Pub Date : 2024-09-17DOI: 10.1101/2024.09.17.613493
Anna E. Lindell, Anne Griesshammer, Lena Michaelis, Dimitrios Papagiannidis, Hannah Ochner, Stephan Kamrad, Rui Guan, Sonja Blasche, Leandro Ventimiglia, Bini Ramachandran, Hilal Ozgur, Aleksej Zelezniak, Nonantzin Beristain-Covarrubias, Juan Carlos Yam-Puc, Indra Roux, Leon P. Barron, Alexandra K. Richardson, Maria Guerra Martin, Vladimir Benes, Nobuhiro Morone, James Thaventhiran, Tanmay A.M. Bharat, Mikhail Savitski, Lisa Maier, Kiran Raosaheb Patil
Per- and polyfluoroalkyl Substances (PFAS) - the so-called 'forever chemicals' - are a major cause of environmental and health concern due to their toxicity and long-term persistence[1,2]. Yet, no efficient mechanisms for their removal have been identified. Here we report bioaccumulation of PFAS by several gut bacterial species over a wide range of concentrations from nanomolar up to 500 μM. For bioaccumulating Bacteroides uniformis, a highly prevalent species, we estimate intracellular PFAS concentration in the mM range - above that of most native metabolites. Despite this high bioaccumulation, B. uniformis cells could grow appreciably up to 250 μM perfluorononanoic acid (PFNA) exposure. Escherichia coli, which accumulated PFAS to a much lesser extent, substantially increased PFAS bioaccumulation when lacking TolC efflux pump indicating trans-membrane transport in PFAS bioaccumulation. Electron microscopy and cryogenic Focused Ion Beam-Secondary Ion Mass-spectrometry revealed distinct morphological changes and intracellular localisation of PFNA aggregates. Bioaccumulation of PFAS and transmembrane transport is also evident in proteomics, metabolomics, thermal proteome profiling, and mutations following adaptive laboratory evolution. In an in vivo context, mice colonized with human gut bacteria showed, compared to germ-free controls or those colonized with low-bioaccumulating bacteria, higher PFNA levels in excreted feces. As the gut microbiota is a critical interface between exposure and human body, our results have implications for understanding and utilizing microbial contribution to PFAS clearance.
{"title":"Extensive PFAS accumulation by human gut bacteria","authors":"Anna E. Lindell, Anne Griesshammer, Lena Michaelis, Dimitrios Papagiannidis, Hannah Ochner, Stephan Kamrad, Rui Guan, Sonja Blasche, Leandro Ventimiglia, Bini Ramachandran, Hilal Ozgur, Aleksej Zelezniak, Nonantzin Beristain-Covarrubias, Juan Carlos Yam-Puc, Indra Roux, Leon P. Barron, Alexandra K. Richardson, Maria Guerra Martin, Vladimir Benes, Nobuhiro Morone, James Thaventhiran, Tanmay A.M. Bharat, Mikhail Savitski, Lisa Maier, Kiran Raosaheb Patil","doi":"10.1101/2024.09.17.613493","DOIUrl":"https://doi.org/10.1101/2024.09.17.613493","url":null,"abstract":"Per- and polyfluoroalkyl Substances (PFAS) - the so-called 'forever chemicals' - are a major cause of environmental and health concern due to their toxicity and long-term persistence[1,2]. Yet, no efficient mechanisms for their removal have been identified. Here we report bioaccumulation of PFAS by several gut bacterial species over a wide range of concentrations from nanomolar up to 500 μM. For bioaccumulating <em>Bacteroides uniformis</em>, a highly prevalent species, we estimate intracellular PFAS concentration in the mM range - above that of most native metabolites. Despite this high bioaccumulation, <em>B. uniformis</em> cells could grow appreciably up to 250 μM perfluorononanoic acid (PFNA) exposure. <em>Escherichia coli</em>, which accumulated PFAS to a much lesser extent, substantially increased PFAS bioaccumulation when lacking TolC efflux pump indicating trans-membrane transport in PFAS bioaccumulation. Electron microscopy and cryogenic Focused Ion Beam-Secondary Ion Mass-spectrometry revealed distinct morphological changes and intracellular localisation of PFNA aggregates. Bioaccumulation of PFAS and transmembrane transport is also evident in proteomics, metabolomics, thermal proteome profiling, and mutations following adaptive laboratory evolution. In an in vivo context, mice colonized with human gut bacteria showed, compared to germ-free controls or those colonized with low-bioaccumulating bacteria, higher PFNA levels in excreted feces. As the gut microbiota is a critical interface between exposure and human body, our results have implications for understanding and utilizing microbial contribution to PFAS clearance.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259495","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.17.613397
