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Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles. 不同的培养基和纯化方法揭示了弗氏丙酸杆菌来源的细胞外囊泡的核心蛋白质组。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad029
Vinícius de Rezende Rodovalho, Brenda Silva Rosa da Luz, Aurélie Nicolas, Julien Jardin, Valérie Briard-Bion, Edson Luiz Folador, Anderson Rodrigues Santos, Gwénaël Jan, Yves Le Loir, Vasco Ariston de Carvalho Azevedo, Éric Guédon
{"title":"Different culture media and purification methods unveil the core proteome of <i>Propionibacterium freudenreichii</i>-derived extracellular vesicles.","authors":"Vinícius de Rezende Rodovalho,&nbsp;Brenda Silva Rosa da Luz,&nbsp;Aurélie Nicolas,&nbsp;Julien Jardin,&nbsp;Valérie Briard-Bion,&nbsp;Edson Luiz Folador,&nbsp;Anderson Rodrigues Santos,&nbsp;Gwénaël Jan,&nbsp;Yves Le Loir,&nbsp;Vasco Ariston de Carvalho Azevedo,&nbsp;Éric Guédon","doi":"10.1093/femsml/uqad029","DOIUrl":"https://doi.org/10.1093/femsml/uqad029","url":null,"abstract":"<p><p>Bacterial extracellular vesicles (EVs) are natural lipidic nanoparticles implicated in intercellular communication. Although EV research focused mainly on pathogens, the interest in probiotic-derived EVs is now rising. One example is <i>Propionibacterium freudenreichii</i>, which produces EVs with anti-inflammatory effects on human epithelial cells. Our previous study with <i>P. freudenreichii</i> showed that EVs purified by size exclusion chromatography (SEC) displayed variations in protein content according to bacterial growth conditions. Considering these content variations, we hypothesized that a comparative proteomic analysis of EVs recovered in different conditions would elucidate whether a representative vesicular proteome existed, possibly providing a robust proteome dataset for further analysis. Therefore, <i>P. freudenreichii</i> was grown in two culture media, and EVs were purified by sucrose density gradient ultracentrifugation (UC). Microscopic and size characterization confirmed EV purification, while shotgun proteomics unveiled that they carried a diverse set of proteins. A comparative analysis of the protein content of UC- and SEC-derived EVs, isolated from cultures either in UF (cow milk ultrafiltrate medium) or YEL (laboratory yeast extract lactate medium), showed that EVs from all these conditions shared 308 proteins. This EV core proteome was notably enriched in proteins related to immunomodulation. Moreover, it showed distinctive features, including highly interacting proteins, compositional biases for some specific amino acids, and other biochemical parameters. Overall, this work broadens the toolset for the purification of <i>P. freudenreichii</i>-derived EVs, identifies a representative vesicular proteome, and enumerates conserved features in vesicular proteins. These results hold the potential for providing candidate biomarkers of purification quality, and insights into the mechanisms of EV biogenesis and cargo sorting.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad029"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/57/2b/uqad029.PMC10265600.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9656045","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: 1
The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status. 非洲儿童的真核体受地理位置、肠道生物地理和营养状况的影响。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad033
Pascale Vonaesch, Vincent Billy, Allison E Mann, Evan Morien, Azimdine Habib, Jean-Marc Collard, Michel Dédé, Nathalie Kapel, Philippe J Sansonetti, Laura Wegener Parfrey
{"title":"The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status.","authors":"Pascale Vonaesch,&nbsp;Vincent Billy,&nbsp;Allison E Mann,&nbsp;Evan Morien,&nbsp;Azimdine Habib,&nbsp;Jean-Marc Collard,&nbsp;Michel Dédé,&nbsp;Nathalie Kapel,&nbsp;Philippe J Sansonetti,&nbsp;Laura Wegener Parfrey","doi":"10.1093/femsml/uqad033","DOIUrl":"https://doi.org/10.1093/femsml/uqad033","url":null,"abstract":"<p><p>Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of <i>Fusarium equiseti</i>, a mycotoxin producing fungus, and lower levels of the protist <i>Blastocystis</i> in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad033"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10481997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10186521","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
The symbolic power of nucleotide second messengers - or how prokaryotes link sensing and responding to their outside world. 核苷酸第二信使的象征力量-或者原核生物如何将感知和响应外部世界联系起来。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad036
Regine Hengge
