Pub Date : 2024-11-19Epub Date: 2024-10-24DOI: 10.1128/msystems.00970-23
Elena Lucy Carter, Nicholas R Waterfield, Chrystala Constantinidou, Mohammad Tauqeer Alam
Photorhabdus is a bacterial genus containing both insect and emerging human pathogens. Most insect-restricted species display temperature restriction, unable to grow above 34°C, while Photorhabdus asymbiotica can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. Metabolic adaptations have been proposed to facilitate the survival of this pathogen at higher temperatures, yet the biological mechanisms underlying these are poorly understood. We have reconstructed an extensively manually curated genome-scale metabolic model of P. asymbiotica (iEC1073, BioModels ID MODEL2309110001), validated through in silico gene knockout and nutrient utilization experiments with an excellent agreement between experimental data and model predictions. Integration of iEC1073 with transcriptomics data obtained for P. asymbiotica at temperatures of 28°C and 37°C allowed the development of temperature-specific reconstructions representing metabolic adaptations the pathogen undergoes when shifting to a higher temperature in a mammalian compared to insect host. Analysis of these temperature-specific reconstructions reveals that nucleotide metabolism is enriched with predicted upregulated and downregulated reactions. iEC1073 could be used as a powerful tool to study the metabolism of P. asymbiotica, in different genetic or environmental conditions.
Importance: Photorhabdus bacterial species contain both human and insect pathogens, and most of these species cannot grow in higher temperatures. However, Photorhabdus asymbiotica, which infects both humans and insects, can grow in higher temperatures and undergoes metabolic adaptations at a temperature of 37°C compared to that of insect body temperature. Therefore, it is important to examine how this bacterial species can metabolically adapt to survive in higher temperatures. In this work, using a mathematical model, we have examined the metabolic shift that takes place when the bacteria switch from growth conditions in 28°C to 37°C. We show that P. asymbiotica potentially experiences predicted temperature-induced metabolic adaptations at 37°C predominantly clustered within the nucleotide metabolism pathway.
{"title":"A temperature-induced metabolic shift in the emerging human pathogen <i>Photorhabdus asymbiotica</i>.","authors":"Elena Lucy Carter, Nicholas R Waterfield, Chrystala Constantinidou, Mohammad Tauqeer Alam","doi":"10.1128/msystems.00970-23","DOIUrl":"10.1128/msystems.00970-23","url":null,"abstract":"<p><p><i>Photorhabdus</i> is a bacterial genus containing both insect and emerging human pathogens. Most insect-restricted species display temperature restriction, unable to grow above 34°C, while <i>Photorhabdus asymbiotica</i> can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. Metabolic adaptations have been proposed to facilitate the survival of this pathogen at higher temperatures, yet the biological mechanisms underlying these are poorly understood. We have reconstructed an extensively manually curated genome-scale metabolic model of <i>P. asymbiotica</i> (iEC1073, BioModels ID MODEL2309110001), validated through <i>in silico</i> gene knockout and nutrient utilization experiments with an excellent agreement between experimental data and model predictions. Integration of iEC1073 with transcriptomics data obtained for <i>P. asymbiotica</i> at temperatures of 28°C and 37°C allowed the development of temperature-specific reconstructions representing metabolic adaptations the pathogen undergoes when shifting to a higher temperature in a mammalian compared to insect host. Analysis of these temperature-specific reconstructions reveals that nucleotide metabolism is enriched with predicted upregulated and downregulated reactions. iEC1073 could be used as a powerful tool to study the metabolism of <i>P. asymbiotica,</i> in different genetic or environmental conditions.</p><p><strong>Importance: </strong><i>Photorhabdus</i> bacterial species contain both human and insect pathogens, and most of these species cannot grow in higher temperatures. However, <i>Photorhabdus asymbiotica</i>, which infects both humans and insects, can grow in higher temperatures and undergoes metabolic adaptations at a temperature of 37°C compared to that of insect body temperature. Therefore, it is important to examine how this bacterial species can metabolically adapt to survive in higher temperatures. In this work, using a mathematical model, we have examined the metabolic shift that takes place when the bacteria switch from growth conditions in 28°C to 37°C. We show that <i>P. asymbiotica</i> potentially experiences predicted temperature-induced metabolic adaptations at 37°C predominantly clustered within the nucleotide metabolism pathway.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0097023"},"PeriodicalIF":5.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Obtaining these signatures would significantly enhance our understanding of the underlying pathophysiological processes of this condition and foster the development of improved therapeutic strategies, potentially personalized to individual patients. Here, we sequenced newly collected samples from 24 patients with periodontitis, and we collected available oral microbiome data from 24 samples in patients with periodontitis and from 214 samples in healthy individuals (n = 262). Data were harmonized, and we performed a pooled analysis of individual patient data. By metagenomic sequencing of the plaque microbiome, we found microbial signatures for periodontitis and defined a periodontitis-related complex, composed by the most discriminative bacteria. A simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, was associated with periodontitis with high accuracy (area under the curve: 0.94). Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.