Shauna Richards, Davide Pagnossin, Paul Samson Buyugu, Oliver Manangwa, Furaha Mramba, Emmanuel Sindoya, Edith Paxton, Steve J. Torr, Ryan Ritchie, Giovanni E. Rossi, Lawrence Nnadozie Anyanwu, Michael Barrett, Liam J. Morrison, Harriet Auty
African animal trypanosomosis (AAT) in cattle is primarily managed through trypanocide administration and insecticide application. Trypanocides can be used for both treatment and prophylaxis, but failure is often reported; this may occur due to resistance, substandard drugs, or inappropriate administration. This study in Tanzania aims to quantify reasons for trypanocide failure. An observational year-long longitudinal study was conducted in high-risk AAT areas in Serengeti District from December 2019-October 2022. Purposive sampling targeted herds with high utilization of the prophylactic trypanocide isometamidium chloride (ISM). When a farmer administered a trypanocide (ISM, diminazine aceturate, homidium), the project veterinarian assessed administration and treatment outcomes were determined based on PCR results from blood samples. A multivariable mixed model was utilized to evaluate risk factors for prophylaxis failure. Quality analysis was performed on trypanocide samples using High Performance Liquid Chromatography. A total of 630 cattle from 21 farms were monitored for a year-long period. A total of 295 trypanocide administrations were reported, predominantly being ISM (56%) used for prophylaxis (87%). One-third of trypanocide administrations were not given adequately, and many trypanocides were given to animals that tested negative for trypanosome infections by PCR. Failures occurred in 7% (95% CI 3.0-14%) of curative treatments, and 44% (95% CI 35-42%) of prophylactic administrations. The brand of ISM was significantly associated with odds of prophylaxis failure (p = 0.011). On quality analysis, two ISM samples had no detectable ISM isomers, but the remainder of ISM and DA samples (n=46) fell within the range of acceptable levels. Drug counterfeiting, inadequate use of trypanocides, and resistance are all contributing to trypanocide failure, limiting effective AAT control and with implications for human disease risk. In order to curb trypanocide failure a multi-modal approach to managing the use of trypanocides is required to address all contributing factors.
牛的非洲动物锥虫病（AAT）主要通过使用杀锥虫剂和杀虫剂来控制。杀锥虫剂可用于治疗和预防，但经常有失败的报道；失败的原因可能是抗药性、药物不达标或用药不当。这项在坦桑尼亚开展的研究旨在量化杀锥虫失败的原因。从 2019 年 12 月到 2022 年 10 月，在塞伦盖蒂区的高风险 AAT 地区开展了为期一年的纵向观察研究。有目的的取样以预防性杀锥虫药异甲脒氯化物（ISM）使用率高的牧群为目标。当牧场主施用杀锥虫剂（ISM、乙酸二甲脒、高脒）时，项目兽医会对施用情况进行评估，并根据血样的 PCR 结果确定治疗效果。采用多变量混合模型评估预防失败的风险因素。使用高效液相色谱法对杀灭锥虫剂样本进行了质量分析。对 21 个农场的 630 头牛进行了为期一年的监测。报告共使用了 295 次杀灭锥虫药物，主要是用于预防的 ISM（56%）（87%）。三分之一的锥虫灭活剂使用不充分，许多锥虫灭活剂是给经 PCR 检测锥虫感染呈阴性的动物使用的。7%（95% CI 3.0-14%）的治疗性用药和44%（95% CI 35-42%）的预防性用药出现失败。ISM的品牌与预防失败的几率明显相关（p = 0.011）。在质量分析中，有两个 ISM 样品未检测到 ISM 异构体，但其余的 ISM 和 DA 样品（n=46）均在可接受水平范围内。药物造假、杀灭锥虫剂使用不当以及抗药性都是导致杀灭锥虫剂失效的原因，从而限制了对急性疟原虫的有效控制，并对人类疾病风险产生了影响。为了遏制杀灭锥虫失败，需要采取多模式方法来管理杀灭锥虫剂的使用，以解决所有诱因。
{"title":"Title Longitudinal Observational (single cohort) Study on the Causes of Trypanocide Failure in cases of African Animal Trypanosomosis in Cattle Near Wildlife Protected Areas of Northern Tanzania","authors":"Shauna Richards, Davide Pagnossin, Paul Samson Buyugu, Oliver Manangwa, Furaha Mramba, Emmanuel Sindoya, Edith Paxton, Steve J. Torr, Ryan Ritchie, Giovanni E. Rossi, Lawrence Nnadozie Anyanwu, Michael Barrett, Liam J. Morrison, Harriet Auty","doi":"10.1101/2024.09.17.613397","DOIUrl":"https://doi.org/10.1101/2024.09.17.613397","url":null,"abstract":"African animal trypanosomosis (AAT) in cattle is primarily managed through trypanocide administration and