microLife最新文献_第4页

Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. 完善感染铜绿假单胞菌的毒性噬菌体不同支系的转录景观。

microLife Pub Date : 2024-02-28 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae002

Leena Putzeys, Laura Wicke, Maarten Boon, Vera van Noort, Jörg Vogel, Rob Lavigne

{"title":"Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa.","authors":"Leena Putzeys, Laura Wicke, Maarten Boon, Vera van Noort, Jörg Vogel, Rob Lavigne","doi":"10.1093/femsml/uqae002","DOIUrl":"10.1093/femsml/uqae002","url":null,"abstract":"The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae002"},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10914365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140041097","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

Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks. 宿主细菌和非宿主细菌支持噬菌体沿着菌丝体和非生物传播网络进行传播。

microLife Pub Date : 2024-02-20 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae004

Claire Périat, Thierry Kuhn, Matteo Buffi, Andrea Corona-Ramirez, Mathilda Fatton, Guillaume Cailleau, Patrick S Chain, Claire E Stanley, Lukas Y Wick, Saskia Bindschedler, Diego Gonzalez, Xiang-Yi Li Richter, Pilar Junier

{"title":"Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks.","authors":"Claire Périat, Thierry Kuhn, Matteo Buffi, Andrea Corona-Ramirez, Mathilda Fatton, Guillaume Cailleau, Patrick S Chain, Claire E Stanley, Lukas Y Wick, Saskia Bindschedler, Diego Gonzalez, Xiang-Yi Li Richter, Pilar Junier","doi":"10.1093/femsml/uqae004","DOIUrl":"10.1093/femsml/uqae004","url":null,"abstract":"Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of 'fungal highways' (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect Pseudomonas putida DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in Pythium ultimum-formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae004"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10924533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095307","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

Polar accumulation of pyoverdin and exit from stationary phase. pyoverdin 极性积累并退出静止期。

microLife Pub Date : 2024-02-14 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae001

Clara Moreno-Fenoll, Maxime Ardré, Paul B Rainey

{"title":"Polar accumulation of pyoverdin and exit from stationary phase.","authors":"Clara Moreno-Fenoll, Maxime Ardré, Paul B Rainey","doi":"10.1093/femsml/uqae001","DOIUrl":"10.1093/femsml/uqae001","url":null,"abstract":"Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus Pseudomonas and used for the acquisition of insoluble ferric iron. Although freely diffusible in aqueous environments, preferential dissemination of pyoverdin among adjacent cells, fine-tuning of intracellular siderophore concentrations, and fitness advantages to pyoverdin-producing versus nonproducing cells, indicate control of location and release. Here, using time-lapse fluorescence microscopy to track single cells in growing microcolonies of Pseudomonas fluorescens SBW25, we show accumulation of pyoverdin at cell poles. Accumulation occurs on cessation of cell growth, is achieved by cross-feeding in pyoverdin-nonproducing mutants and is reversible. Moreover, accumulation coincides with localization of a fluorescent periplasmic reporter, suggesting that pyoverdin accumulation at cell poles is part of the general cellular response to starvation. Compatible with this conclusion is absence of non-accumulating phenotypes in a range of pyoverdin mutants. Analysis of the performance of pyoverdin-producing and nonproducing cells under conditions promoting polar accumulation shows an advantage to accumulation on resumption of growth after stress. Examination of pyoverdin polar accumulation in a multispecies community and in a range of laboratory and natural species of Pseudomonas, including P. aeruginosa PAO1 and P. putida KT2440, confirms that the phenotype is characteristic of Pseudomonas.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae001"},"PeriodicalIF":0.0,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10873284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900970","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

Archaeal virus entry and egress 古细菌病毒的进入和排出

microLife Pub Date : 2024-01-03 DOI: 10.1093/femsml/uqad048

Bastiaan P Kuiper, Anna M C Schöntag, H. M. Oksanen, Bertram Daum, Tessa E. F. Quax

引用次数: 0

Agtrevirus phage AV101 recognizes four different O-antigens infecting diverse E. coli 姬状病毒噬菌体 AV101 可识别感染不同大肠杆菌的四种不同 O 抗原

microLife Pub Date : 2023-12-20 DOI: 10.1093/femsml/uqad047

Anders Nørgaard Sørensen, Dorottya Kalmar, V. T. Lutz, Victor Klein-Sousa, Nicholas M I Taylor, M. C. H. Sørensen, L. Brøndsted