{"title":"The symbolic power of nucleotide second messengers - or how prokaryotes link sensing and responding to their outside world.","authors":"Regine Hengge","doi":"10.1093/femsml/uqad036","DOIUrl":"https://doi.org/10.1093/femsml/uqad036","url":null,"abstract":"Editorial Nucleotide second messengers are k e y components of molecular information processing pathways and networks that allow bacteria and archaea to navigate and adapt to an e v er c hanging exter-nal world. Being produced and/or degraded by often membrane-associated enzymes that can sense and react to environmental or cellular changes, the intracellular second messenger molecules are in turn sensed by cellular effectors—usually proteins or protein domains , sometimes ribos witc hes—that trigger dir ectl y associated target systems to produce specific molecular reactions. T hus , second messengers are informational molecules, which stand as intracellular molecular symbols or signs for something else, namel y, some potentiall y life-thr eatening condition, and which inform the executive machinery of the cell that an a ppr o-priate ada ptiv e r esponse is ur gentl y needed. It is pr obabl y not accidental that two major classes of intracellular molecules with symbolic functions are both deri vati ves of n ucleotides although there is a clear functional division of labour between them. The nucleotide polymers DNA and RNA function in the stor a ge and ef-fectuation of genetic information that has to be maintained over long times. By constrast, nucleotide second messengers are tiny RNAs, which consist only of one or two, often cyclic nucleotides, that have to transiently represent environmental or cellular states in real time . T his requires high dynamics of second messenger pr oduction and degr adation by specific enzymes whose expr es-sion and activity has to be tightl y contr olled by sensory input. It is likely that second messenger signaling is the evolutionary oldest form of molecular information processing, rudimentary forms of which ma y ha ve already evolved in the early RN A w orld. The cur-r ent pictur e of second messenger signaling in Pr okary otes, ho we","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad036"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/66/13/uqad036.PMC10449370.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10099795","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
The role of site-2-proteases in bacteria: a review on physiology, virulence, and therapeutic potential. 2-位点蛋白酶在细菌中的作用:生理、毒力和治疗潜力的综述。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad025
Sofie S Kristensen, Dzung B Diep, Morten Kjos, Geir Mathiesen
{"title":"The role of site-2-proteases in bacteria: a review on physiology, virulence, and therapeutic potential.","authors":"Sofie S Kristensen,&nbsp;Dzung B Diep,&nbsp;Morten Kjos,&nbsp;Geir Mathiesen","doi":"10.1093/femsml/uqad025","DOIUrl":"https://doi.org/10.1093/femsml/uqad025","url":null,"abstract":"<p><p>Site-2-proteases are a class of intramembrane proteases involved in regulated intramembrane proteolysis. Regulated intramembrane proteolysis is a highly conserved signaling mechanism that commonly involves sequential digestion of an anti-sigma factor by a site-1- and site-2-protease in response to external stimuli, resulting in an adaptive transcriptional response. Variation of this signaling cascade continues to emerge as the role of site-2-proteases in bacteria continues to be explored. Site-2-proteases are highly conserved among bacteria and play a key role in multiple processes, including iron uptake, stress response, and pheromone production. Additionally, an increasing number of site-2-proteases have been found to play a pivotal role in the virulence properties of multiple human pathogens, such as alginate production in <i>Pseudomonas aeruginosa</i>, toxin production in <i>Vibrio cholerae</i>, resistance to lysozyme in enterococci and antimicrobials in several <i>Bacillus</i> spp, and cell-envelope lipid composition in <i>Mycobacterium tuberculosis</i>. The prominent role of site-2-proteases in bacterial pathogenicity highlights the potential of site-2-proteases as novel targets for therapeutic intervention. In this review, we summarize the role of site-2-proteases in bacterial physiology and virulence, as well as evaluate the therapeutic potential of site-2-proteases.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad025"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518993","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: 1
Characterization of a soluble library of the Pseudomonas aeruginosa PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. 铜绿假单胞菌PAO1膜蛋白组可溶性文库的表征,重点研究c-二- gmp转换酶。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad028
Anna Scherhag, Markus Räschle, Niklas Unbehend, Benedikt Venn, David Glueck, Timo Mühlhaus, Sandro Keller, Eugenio Pérez Patallo, Susanne Zehner, Nicole Frankenberg-Dinkel
{"title":"Characterization of a soluble library of the <i>Pseudomonas aeruginosa</i> PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes.","authors":"Anna Scherhag,&nbsp;Markus Räschle,&nbsp;Niklas Unbehend,&nbsp;Benedikt Venn,&nbsp;David Glueck,&nbsp;Timo Mühlhaus,&nbsp;Sandro Keller,&nbsp;Eugenio Pérez Patallo,&nbsp;Susanne Zehner,&nbsp;Nicole Frankenberg-Dinkel","doi":"10.1093/femsml/uqad028","DOIUrl":"https://doi.org/10.1093/femsml/uqad028","url":null,"abstract":"<p><p>Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen <i>Pseudomonas aeruginosa</i>, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of <i>P. aeruginosa</i> for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad028"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e6/b3/uqad028.PMC10335732.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9872409","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