insecticide application. Trypanocides can be used for both treatment and prophylaxis, but failure is often reported; this may occur due to resistance, substandard drugs, or inappropriate administration. This study in Tanzania aims to quantify reasons for trypanocide failure. An observational year-long longitudinal study was conducted in high-risk AAT areas in Serengeti District from December 2019-October 2022. Purposive sampling targeted herds with high utilization of the prophylactic trypanocide isometamidium chloride (ISM). When a farmer administered a trypanocide (ISM, diminazine aceturate, homidium), the project veterinarian assessed administration and treatment outcomes were determined based on PCR results from blood samples. A multivariable mixed model was utilized to evaluate risk factors for prophylaxis failure. Quality analysis was performed on trypanocide samples using High Performance Liquid Chromatography. A total of 630 cattle from 21 farms were monitored for a year-long period. A total of 295 trypanocide administrations were reported, predominantly being ISM (56%) used for prophylaxis (87%). One-third of trypanocide administrations were not given adequately, and many trypanocides were given to animals that tested negative for trypanosome infections by PCR. Failures occurred in 7% (95% CI 3.0-14%) of curative treatments, and 44% (95% CI 35-42%) of prophylactic administrations. The brand of ISM was significantly associated with odds of prophylaxis failure (p = 0.011). On quality analysis, two ISM samples had no detectable ISM isomers, but the remainder of ISM and DA samples (n=46) fell within the range of acceptable levels. Drug counterfeiting, inadequate use of trypanocides, and resistance are all contributing to trypanocide failure, limiting effective AAT control and with implications for human disease risk. In order to curb trypanocide failure a multi-modal approach to managing the use of trypanocides is required to address all contributing factors.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259489","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.08.611882
Gursonika Binepal, Emil Jurga, Duncan Carruthers-Lay, Sören Krüger, Sandra Zittermann, Jessica Minion, Mathew Diggle, David C. Alexander, Irene Martin, Vanessa Allen, John Parkinson, Scott D. Gray-Owen
The incidence of disseminated gonococcal infection (DGI) has remained low since the advent of antibiotics, however recent surge in DGI have inexplicably emerged within several regions during the past decade. In an effort to understand whether Neisseria gonorrhoeae that cause disseminated disease can be differentiated from non-invasive strains, we have performed a phenotypic and genotypic analysis on a selection of isolates obtained from invasive and uncomplicated infections in Canada. Phenotypic analysis of a matched subset of 19 isolates obtained since 2013 found that these varied in their capacity to aggregate in suspension and in their association with serum complement proteins, however these interactions did not discriminate between the invasive and mucosal isolates. Sequence typing of 360 Canadian isolates revealed that two porB alleles are significantly associated with the DGI strains, one of these being present throughout the past decade whereas the other became associated more recently. A PopNet-based population dynamics analysis, which instead establishes relationships based upon variance among discrete chromosomal segments, found that DGI isolates were restricted in their phylogenetic distribution. While this implies a genetically-linked potential to cause invasive disease, it cannot distinguish between an inherent difference in the phenotype of these populations or the horizontal exchange of some virulence factor among closely related strains. Regardless, a large number of genetic determinants are enriched in the DGI strains, making these enticing candidates for future work to understand how they might either promote the gonococcal capacity to cause systemic infection or reduce the presentation of clinical symptoms from localized infection so that it remains untreated.