{"title":"Agtrevirus phage AV101 recognizes four different O-antigens infecting diverse E. coli","authors":"Anders Nørgaard Sørensen, Dorottya Kalmar, V. T. Lutz, Victor Klein-Sousa, Nicholas M I Taylor, M. C. H. Sørensen, L. Brøndsted","doi":"10.1093/femsml/uqad047","DOIUrl":"https://doi.org/10.1093/femsml/uqad047","url":null,"abstract":"\u0000 Bacteriophages in the Agtrevirus genus are known for expressing multiple tail spike proteins (TSPs), but little is known about their genetic diversity and host recognition apart from their ability to infect diverse Enterobacteriaceae species. Here we aim to determine the genetic differences that may account for the diverse host ranges of Agrevirus phages. We performed comparative genomics of 14 Agtrevirus and identified only a few genetic differences including genes involved in nucleotide metabolism. Most notably was the diversity of the tsp gene cluster, specifically in the receptor binding domains that were unique among most of the phages. We further characterized agtrevirus AV101 infecting nine diverse Extended Spectrum β-lactamase (ESBL) E. coli and demonstrated that this phage encoded four unique TSPs among Agtrevirus. Purified TSPs formed translucent zones and inhibited AV101 infection of specific hosts, demonstrating that TSP1, TSP2, TSP3, and TSP4 recognize O8, O82, O153, and O159 O-antigens of E. coli, respectively. BLASTp analysis showed that the receptor binding domain of TSP1, TSP2, TSP3 and TSP4 are similar to TSPs encoded by E. coli prophages and distant related virulent phages. Thus, Agtrevirus may have gained their receptor binding domains by recombining with prophages or virulent phages. Overall, combining bioinformatic and biological data expands the understanding of TSP host recognition of Agtrevirus and give new insight into the origin and acquisition of receptor binding domains of Ackermannviridae phages.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138954605","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: 0

A native phosphoglycolate salvage pathway of the synthetic autotrophic yeast Komagataella phaffii. 合成自养酵母 Komagataella phaffii 的原生磷酸乙酸盐挽救途径。

microLife Pub Date : 2023-12-11 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqad046

Michael Baumschabl, Bernd M Mitic, Christina Troyer, Stephan Hann, Özge Ata, Diethard Mattanovich

{"title":"A native phosphoglycolate salvage pathway of the synthetic autotrophic yeast Komagataella phaffii.","authors":"Michael Baumschabl, Bernd M Mitic, Christina Troyer, Stephan Hann, Özge Ata, Diethard Mattanovich","doi":"10.1093/femsml/uqad046","DOIUrl":"10.1093/femsml/uqad046","url":null,"abstract":"Synthetic autotrophs can serve as chassis strains for bioproduction from CO2 as a feedstock to take measures against the climate crisis. Integration of the Calvin-Benson-Bassham (CBB) cycle into the methylotrophic yeast Komagataella phaffii (Pichia pastoris) enabled it to use CO2 as the sole carbon source. The key enzyme in this cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzing the carboxylation step. However, this enzyme is error prone to perform an oxygenation reaction leading to the production of toxic 2-phosphoglycolate. Native autotrophs have evolved different recycling pathways for 2-phosphoglycolate. However, for synthetic autotrophs, no information is available for the existence of such pathways. Deletion of CYB2 in the autotrophic K. phaffii strain led to the accumulation of glycolate, an intermediate in phosphoglycolate salvage pathways, suggesting that such a pathway is enabled by native K. phaffii enzymes. 13C tracer analysis with labeled glycolate indicated that the yeast pathway recycling phosphoglycolate is similar to the plant salvage pathway. This orthogonal yeast pathway may serve as a sensor for RuBisCO oxygenation, and as an engineering target to boost autotrophic growth rates in K. phaffii.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqad046"},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10791038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139486758","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