Correction to: control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP. 修正:通过第二信使环二gmp控制蓝藻的光依赖性行为。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad035
{"title":"Correction to: control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP.","authors":"","doi":"10.1093/femsml/uqad035","DOIUrl":"https://doi.org/10.1093/femsml/uqad035","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/femsml/uqad019.].</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad035"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10430786/pdf/uqad035.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10022106","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
Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles. 昆基芽孢杆菌释放rna相关的膜囊泡和蛋白质纳米颗粒。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad037
Christian Seeger, Karl Dyrhage, Kristina Näslund, Siv G E Andersson
{"title":"<i>Apilactobacillus kunkeei</i> releases RNA-associated membrane vesicles and proteinaceous nanoparticles.","authors":"Christian Seeger,&nbsp;Karl Dyrhage,&nbsp;Kristina Näslund,&nbsp;Siv G E Andersson","doi":"10.1093/femsml/uqad037","DOIUrl":"https://doi.org/10.1093/femsml/uqad037","url":null,"abstract":"<p><p>Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of <i>Apilactobacillus kunkeei</i>, a defensive symbiont of honeybees. The membrane vesicles were separated from the extracellular particles using density gradient ultracentrifugation. The peaks of the RNA and protein distributions were separated from each other and the highest concentration of RNA was observed in the fractions that contained the membrane vesicles while the highest protein concentration coincided with the fractions that contained extracellular particles. A comparative proteomics analysis by LC-MS/MS showed that 37 proteins with type-I signal peptides were consistently identified across the fractionated samples obtained from the cell-free pellets, of which 29 were orthologs detected in both strains. Functional predictions of the extracellular proteins revealed the presence of glycoside hydrolases, glycosyltransferases, giant proteins and peptidases. The extracellular transcriptomes mapped to a broad set of genes with a similar functional profile as the whole cell transcriptome. This study provides insights into the composition of membrane vesicles and extracellular proteins of a bee-associated symbiont.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad037"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10496945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10262986","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
Mycobacterium tuberculosis infection triggers epigenetic changes that are enriched in a type I IFN signature. 结核分枝杆菌感染触发了I型IFN特征丰富的表观遗传变化。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad006
Katrina Madden, Rayan El Hamra, Stefania Berton, Jake Felker, Gonzalo G Alvarez, Alexandre Blais, Jim Sun
{"title":"<i>Mycobacterium tuberculosis</i> infection triggers epigenetic changes that are enriched in a type I IFN signature.","authors":"Katrina Madden,&nbsp;Rayan El Hamra,&nbsp;Stefania Berton,&nbsp;Jake Felker,&nbsp;Gonzalo G Alvarez,&nbsp;Alexandre Blais,&nbsp;Jim Sun","doi":"10.1093/femsml/uqad006","DOIUrl":"https://doi.org/10.1093/femsml/uqad006","url":null,"abstract":"<p><p>Tuberculosis, a deadly infectious lung disease caused by <i>Mycobacterium tuberculosis</i> (Mtb), remains the leading cause of bacterial disease-related deaths worldwide. Mtb reprograms and disables key antibacterial response pathways, many of which are regulated by epigenetic mechanisms that control the accessibility of chromatin to the transcriptional machinery. Recent reports suggest that host phosphatases, such as PPM1A, contribute to regulating chromatin accessibility during bacterial infections. However, changes in genome-wide chromatin accessibility during Mtb infection and whether PPM1A plays a role in this process remains unknown. Herein, we use combinatorial chromatin accessibility (ATAC-seq) and transcriptomic (RNA-seq) profiling of wild-type, PPM1A knockout and PPM1A overexpressing macrophages to demonstrate that Mtb infection induces global chromatin remodelling consistent with changes in gene expression. The strongest concordant changes to chromatin accessibility and gene expression triggered by Mtb infection were enriched for genes involved in type I interferon (IFN) signalling pathways. A panel of 15 genes with the strongest concordant changes in chromatin accessibility and gene expression were validated to be significantly upregulated in Mtb-infected human monocyte-derived macrophages. PPM1A expression affects chromatin accessibility profiles during Mtb infection that are reflected in the total number, chromosome location, and directionality of change. Transcription factor binding motif analysis revealed enrichment for transcription factors involved in the type I IFN pathway during Mtb infection, including members of the IRF, MEF2, and AP-1 families. Our study shows that altered type I IFN responses in Mtb-infected macrophages occur due to genome-wide changes in chromatin accessibility, and that PPM1A could influence a subset of these signatures.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad006"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c4/35/uqad006.PMC9936219.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9317032","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: 1