Importance: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.
{"title":"Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis.","authors":"Assem Soueidan, Katia Idiri, Camille Becchina, Pauline Esparbès, Arnaud Legrand, Quentin Le Bastard, Emmanuel Montassier","doi":"10.1128/msystems.00930-24","DOIUrl":"10.1128/msystems.00930-24","url":null,"abstract":"<p><p>Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Obtaining these signatures would significantly enhance our understanding of the underlying pathophysiological processes of this condition and foster the development of improved therapeutic strategies, potentially personalized to individual patients. Here, we sequenced newly collected samples from 24 patients with periodontitis, and we collected available oral microbiome data from 24 samples in patients with periodontitis and from 214 samples in healthy individuals (<i>n</i> = 262). Data were harmonized, and we performed a pooled analysis of individual patient data. By metagenomic sequencing of the plaque microbiome, we found microbial signatures for periodontitis and defined a periodontitis-related complex, composed by the most discriminative bacteria. A simple two-factor decision tree, based on <i>Tannerella forsythia</i> and <i>Fretibacterium fastidiosum</i>, was associated with periodontitis with high accuracy (area under the curve: 0.94). Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.</p><p><strong>Importance: </strong>Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on <i>Tannerella forsythia</i> and <i>Fretibacterium fastidiosum</i>, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0093024"},"PeriodicalIF":5.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19Epub Date: 2024-10-18DOI: 10.1128/msystems.01289-24
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford, Promi Das, Justin P Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A Gilbert, Rob Knight
{"title":"Correction for Zhu et al., \"Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy\".","authors":"Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford, Promi Das, Justin P Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A Gilbert, Rob Knight","doi":"10.1128/msystems.01289-24","DOIUrl":"10.1128/msystems.01289-24","url":null,"abstract":"","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0128924"},"PeriodicalIF":5.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) strains present a significant global public health threat due to their high mortality rates. This study investigated the genomic characteristics of seven ST11-K1 CR-hvKP isolates harboring highly homologous KPC-2-encoding multidrug-resistance plasmids. The strains were isolated from a Chinese tertiary hospital between 2017 and 2020. Whole-genome sequencing and bioinformatic analysis revealed various antibiotic resistance genes (ARGs) and virulence determinants. The blaKPC-2-bearing plasmids that contain multiple antibiotic-resistance genes were also identified in these strains. ISfinder and Orifinder were applied to identify insertion sequences (IS) and conjugation-related factors among these blaKPC-2-bearing plasmids. The blaKPC-2 was highly consistent in seven blaKPC-2-bearing plasmids (ISKpn6-blaKPC-2-ISKpn27-ISYps3-IS26). In addition, we found a region composed of ISIR, Tn5393, and IS26. It was located upstream of the blaCTX-M-15 gene and presented in six blaKPC-2-bearing plasmids, with pCR-hvKP221-KPC-P3 as an exception. Conjugation experiments demonstrated the horizontal transfer of resistance plasmids pCR-hvKP128-KPC-P1 and pCR-hvKP132-KPC-P1 across species. Notably, pLVPK-like virulence plasmids carrying virulence gene clusters pCR-hvKP173-Vir-P1, and pCR-hvKP221-Vir-P1 were also detected. A fusional plasmid pCR-hvKP221-Vir-P2, which carries virulence gene clusters and ARGs, was also identified. Five CR-hvKP strains displayed enhanced biofilm formation and high virulence in vivo infection models. Phylogenetic and single nucleotide polymorphism (SNP) analyses indicated a close genetic relationship among the isolates, suggesting a subclade. These findings highlight the complex genetic profiles and potential transmission mechanisms of CR-hvKP strains.