{"title":"Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada","authors":"Gursonika Binepal, Emil Jurga, Duncan Carruthers-Lay, Sören Krüger, Sandra Zittermann, Jessica Minion, Mathew Diggle, David C. Alexander, Irene Martin, Vanessa Allen, John Parkinson, Scott D. Gray-Owen","doi":"10.1101/2024.09.08.611882","DOIUrl":"https://doi.org/10.1101/2024.09.08.611882","url":null,"abstract":"The incidence of disseminated gonococcal infection (DGI) has remained low since the advent of antibiotics, however recent surge in DGI have inexplicably emerged within several regions during the past decade. In an effort to understand whether Neisseria gonorrhoeae that cause disseminated disease can be differentiated from non-invasive strains, we have performed a phenotypic and genotypic analysis on a selection of isolates obtained from invasive and uncomplicated infections in Canada. Phenotypic analysis of a matched subset of 19 isolates obtained since 2013 found that these varied in their capacity to aggregate in suspension and in their association with serum complement proteins, however these interactions did not discriminate between the invasive and mucosal isolates. Sequence typing of 360 Canadian isolates revealed that two porB alleles are significantly associated with the DGI strains, one of these being present throughout the past decade whereas the other became associated more recently. A PopNet-based population dynamics analysis, which instead establishes relationships based upon variance among discrete chromosomal segments, found that DGI isolates were restricted in their phylogenetic distribution. While this implies a genetically-linked potential to cause invasive disease, it cannot distinguish between an inherent difference in the phenotype of these populations or the horizontal exchange of some virulence factor among closely related strains. Regardless, a large number of genetic determinants are enriched in the DGI strains, making these enticing candidates for future work to understand how they might either promote the gonococcal capacity to cause systemic infection or reduce the presentation of clinical symptoms from localized infection so that it remains untreated.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259446","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}
In the oceans, the diversity of phytoplankton primary products supports a wide range of microbial heterotrophs, including bacteria and fungi. The organic substrate dynamics within pelagic microbial communities are strongly controlled by microorganismal interactions, resulting in a dense interactome. While the role of bacteria in the microbial loop is well documented, the degradation capacity and substrate specificity of marine fungi, as well as their role and function in metabolic guilds with bacteria, is comparatively less understood. We chose the polysaccharide laminarin, a major product of marine primary production, as well as oligomeric laminarin subunits and monomeric glucose, to study the degradation capacity of eleven marine yeast isolates from the pelagic microbial community of Helgoland Roads. Our aim was to measure yeast growth and correlate degradation yields and putative intermediate degradation products with the size of laminarin-based organic precursor substrates. We developed a reproducible, temporally resolved, high-throughput growth protocol to measure resource-specific yeast growth. Measurement of temporally fine-scaled growth kinetic models of isolates were accompanied with qualitative and quantitative chemical analyses of substrates and degradation intermediates. Our data showed that yeast growth was negatively correlated with oligomer length. Fluorophore-assisted carbohydrate electrophoresis suggested the lack of enzymatic endo-activity for laminarin in yeasts under investigation, suggesting they may occupy a niche in the microbial loop, benefitting from extracellular hydrolysis of carbohydrates by other microorganisms. In terrestrial environments, namely forest soil ecosystems, yeasts have been assigned a similar niche, supporting a prominent role of yeasts in microbial interactomes.
