cyclase and phosphodiesterase enzymes to catalyse formation or hydrolysis of c-di-GMP, both enzymatic domains often occur in a single protein. It is tacitly assumed that one of the two enzymatic activities is dominant, and that additional domains and protein interactions enable responses to environmental conditions and control activity. Here we report the structure of the phosphodiesterase domain of the membrane protein RbdA (regulator of biofilm dispersal) in a dimeric, activated state and show that phosphodiesterase activity is controlled by the linked cyclase. The phosphodiesterase region around helices α5/α6 forms the dimer interface, providing a rationale for activation, as this region was seen in contact with the cyclase domain in an auto-inhibited structure previously described. Kinetic analysis supports this model, as the activity of the phosphodiesterase alone is lower when linked to the cyclase. Analysis of a computed model of the RbdA periplasmatic domain reveals an all-helical architecture with a large binding pocket that could accommodate putative ligands. Unravelling the regulatory circuits in multi-domain phosphodiesterases like RbdA is important to develop strategies to manipulate or disperse bacterial biofilms.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11372557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142157190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0