Importance: We reported seven CR-hvKP strains all carried a highly homologous blaKPC-2 integrated IncFⅡ-resistant plasmid, and two strains harbored virulence plasmids. Conjugation experiments confirmed the transferability of these plasmids, indicating a potential for resistance spread. Phylogenetic analysis clarified the relationship among the CR-hvKP isolates. This study provides insights into the phenotypic and genomic characteristics of seven ST11-K1 CR-hvKP strains. The high prevalence and potential for local outbreaks emphasize the need for effective control measures.
{"title":"Phenotypic and genomic characterization of ST11-K1 CR-hvKP with highly homologous <i>bla</i><sub>KPC-2</sub>-bearing plasmids in China.","authors":"Yu-Ling Han, Hua Wang, Hong-Zhe Zhu, Ying-Ying Lv, Wen Zhao, Yan-Yan Wang, Jian-Xun Wen, Zhi-De Hu, Jun-Rui Wang, Wen-Qi Zheng","doi":"10.1128/msystems.01101-24","DOIUrl":"10.1128/msystems.01101-24","url":null,"abstract":"<p><p>Carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-hvKP) strains present a significant global public health threat due to their high mortality rates. This study investigated the genomic characteristics of seven ST11-K1 CR-hvKP isolates harboring highly homologous KPC-2-encoding multidrug-resistance plasmids. The strains were isolated from a Chinese tertiary hospital between 2017 and 2020. Whole-genome sequencing and bioinformatic analysis revealed various antibiotic resistance genes (ARGs) and virulence determinants. The <i>bla</i><sub>KPC-2</sub>-bearing plasmids that contain multiple antibiotic-resistance genes were also identified in these strains. ISfinder and Orifinder were applied to identify insertion sequences (IS) and conjugation-related factors among these <i>bla</i><sub>KPC-2</sub>-bearing plasmids. The <i>bla</i><sub>KPC-2</sub> was highly consistent in seven <i>bla</i><sub>KPC-2</sub>-bearing plasmids (IS<i>Kpn6-bla</i><sub>KPC-2</sub>-IS<i>Kpn27</i>-IS<i>Yps3</i>-IS<i>26</i>). In addition, we found a region composed of IS<i>IR</i>, Tn<i>5393</i>, and IS<i>26</i>. It was located upstream of the <i>bla</i><sub>CTX-M-15</sub> gene and presented in six <i>bla</i><sub>KPC-2</sub>-bearing plasmids, with pCR-hvKP221-KPC-P3 as an exception. Conjugation experiments demonstrated the horizontal transfer of resistance plasmids pCR-hvKP128-KPC-P1 and pCR-hvKP132-KPC-P1 across species. Notably, pLVPK-like virulence plasmids carrying virulence gene clusters pCR-hvKP173-Vir-P1, and pCR-hvKP221-Vir-P1 were also detected. A fusional plasmid pCR-hvKP221-Vir-P2, which carries virulence gene clusters and ARGs, was also identified. Five CR-hvKP strains displayed enhanced biofilm formation and high virulence <i>in vivo</i> infection models. Phylogenetic and single nucleotide polymorphism (SNP) analyses indicated a close genetic relationship among the isolates, suggesting a subclade. These findings highlight the complex genetic profiles and potential transmission mechanisms of CR-hvKP strains.</p><p><strong>Importance: </strong>We reported seven CR-hvKP strains all carried a highly homologous <i>bla</i><sub>KPC-2</sub> integrated IncFⅡ-resistant plasmid, and two strains harbored virulence plasmids. Conjugation experiments confirmed the transferability of these plasmids, indicating a potential for resistance spread. Phylogenetic analysis clarified the relationship among the CR-hvKP isolates. This study provides insights into the phenotypic and genomic characteristics of seven ST11-K1 CR-hvKP strains. The high prevalence and potential for local outbreaks emphasize the need for effective control measures.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0110124"},"PeriodicalIF":5.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-18DOI: 10.1128/msystems.01403-24
Angel Rain-Franco, Alizée Le Moigne, Lucas Serra Moncadas, Marisa O D Silva, Adrian-Stefan Andrei, Jakob Pernthaler
Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually "refined" into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence.
