microLife最新文献_第5页

Colony morphotype diversification as a signature of bacterial evolution. 菌落形态类型多样化是细菌进化的标志。

microLife Pub Date : 2023-10-10 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad041

Ákos T Kovács

引用次数: 0

Correction to: Putative nucleotide-based second messengers in archaea. 更正：古菌中假定的基于核苷酸的第二信使。

microLife Pub Date : 2023-09-27 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad039

引用次数: 0

A paradox of bacterial persistence and antibiotic resistance: chloramphenicol acetyl transferase as a double barrel shot gun. 细菌持久性和抗生素耐药性的悖论：氯霉素乙酰转移酶作为双管喷枪。

microLife Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad034

Ana Alves da Silva, Inês Jesus Silva, Cecília Maria Arraiano

{"title":"A paradox of bacterial persistence and antibiotic resistance: chloramphenicol acetyl transferase as a double barrel shot gun.","authors":"Ana Alves da Silva, Inês Jesus Silva, Cecília Maria Arraiano","doi":"10.1093/femsml/uqad034","DOIUrl":"https://doi.org/10.1093/femsml/uqad034","url":null,"abstract":"The problematic microbial resistance to antibiotics has led to an increasing interest in bacterial persistence and its impact on infection. Nonetheless, these two mechanisms are often assessed in independent studies, and there is a lack of knowledge about their relation or possible interactions, both at cellular and population levels. This work shows evidence that the insertion of the resistance gene Chloramphenicol Acetyl Transferase (cat) together with its cognate antibiotic chloramphenicol (CAM), is capable to modulate Salmonella Typhimurium persistence to several antibiotics and decrease its survival. This effect is independent of the antibiotics' mechanisms of action or the locus of cat. RelA [p(ppGpp) syntetase] has been shown to be involved in persistence. It was recently proposed that RelA [(p)ppGpp synthetase], binds to uncharged tRNAs, forming RelA.tRNA complexes. These complexes bind to vacant A-sites in the ribosome, and this mechanism is essential for the activation of RelA. In this study, we propose that the antibiotic chloramphenicol blocks the A-site of the ribosome, hindering the binding of RelA.tRNA complexes to the ribosome thus preventing the activation of RelA and (p)ppGpp synthesis, with a consequent decrease in the level of persistence of the population. Our discovery that the concomitant use of chloramphenicol and other antibiotics in chloramphenicol resistant bacteria can decrease the persister levels can be the basis of novel therapeutics aiming to decrease the persisters and recalcitrant infections.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad034"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/22/d7/uqad034.PMC10540939.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41180646","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

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola. 变异克雷伯菌在负频率依赖性选择下出现新的非聚集性变体。

microLife Pub Date : 2023-09-12 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad038

Amandine Nucci, Juliette Janaszkiewicz, Eduardo P C Rocha, Olaya Rendueles

{"title":"Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola.","authors":"Amandine Nucci, Juliette Janaszkiewicz, Eduardo P C Rocha, Olaya Rendueles","doi":"10.1093/femsml/uqad038","DOIUrl":"https://doi.org/10.1093/femsml/uqad038","url":null,"abstract":"Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad038"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1f/bc/uqad038.PMC10540941.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41179793","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

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola 变异克雷伯菌在负频率依赖性选择下出现新的非聚集性变体

microLife Pub Date : 2023-07-10 DOI: 10.1101/2023.07.10.548335

Amandine Nucci, J. Janaszkiewicz, E. Rocha, Olaya Rendueles

{"title":"Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola","authors":"Amandine Nucci, J. Janaszkiewicz, E. Rocha, Olaya Rendueles","doi":"10.1101/2023.07.10.548335","DOIUrl":"https://doi.org/10.1101/2023.07.10.548335","url":null,"abstract":"Klebsiella variicola is an emergent human pathogen causing diverse infections, including in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of loss-of-function yielding reduced fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clone show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and is able to socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had truncated MrkH proteins many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were all isolated from human, mostly from urine. The decreased aggregation of these mutants could have important clinical implications as such clones could better disperse within the host allowing colonisation of other body sites and leading to systemic infections. One-sentence Summary Report of the emergence of a novel non-aggregative colony morphology in K. variicola and the first example of social exploitation in the Klebsiella genus.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47917226","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}