EAM highlights in FEMS 2023: from the Petri dish to planet Earth EAM在FEMS 2023中的亮点:从培养皿到行星地球

microLife Pub Date : 2023-11-03 DOI: 10.1093/femsml/uqad045

Jörg Vogel, Victor de Lorenzo

引用次数: 0

T5-like phage BF23 evades host-mediated DNA restriction and methylation t5样噬菌体BF23逃避宿主介导的DNA限制和甲基化

microLife Pub Date : 2023-10-26 DOI: 10.1093/femsml/uqad044

Mikhail Skutel, Aleksandr Andriianov, Maria Zavialova, Maria Kirsanova, Olufasefunmi Shodunke, Evgenii Zorin, Aleksandr Golovshchinskii, Konstantin Severinov, Artem Isaev

{"title":"T5-like phage BF23 evades host-mediated DNA restriction and methylation","authors":"Mikhail Skutel, Aleksandr Andriianov, Maria Zavialova, Maria Kirsanova, Olufasefunmi Shodunke, Evgenii Zorin, Aleksandr Golovshchinskii, Konstantin Severinov, Artem Isaev","doi":"10.1093/femsml/uqad044","DOIUrl":"https://doi.org/10.1093/femsml/uqad044","url":null,"abstract":"Abstract Bacteriophage BF23 is a close relative of phage T5, a prototypical Tequintavirus that infects Escherichia coli. BF23 was isolated in the middle of the XXth century and was extensively studied as a model object. Like T5, BF23 carries long ∼9.7 kbp terminal repeats, injects its genome into infected cell in a two-stage process, and carries multiple specific nicks in its double-stranded genomic DNA. The two phages rely on different host secondary receptors – FhuA (T5) and BtuB (BF23). Only short fragments of the BF23 genome, including the region encoding receptor interacting proteins, have been determined. Here, we report the full genomic sequence of BF23 and describe the protein content of its virion. T5-like phages represent a unique group that resist restriction by most nuclease-based host immunity systems. We show that BF23, like other Tequintavirus phages, resist Types I/II/III restriction-modification host immunity systems if their recognition sites are located outside the terminal repeats. We also demonstrate that the BF23 avoids host-mediated methylation. We propose that inhibition of methylation is a common feature of Tequintavirus and Epseptimavirus genera phages, that is not, however, associated with their anti-restriction activity.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"10 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135012350","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: 0

The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis. 环二磷酸腺苷在枯草芽孢杆菌生理调控中的诸多作用。

microLife Pub Date : 2023-10-20 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad043

Christina Herzberg, Janek Meißner, Robert Warneke, Jörg Stülke

{"title":"The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis.","authors":"Christina Herzberg, Janek Meißner, Robert Warneke, Jörg Stülke","doi":"10.1093/femsml/uqad043","DOIUrl":"10.1093/femsml/uqad043","url":null,"abstract":"The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis as well as in many bacteria and archaea. Bacillus subtilis possesses three diadenylate cyclases and two phosphodiesterases that synthesize and degrade the molecule, respectively. Among the second messengers, c-di-AMP is unique since it is essential for B. subtilis on the one hand but toxic upon accumulation on the other. This role as an \"essential poison\" is related to the function of c-di-AMP in the control of potassium homeostasis. C-di-AMP inhibits the expression and activity of potassium uptake systems by binding to riboswitches and transporters and activates the activity of potassium exporters. In this way, c-di-AMP allows the adjustment of uptake and export systems to achieve a balanced intracellular potassium concentration. C-di-AMP also binds to two dedicated signal transduction proteins, DarA and DarB. Both proteins seem to interact with other proteins in their apo state, i.e. in the absence of c-di-AMP. For DarB, the (p)ppGpp synthetase/hydrolase Rel and the pyruvate carboxylase PycA have been identified as targets. The interactions trigger the synthesis of the alarmone (p)ppGpp and of the acceptor molecule for the citric acid cycle, oxaloacetate, respectively. In the absence of c-di-AMP, many amino acids inhibit the growth of B. subtilis. This feature can be used to identify novel players in amino acid homeostasis. In this review, we discuss the different functions of c-di-AMP and their physiological relevance.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad043"},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10636490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89721000","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: A leader cell triggers end of lag phase in populations of Pseudomonas fluorescens. 更正：荧光假单胞菌种群中的先导细胞触发滞后期结束。

microLife Pub Date : 2023-10-20 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad040

引用次数: 0