Importance: We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.
{"title":"Dispersal shapes compositional and functional diversity in aquatic microbial communities.","authors":"Angel Rain-Franco, Alizée Le Moigne, Lucas Serra Moncadas, Marisa O D Silva, Adrian-Stefan Andrei, Jakob Pernthaler","doi":"10.1128/msystems.01403-24","DOIUrl":"https://doi.org/10.1128/msystems.01403-24","url":null,"abstract":"<p><p>Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually \"refined\" into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence.</p><p><strong>Importance: </strong>We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0140324"},"PeriodicalIF":5.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-12DOI: 10.1128/msystems.00762-24
Vasni Zavaleta, Laura Pérez-Través, Luis A Saona, Carlos A Villarroel, Amparo Querol, Francisco A Cubillos
<p><p>Hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i> resulted in the emergence of <i>S. pastorianus</i>, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of <i>S. eubayanus</i> parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in <i>S. cerevisiae</i> and <i>S. eubayanus</i>, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The <i>S. cerevisiae</i> parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer <i>S. cerevisiae</i> parental lineages exhibited a volatile compound profile resembling the corresponding <i>S. eubayanus</i> parent. This pattern may result from the dominant inheritance of the <i>S. eubayanus</i> aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer <i>S. cerevisiae</i> lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.</p><p><strong>Importance: </strong>Our study investigates the principles of lager yeast hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i>. This process gave rise to the lager yeast <i>Saccharomyces pastorianus</i>. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the <i>S. cerevisiae</i> parent, with Beer lineage hybrids adopting aroma characteristics from their <i>S. eubayanus</i> parent. These insights reveal the complex genetic interactions in hybrid yeasts, openin
酿酒酵母(Saccharomyces cerevisiae)和酿酒酵母(Saccharomyces eubayanus)杂交产生了酿酒酵母(S. pastorianus),它是啤酒发酵的一种重要酵母。然而,由于 S. eubayanus 亲本菌株的稀缺,我们对这两个物种之间杂交成功率和杂交活力的了解仍然有限。在此,我们探讨了杂交成功率以及杂交对新形成的拉格杂交种的发酵性能和挥发性化合物特征的影响。通过从两个物种中选择不同品系的候选亲本,我们发现啤酒品系和 PB-2 品系分别在 S. cerevisiae 和 S. eubayanus 中表现出很高的杂交成功率。通过自发二倍体杂交技术(稀有交配)产生的多倍体杂交种显示,三倍体和二倍体比四倍体更普遍。尽管在发酵能力方面没有异交现象,但杂交种表现出了表型变异性,特别是受麦芽三糖消耗量的影响。有趣的是,虽然三倍体表现出更大的表型变异性,但倍性水平与发酵能力并无明显关联。S. cerevisiae 亲本品系主要影响挥发性化合物特征,在香气产生方面存在显著差异。有趣的是,从啤酒酿造菌(S. cerevisiae)亲本品系中产生的杂交种表现出与相应的啤酒酿造菌(S. eubayanus)亲本相似的挥发性化合物特征。这种模式可能是由 S. eubayanus 香气特征的显性遗传造成的,与酒精代谢和乙酸酯合成相关的基因在包括啤酒酿造啤酒 S. cerevisiae 品系的杂交种中过度表达也说明了这一点。我们的研究结果表明,亲本品系与杂交结果之间存在复杂的相互作用,凸显了通过杂交策略创造具有独特酿造特性的酵母菌的潜力:我们的研究调查了酿酒酵母与酿酒酵母杂交的原理。这一过程产生了酿酒酵母牧酵母。通过研究这些新型杂交种在发酵过程中的表现及其产生的香气,我们揭示了酿造性状遗传的基因基础。我们利用来自两个亲本物种的不同菌株和品系,主要是三倍体和二倍体,成功地产生了多倍体杂交种。虽然这些杂交种的发酵能力没有得到提高,但它们表现出了不同的性状,尤其是在利用麦芽三糖(酿造中的一种关键糖分)方面。值得注意的是,这些杂交种的香气特征主要受 S. cerevisiae 亲本的影响,而 Beer 系杂交种则采用了其 S. eubayanus 亲本的香气特征。这些发现揭示了杂交酵母中复杂的基因相互作用,为制造具有理想性状的独特酿酒酵母提供了新的可能性。
{"title":"Understanding brewing trait inheritance in <i>de novo</i> Lager yeast hybrids.","authors":"Vasni Zavaleta, Laura Pérez-Través, Luis A Saona, Carlos A Villarroel, Amparo Querol, Francisco A Cubillos","doi":"10.1128/msystems.00762-24","DOIUrl":"https://doi.org/10.1128/msystems.00762-24","url":null,"abstract":"<p><p>Hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i> resulted in the emergence of <i>S. pastorianus</i>, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of <i>S. eubayanus</i> parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in <i>S. cerevisiae</i> and <i>S. eubayanus</i>, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The <i>S. cerevisiae</i> parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer <i>S. cerevisiae</i> parental lineages exhibited a volatile compound profile resembling the corresponding <i>S. eubayanus</i> parent. This pattern may result from the dominant inheritance of the <i>S. eubayanus</i> aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer <i>S. cerevisiae</i> lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.</p><p><strong>Importance: </strong>Our study investigates the principles of lager yeast hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i>. This process gave rise to the lager yeast <i>Saccharomyces pastorianus</i>. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the <i>S. cerevisiae</i> parent, with Beer lineage hybrids adopting aroma characteristics from their <i>S. eubayanus</i> parent. These insights reveal the complex genetic interactions in hybrid yeasts, openin","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0076224"},"PeriodicalIF":5.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-12DOI: 10.1128/msystems.01142-24