{"title":"Utilization and degradation of laminarin-based substrates by marine yeasts suggests their niche-specific role in microbial loop dynamics.","authors":"Berin Arslan-Gatz, Mikkel Schultz-Johansen, Tom-Niklas Hollwedel, Sofie Niggemeier, Rolf Nimzyk, Antje Wichels, Gunnar Gerdts, Jan-Hendrik Hehemann, Tilmann Harder, Marlis Reich","doi":"10.1101/2024.09.13.612705","DOIUrl":"https://doi.org/10.1101/2024.09.13.612705","url":null,"abstract":"In the oceans, the diversity of phytoplankton primary products supports a wide range of microbial heterotrophs, including bacteria and fungi. The organic substrate dynamics within pelagic microbial communities are strongly controlled by microorganismal interactions, resulting in a dense interactome. While the role of bacteria in the microbial loop is well documented, the degradation capacity and substrate specificity of marine fungi, as well as their role and function in metabolic guilds with bacteria, is comparatively less understood. We chose the polysaccharide laminarin, a major product of marine primary production, as well as oligomeric laminarin subunits and monomeric glucose, to study the degradation capacity of eleven marine yeast isolates from the pelagic microbial community of Helgoland Roads. Our aim was to measure yeast growth and correlate degradation yields and putative intermediate degradation products with the size of laminarin-based organic precursor substrates. We developed a reproducible, temporally resolved, high-throughput growth protocol to measure resource-specific yeast growth. Measurement of temporally fine-scaled growth kinetic models of isolates were accompanied with qualitative and quantitative chemical analyses of substrates and degradation intermediates. Our data showed that yeast growth was negatively correlated with oligomer length. Fluorophore-assisted carbohydrate electrophoresis suggested the lack of enzymatic endo-activity for laminarin in yeasts under investigation, suggesting they may occupy a niche in the microbial loop, benefitting from extracellular hydrolysis of carbohydrates by other microorganisms. In terrestrial environments, namely forest soil ecosystems, yeasts have been assigned a similar niche, supporting a prominent role of yeasts in microbial interactomes.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259525","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.17.613401
Indika Senavirathna, Dinesha Jayasundara, Janith Warnasekara, Suneth B Agampodi, Ellie J. Putz, Jarlath E. Nally, Darrell O. Bayles, Reetika Chaurasia, Joseph M. Vinetz
Leptospira borgpetersenii commonly causes human leptospirosis, including severe disease. The first published analysis of L. borgpetersenii, performed on two strains of serovar Hardjo (L550 and JB197), concluded that the L. borgpetersenii genome is in the process of genome decay with functional consequences leading to a more obligately host-dependent life cycle. Yet whole genome analysis has only been carried out on few strains of L. borgpetersenii, with limited closed genomes and comprehensive analysis. Herein we report the complete, circularized genomes of seven non-Hardjo Leptospira borgpetersenii isolates from human leptospirosis patients in Sri Lanka. These isolates (all ST144) were found to be nearly identical by whole genome analysis; serotyping showed they are a novel serovar. We show that the L. borgpetersenii isolated from humans in Sri Lanka are less genomically decayed than previously reported isolates: fewer pseudogenes (N=141) and Insertion Sequence (IS) elements (N=46) compared to N=248, N=270, and N=400 pseudogenes, and N=121 and N=116 IS elements in published L. borgpetersenii Hardjo genomes (L550, JB197 and TC112). Compared to previously published L. borgpetersenii whole genome analyses showing two to three VM proteins in L. borgpetersenii isolates from cattle, rats and humans, we found that all of the human L. borgpetersenii isolates from Sri Lanka, including previously reported serovar Piyasena, have 4 encoded VM proteins, one ortholog of L. interrogans Copenhageni LIC12339 and 3 orthologs of LIC12844. Our findings of fewer pseudogenes, IS elements and expansion of the LIC12844 homologs of the PF07598 family in these human isolates suggests that this newly identified L. borgpetersenii serovar from Sri Lanka has unique pathogenicity. Comparative genome analysis and experimental studies of these L. borgpetersenii isolates will enable deeper insights into the molecular and cellular mechanisms of leptospirosis pathogenesis.