引用次数: 1

Putative nucleotide-based second messengers in archaea. 古菌中假定的基于核苷酸的第二信使。

microLife Pub Date : 2023-06-05 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad027

Chris van der Does, Frank Braun, Hongcheng Ren, Sonja-Verena Albers

{"title":"Putative nucleotide-based second messengers in archaea.","authors":"Chris van der Does, Frank Braun, Hongcheng Ren, Sonja-Verena Albers","doi":"10.1093/femsml/uqad027","DOIUrl":"10.1093/femsml/uqad027","url":null,"abstract":"Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad027"},"PeriodicalIF":0.0,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/90/0b/uqad027.PMC10249747.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9612316","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

Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes. (p)ppGpp 在真菌的抗生素耐药性、耐受性、持久性和生存中的作用。

microLife Pub Date : 2023-03-11 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad009

Andrea Salzer, Christiane Wolz

{"title":"Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes.","authors":"Andrea Salzer, Christiane Wolz","doi":"10.1093/femsml/uqad009","DOIUrl":"10.1093/femsml/uqad009","url":null,"abstract":"The stringent response and its signalling nucleotides, pppGpp and ppGpp, have been the subject of intense research since the discovery of (p)ppGpp in 1969. Recent studies have revealed that the downstream events that follow (p)ppGpp accumulation vary among species. Consequently, the stringent response as initially characterized in Escherichia coli largely differs from the response in Firmicutes (Bacillota), wherein synthesis and degradation of the messengers (p)ppGpp are orchestrated by the bifunctional Rel enzyme with synthetase and hydrolase activity and the two synthetases SasA/RelP and SasB/RelQ. Here we will summarize recent studies supporting the role of (p)ppGpp in the development of antibiotic resistance and tolerance as well as survival under adverse environmental conditions in Firmicutes. We will also discuss the impact of elevated (p)ppGpp levels on the development of persister cells and the establishment of persistent infections. (p)ppGpp levels are usually tightly controlled to allow optimal growth under non-stressed conditions. Upon the onset of certain 'stringent conditions' the sudden increase in (p)ppGpp levels limits growth while exerting protective effects. In Firmicutes, the (p)ppGpp-mediated restriction of GTP accumulation is one major mechanism of protection and survival under stresses such as antibiotic exposure.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad009"},"PeriodicalIF":0.0,"publicationDate":"2023-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9570012","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

Microbiology education: a significant path to sustainably improve the human and biosphere condition. 微生物学教育：可持续改善人类和生物圈状况的重要途径。

microLife Pub Date : 2023-03-10 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad013

Kenneth Timmis

引用次数: 0

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics. 通过核糖体分析和蛋白质组学揭示植物共生体瓜萎镰刀菌（Sinorhizobium meliloti）的小蛋白质组。

microLife Pub Date : 2023-03-10 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad012

Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H Ahrens, Cynthia M Sharma, Elena Evguenieva-Hackenberg

{"title":"Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics.","authors":"Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H Ahrens, Cynthia M Sharma, Elena Evguenieva-Hackenberg","doi":"10.1093/femsml/uqad012","DOIUrl":"10.1093/femsml/uqad012","url":null,"abstract":"The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad012"},"PeriodicalIF":0.0,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522021","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

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. 结合核糖体图谱分析和小蛋白优化质谱分析，揭示火山火绒菌的小蛋白质组。

microLife Pub Date : 2023-01-16 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad001

Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M Sharma, Anita Marchfelder

{"title":"Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry.","authors":"Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M Sharma, Anita Marchfelder","doi":"10.1093/femsml/uqad001","DOIUrl":"10.1093/femsml/uqad001","url":null,"abstract":"In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad001"},"PeriodicalIF":0.0,"publicationDate":"2023-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/78/30/uqad001.PMC10117724.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518992","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