Ye Jin, Chenyang Gao, Gaoqin Teng, Zhenchao Zhou, Wangxiao Zhou, Man Huang
<p><p><i>Staphylococcus aureus</i> sequence type (ST) 88, encompassing both methicillin-resistant <i>S. aureus</i> (MRSA) and methicillin-sensitive <i>S. aureus</i> (MSSA) phenotypes, is globally prevalent and commonly associated with skin and soft tissue infections. Despite its widespread occurrence, comprehensive genomic studies on this clone remain scarce. In this study, we performed detailed genomic analyses on 130 ST88 isolates derived from severe bloodstream infections alongside 275 publicly available ST88 sequences. Our phylogenetic analysis identified four distinct clades, with evidence suggesting independent evolution and significant clonal expansion of ST88 in China, particularly within clade I, which appeared to have emerged circa 1964. We documented notable interregional, international, and even intercontinental transmission of ST88 isolates. Variability in the distribution of SCC<i>mec</i> and <i>spa</i> types was observed across clades. Our <i>in silico</i> analyses indicated distinct patterns in the distribution of resistance genes, virulence genes, and mobile genetic elements among the clades, with clade I notably harboring the highest prevalence of the intact <i>sraP</i> gene and an independently acquired novel prophage, φST88-1. Conversely, clade IV exhibited deletions within the <i>sasC</i> gene, with certain sub-clades lacking the <i>sdrDE</i> and <i>fnbB</i> genes, underscoring the superior adhesive capabilities of clade I. <i>In vitro</i> experiments confirmed enhanced biofilm formation in clade I isolates, although the levels of hemolysis and cytotoxicity were similar across clades. Pan-genome-wide association study revealed that core SNPs, rather than the accessory genome, are the primary contributors to the diversification of the ST88 clades. These findings enrich our understanding of the genetic foundations underpinning the transmission dynamics and phenotypic diversity of ST88 clones globally.IMPORTANCEUnderstanding the evolution and transmission of <i>Staphylococcus aureus</i> ST88 clones is critically important due to their spread within food, hospital, and community environments, leading to significant health issues. Despite its prevalence, detailed genomic insights into ST88, particularly regarding its diversity and evolutionary dynamics, have been lacking. Our comprehensive genomic analysis of 130 ST88 isolates from severe bloodstream infections, alongside 275 sequences from public databases, significantly advances our understanding of this pathogen. We identified four distinct evolutionary clades, demonstrating the independent evolution and substantial clonal expansion of ST88 in China, as well as its ability to spread across regions and continents. The diversity among the isolates was evident in their unique profiles of <i>SCCmec</i> elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. Our findings underscore the critical role of core genomic variations over accessory elements in d
{"title":"Dissecting the genetic features and evolution of <i>Staphylococcus aureus</i> sequence type 88: a global perspective.","authors":"Ye Jin, Chenyang Gao, Gaoqin Teng, Zhenchao Zhou, Wangxiao Zhou, Man Huang","doi":"10.1128/msystems.01142-24","DOIUrl":"https://doi.org/10.1128/msystems.01142-24","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> sequence type (ST) 88, encompassing both methicillin-resistant <i>S. aureus</i> (MRSA) and methicillin-sensitive <i>S. aureus</i> (MSSA) phenotypes, is globally prevalent and commonly associated with skin and soft tissue infections. Despite its widespread occurrence, comprehensive genomic studies on this clone remain scarce. In this study, we performed detailed genomic analyses on 130 ST88 isolates derived from severe bloodstream infections alongside 275 publicly available ST88 sequences. Our phylogenetic analysis identified four distinct clades, with evidence suggesting independent evolution and significant clonal expansion of ST88 in China, particularly within clade I, which appeared to have emerged circa 1964. We documented notable interregional, international, and even intercontinental transmission of ST88 isolates. Variability in the distribution of SCC<i>mec</i> and <i>spa</i> types was observed across clades. Our <i>in silico</i> analyses indicated distinct patterns in the distribution of resistance genes, virulence genes, and mobile genetic elements among the clades, with clade I notably harboring the highest prevalence of the intact <i>sraP</i> gene and an independently acquired