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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

Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. 真菌滴剂:真菌菌丝生长的宏观和微观分析的新方法。

microLife Pub Date : 2023-10-18 eCollection Date: 2023-01-01 DOI: 10.1093/femsml/uqad042

Matteo Buffi, Guillaume Cailleau, Thierry Kuhn, Xiang-Yi Li Richter, Claire E Stanley, Lukas Y Wick, Patrick S Chain, Saskia Bindschedler, Pilar Junier

{"title":"Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth.","authors":"Matteo Buffi, Guillaume Cailleau, Thierry Kuhn, Xiang-Yi Li Richter, Claire E Stanley, Lukas Y Wick, Patrick S Chain, Saskia Bindschedler, Pilar Junier","doi":"10.1093/femsml/uqad042","DOIUrl":"10.1093/femsml/uqad042","url":null,"abstract":"This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad042"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10642649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107592977","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

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