An archaeal Cas3 protein facilitates rapid recovery from DNA damage. 一种古细菌Cas3蛋白促进DNA损伤的快速恢复。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqad007
Guy Miezner, Israela Turgeman-Grott, Kelly M Zatopek, Andrew F Gardner, Leah Reshef, Deepak K Choudhary, Martina Alstetter, Thorsten Allers, Anita Marchfelder, Uri Gophna
{"title":"An archaeal Cas3 protein facilitates rapid recovery from DNA damage.","authors":"Guy Miezner,&nbsp;Israela Turgeman-Grott,&nbsp;Kelly M Zatopek,&nbsp;Andrew F Gardner,&nbsp;Leah Reshef,&nbsp;Deepak K Choudhary,&nbsp;Martina Alstetter,&nbsp;Thorsten Allers,&nbsp;Anita Marchfelder,&nbsp;Uri Gophna","doi":"10.1093/femsml/uqad007","DOIUrl":"https://doi.org/10.1093/femsml/uqad007","url":null,"abstract":"<p><p>CRISPR-Cas systems provide heritable acquired immunity against viruses to archaea and bacteria. Cas3 is a CRISPR-associated protein that is common to all Type I systems, possesses both nuclease and helicase activities, and is responsible for degradation of invading DNA. Involvement of Cas3 in DNA repair had been suggested in the past, but then set aside when the role of CRISPR-Cas as an adaptive immune system was realized. Here we show that in the model archaeon <i>Haloferax volcanii</i> a <i>cas3</i> deletion mutant exhibits increased resistance to DNA damaging agents compared with the wild-type strain, but its ability to recover quickly from such damage is reduced. Analysis of <i>cas3</i> point mutants revealed that the helicase domain of the protein is responsible for the DNA damage sensitivity phenotype. Epistasis analysis indicated that <i>cas3</i> operates with <i>mre11</i> and <i>rad50</i> in restraining the homologous recombination pathway of DNA repair. Mutants deleted for Cas3 or deficient in its helicase activity showed higher rates of homologous recombination, as measured in pop-in assays using non-replicating plasmids. These results demonstrate that Cas proteins act in DNA repair, in addition to their role in defense against selfish elements and are an integral part of the cellular response to DNA damage.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad007"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516282","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
Bacteria without their phages are just not competitive. 没有噬菌体的细菌是没有竞争力的。
microLife Pub Date : 2023-01-01 DOI: 10.1093/femsml/uqac024
Sarah Wettstadt
{"title":"Bacteria without their phages are just not competitive.","authors":"Sarah Wettstadt","doi":"10.1093/femsml/uqac024","DOIUrl":"https://doi.org/10.1093/femsml/uqac024","url":null,"abstract":"As a veterinarian by training, José Penadés never thought he would stick with a scientific career. For his PhD, he already switched gears and worked on the human autoimmune disease Goodpasture syndrome. However, he quickly realised that studying autoantigens gave him quite a hard time and ‘immunology was just not [my] his thing’. Afterwards he decided to stay in Valencia, Spain, and get some teaching experience at a private school. Yet, here, he recognised that indeed he was missing research. So, José chose to go back to a previous lab where he could apply his newly acquired molecular biology toolbox to their project on bacterial biofilms. He focused on the Gram-positive Staphylococcus aureus and studied how this pathogen forms biofilms to persist in the host. He and his team found a new cell-wall associated protein that they called Bap for biofilm-associated protein showing that proteins are integral parts of bacterial biofilms (Cucarella et al. 2001). They discovered that S. aureus produces Bap and attaches it to its outer membrane as a sensor. Upon contact with a surface or another cell, for example during infection, Bap is cleaved off the bacterial membrane and released to the surrounding. During an inflammatory response in the human body, the pH of the local environment drops. This triggers the N-terminal amyloid-like regions of Bap to form aggregates that further become functional scaffolds of the biofilm matrix (Taglialegna et al. 2016). With this dip into the microbiology world, José was more determined and started to enjoy the scientific process. In comparison with immunological studies, he found microbiological experiments more rewarding, since ‘it is easier to see a phenotype. You can complement and move genes between bacteria as you like and you are pretty confident about the results that you see.’","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqac024"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cb/fc/uqac024.PMC10117707.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518988","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
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