novel prophage, φST88-1. Conversely, clade IV exhibited deletions within the <i>sasC</i> gene, with certain sub-clades lacking the <i>sdrDE</i> and <i>fnbB</i> genes, underscoring the superior adhesive capabilities of clade I. <i>In vitro</i> experiments confirmed enhanced biofilm formation in clade I isolates, although the levels of hemolysis and cytotoxicity were similar across clades. Pan-genome-wide association study revealed that core SNPs, rather than the accessory genome, are the primary contributors to the diversification of the ST88 clades. These findings enrich our understanding of the genetic foundations underpinning the transmission dynamics and phenotypic diversity of ST88 clones globally.IMPORTANCEUnderstanding the evolution and transmission of <i>Staphylococcus aureus</i> ST88 clones is critically important due to their spread within food, hospital, and community environments, leading to significant health issues. Despite its prevalence, detailed genomic insights into ST88, particularly regarding its diversity and evolutionary dynamics, have been lacking. Our comprehensive genomic analysis of 130 ST88 isolates from severe bloodstream infections, alongside 275 sequences from public databases, significantly advances our understanding of this pathogen. We identified four distinct evolutionary clades, demonstrating the independent evolution and substantial clonal expansion of ST88 in China, as well as its ability to spread across regions and continents. The diversity among the isolates was evident in their unique profiles of <i>SCCmec</i> elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. Our findings underscore the critical role of core genomic variations over accessory elements in d","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0114224"},"PeriodicalIF":5.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microbial transformation is a favored approach for environmental remediation. However, the effectiveness of microbial remediation has been limited by the lack of chassis cells with satisfactory contaminant degradation performance. Pseudomonas putida B6-2, with a wide substrate spectrum and high solvent tolerance, is a chassis strain with great potential for application in environmental remediation. Here, guided by bioinformatic analyses and genome-scale metabolic model (GEM) predictions, we successfully optimized P. putida B6-2 by rationally reducing its nonessential genetic components and generating a more robust genome-streamlined strain, P. putida BGR4. Several improvements were observed compared with the original P. putida B6-2 strain, including a 1.4 × 105-fold increase in electroporation efficiency, an 8.3-fold increase in conjugation efficiency, improved glycerol utilization capability, and increased phenol utilization after heterologous expression of the phenol monooxygenase encoded by dmpKLMNOP. Additionally, P. putida BGR4 exhibited enhanced tolerance to several stressors, including starvation, oxidative stress, and DNA damage. Transcriptomic analysis revealed that genome streamlining led to the upregulation of genes involved in the "carbon metabolism" and "tricarboxylic acid cycle" pathways in P. putida BGR4, which likely contributed to the superior phenotype of P. putida BGR4 in terms of carbon source utilization and contaminant degradation capabilities. Furthermore, the absence of four prophages was identified as a potential cause of the enhanced stress resistance observed in P. putida BGR4. Overall, we developed a combined genome-streamlining strategy involving bioinformatic analyses and GEM predictions and generated a more robust chassis strain, P. putida BGR4, which expands the repertoire of chassis cells for environmental remediation.IMPORTANCEDespite the development of many chassis cells, there is still a lack of robust chassis cells with satisfactory contaminant degradation performance. Targeted genome streamlining is an effective way to provide powerful chassis cells. However, genome streamlining does not always lead to the improved phenotypes of genome-streamlined chassis cells. In this research, a novel procedure that combined bioinformatic analyses and GEM predictions was proposed to guide genome streamlining and predict the effects of genome streamlining. This genome streamlining procedure was successfully applied to Pseudomonas putida B6-2, which was a chassis cell with great potential for application in environmental remediation and resulted in the generation of a more robust chassis cell, P. putida BGR4, thereby providing a superior chassis cell for efficient and sustainable environmental remediation and a valuable framework for guiding the genome streamlining of strains for other applications.
微生物转化是环境修复的首选方法。然而,由于缺乏具有令人满意的污染物降解性能的基质细胞,微生物修复的有效性受到了限制。普氏假单胞菌 B6-2 具有广泛的底物谱和较高的溶剂耐受性,是一种在环境修复中具有巨大应用潜力的基质菌株。在此,我们以生物信息学分析和基因组尺度代谢模型(GEM)预测为指导,通过合理减少非必要的基因成分,成功优化了假单胞菌 B6-2,并产生了一个更强大的基因组精简菌株--假单胞菌 BGR4。与原始的 P. putida B6-2 菌株相比,我们观察到了一些改进,包括电穿孔效率提高了 1.4 × 105 倍,共轭效率提高了 8.3 倍,甘油利用能力提高了,以及异源表达由 dmpKLMNOP 编码的苯酚单加氧酶后苯酚利用率提高了。此外,P. putida BGR4 对饥饿、氧化应激和 DNA 损伤等几种胁迫的耐受性也有所增强。转录组分析表明,基因组精简导致参与 P. putida BGR4 中 "碳代谢 "和 "三羧酸循环 "途径的基因上调,这可能是 P. putida BGR4 在碳源利用和污染物降解能力方面表现出优异表型的原因。此外,四种噬菌体的缺失也是导致 P. putida BGR4 抗逆性增强的潜在原因。总之,我们开发了一种涉及生物信息学分析和 GEM 预测的联合基因组精简策略,并产生了一种更稳健的底盘菌株 P. putida BGR4,从而扩大了用于环境修复的底盘细胞的范围。重要意义尽管开发了许多底盘细胞,但仍然缺乏具有令人满意的污染物降解性能的稳健底盘细胞。有针对性地精简基因组是提供强大底盘细胞的有效方法。然而,基因组精简并不总能改善基因组精简后底盘细胞的表型。本研究提出了一种结合生物信息学分析和 GEM 预测的新程序,用于指导基因组精简和预测基因组精简的效果。该基因组精简程序被成功应用于具有环境修复巨大应用潜力的假单胞菌 B6-2,并产生了更强健的假单胞菌 BGR4,从而为高效和可持续的环境修复提供了一个卓越的底盘细胞,并为指导其他应用菌株的基因组精简提供了一个有价值的框架。
{"title":"Genome streamlining of <i>Pseudomonas putida</i> B6-2 for bioremediation.","authors":"Siqing Fan, Hao Ren, Xueni Fu, Xiangyu Kong, Hao Wu, Zhenmei Lu","doi":"10.1128/msystems.00845-24","DOIUrl":"https://doi.org/10.1128/msystems.00845-24","url":null,"abstract":"<p><p>Microbial transformation is a favored approach for environmental remediation. However, the effectiveness of microbial remediation has been limited by the lack of chassis cells with satisfactory contaminant degradation performance. <i>Pseudomonas putida</i> B6-2, with a wide substrate spectrum and high solvent tolerance, is a chassis strain with great potential for application in environmental remediation. Here, guided by bioinformatic analyses and genome-scale metabolic model (GEM) predictions, we successfully optimized <i>P. putida</i> B6-2 by rationally reducing its nonessential genetic components and generating a more robust genome-streamlined strain, <i>P. putida</i> BGR4. Several improvements were observed compared with the original <i>P. putida</i> B6-2 strain, including a 1.4 × 10<sup>5</sup>-fold increase in electroporation efficiency, an 8.3-fold increase in conjugation efficiency, improved glycerol utilization capability, and increased phenol utilization after heterologous expression of the phenol monooxygenase encoded by <i>dmpKLMNOP</i>. Additionally, <i>P. putida</i> BGR4 exhibited enhanced tolerance to several stressors, including starvation, oxidative stress, and DNA damage. Transcriptomic analysis revealed that genome streamlining led to the upregulation of genes involved in the \"carbon metabolism\" and \"tricarboxylic acid cycle\" pathways in <i>P. putida</i> BGR4, which likely contributed to the superior phenotype of <i>P. putida</i> BGR4 in terms of carbon source utilization and contaminant degradation capabilities. Furthermore, the absence of four prophages was identified as a potential cause of the enhanced stress resistance observed in <i>P. putida</i> BGR4. Overall, we developed a combined genome-streamlining strategy involving bioinformatic analyses and GEM predictions and generated a more robust chassis strain, <i>P. putida</i> BGR4, which expands the repertoire of chassis cells for environmental remediation.IMPORTANCEDespite the development of many chassis cells, there is still a lack of robust chassis cells with satisfactory contaminant degradation performance. Targeted genome streamlining is an effective way to provide powerful chassis cells. However, genome streamlining does not always lead to the improved phenotypes of genome-streamlined chassis cells. In this research, a novel procedure that combined bioinformatic analyses and GEM predictions was proposed to guide genome streamlining and predict the effects of genome streamlining. This genome streamlining procedure was successfully applied to <i>Pseudomonas putida</i> B6-2, which was a chassis cell with great potential for application in environmental remediation and resulted in the generation of a more robust chassis cell, <i>P. putida</i> BGR4, thereby providing a superior chassis cell for efficient and sustainable environmental remediation and a valuable framework for guiding the genome streamlining of strains for other applications.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0084524"},"PeriodicalIF":5.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-11DOI: 10.1128/msystems.01004-24
Harley O'Connor Mount, Malene L Urbanus, Dayag Sheykhkarimli, Atina G Coté, Florent Laval, Georges Coppin, Nishka Kishore, Roujia Li, Kerstin Spirohn-Fitzgerald, Morgan O Petersen, Jennifer J Knapp, Dae-Kyum Kim, Jean-Claude Twizere, Michael A Calderwood, Marc Vidal, Frederick P Roth, Alexander W Ensminger
Legionella pneumophila uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified L. pneumophila effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are "metaeffectors," a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein-protein interactions among all L. pneumophila effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector-effector interactions (doubling the number of known effector-effector interactions).
Importance: Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These "effectors of effectors" or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of Legionella pneumophila, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between L. pneumophila effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.
{"title":"A comprehensive two-hybrid analysis to explore the <i>Legionella pneumophila</i> effector-effector interactome.","authors":"Harley O'Connor Mount, Malene L Urbanus, Dayag Sheykhkarimli, Atina G Coté, Florent Laval, Georges Coppin, Nishka Kishore, Roujia Li, Kerstin Spirohn-Fitzgerald, Morgan O Petersen, Jennifer J Knapp, Dae-Kyum Kim, Jean-Claude Twizere, Michael A Calderwood, Marc Vidal, Frederick P Roth, Alexander W Ensminger","doi":"10.1128/msystems.01004-24","DOIUrl":"https://doi.org/10.1128/msystems.01004-24","url":null,"abstract":"<p><p><i>Legionella pneumophila</i> uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified <i>L. pneumophila</i> effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are \"metaeffectors,\" a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein-protein interactions among all <i>L. pneumophila</i> effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector-effector interactions (doubling the number of known effector-effector interactions).</p><p><strong>Importance: </strong>Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These \"effectors of effectors\" or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of <i>Legionella pneumophila</i>, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between <i>L. pneumophila</i> effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0100424"},"PeriodicalIF":5.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-11DOI: 10.1128/msystems.01416-24
Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert
{"title":"Microbial solutions must be deployed against climate catastrophe.","authors":"Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert","doi":"10.1128/msystems.01416-24","DOIUrl":"https://doi.org/10.1128/msystems.01416-24","url":null,"abstract":"","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0141624"},"PeriodicalIF":5.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}