博格特氏钩端螺旋体（Leptospira borgpetersenii）通常会引起人类钩端螺旋体病，包括严重的疾病。首次发表的对 L. borgpetersenii 的分析是在两个血清 Hardjo 菌株（L550 和 JB197）上进行的，得出的结论是 L. borgpetersenii 基因组正处于基因组衰变过程中，其功能性后果导致其生命周期更加依赖于宿主。然而，全基因组分析只在少数 L. borgpetersenii 菌株上进行过，封闭基因组和全面分析有限。在此，我们报告了从斯里兰卡人类钩端螺旋体病患者中分离出的七株非哈氏钩端螺旋体的完整环化基因组。通过全基因组分析发现，这些分离株（均为 ST144）几乎完全相同；血清分型显示它们是一个新的血清型。我们的研究表明，从斯里兰卡人体内分离出的 L. borgpetersenii 的基因组衰变程度低于之前报道的分离株：与已发表的 L. borgpetersenii Hardjo 基因组（L550、JB197 和 TC112）中的 N=248、N=270 和 N=400 个假基因以及 N=121 和 N=116 个 IS 元素相比，假基因（N=141）和插入序列（IS）元素（N=46）较少。以前发表的 L. borgpetersenii 全基因组分析显示，来自牛、大鼠和人类的 L. borgpetersenii 分离物中有 2 到 3 个 VM 蛋白，与此相比，我们发现来自斯里兰卡的所有人类 L. borgpetersenii 分离物（包括以前报道的 Piyasena 血清菌株）都有 4 个编码的 VM 蛋白，其中一个是 L. interrogans Copenhageni LIC12339 的直向同源物，另一个是 LIC12844 的 3 个直向同源物。我们在这些人类分离株中发现了较少的假基因、IS元件和 PF07598 家族 LIC12844 同源物的扩增，这表明斯里兰卡新发现的 L. borgpetersenii 血清菌具有独特的致病性。对这些 L. borgpetersenii 分离物进行基因组比较分析和实验研究，将有助于深入了解钩端螺旋体病致病的分子和细胞机制。
{"title":"Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates","authors":"Indika Senavirathna, Dinesha Jayasundara, Janith Warnasekara, Suneth B Agampodi, Ellie J. Putz, Jarlath E. Nally, Darrell O. Bayles, Reetika Chaurasia, Joseph M. Vinetz","doi":"10.1101/2024.09.17.613401","DOIUrl":"https://doi.org/10.1101/2024.09.17.613401","url":null,"abstract":"Leptospira borgpetersenii commonly causes human leptospirosis, including severe disease. The first published analysis of L. borgpetersenii, performed on two strains of serovar Hardjo (L550 and JB197), concluded that the L. borgpetersenii genome is in the process of genome decay with functional consequences leading to a more obligately host-dependent life cycle. Yet whole genome analysis has only been carried out on few strains of L. borgpetersenii, with limited closed genomes and comprehensive analysis. Herein we report the complete, circularized genomes of seven non-Hardjo Leptospira borgpetersenii isolates from human leptospirosis patients in Sri Lanka. These isolates (all ST144) were found to be nearly identical by whole genome analysis; serotyping showed they are a novel serovar. We show that the L. borgpetersenii isolated from humans in Sri Lanka are less genomically decayed than previously reported isolates: fewer pseudogenes (N=141) and Insertion Sequence (IS) elements (N=46) compared to N=248, N=270, and N=400 pseudogenes, and N=121 and N=116 IS elements in published L. borgpetersenii Hardjo genomes (L550, JB197 and TC112). Compared to previously published L. borgpetersenii whole genome analyses showing two to three VM proteins in L. borgpetersenii isolates from cattle, rats and humans, we found that all of the human L. borgpetersenii isolates from Sri Lanka, including previously reported serovar Piyasena, have 4 encoded VM proteins, one ortholog of L. interrogans Copenhageni LIC12339 and 3 orthologs of LIC12844. Our findings of fewer pseudogenes, IS elements and expansion of the LIC12844 homologs of the PF07598 family in these human isolates suggests that this newly identified L. borgpetersenii serovar from Sri Lanka has unique pathogenicity. Comparative genome analysis and experimental studies of these L. borgpetersenii isolates will enable deeper insights into the molecular and cellular mechanisms of leptospirosis pathogenesis.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259444","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.17.613263
Oliver JD Charity, Gaetan Thilliez, Haider Al-Khanaq, Luke Acton, Rafal Kolenda, Matt Bawn, Liljana Petrovska, Robert A Kingsley
Bacteriophage (phage) are promising novel antimicrobials but a key challenge to their effective implementation is the rapid emergence of phage resistance. An improved understanding of phage-host interactions is therefore needed. The Anderson phage typing scheme differentiates closely related strains of Salmonella enterica serovar Typhimurium (S. Typhimurium) based on sensitivity to a panel of phage preparations. Switches in phage type are indicative of changes in phage sensitivity and inform on the dynamics of phage interaction with their host bacteria. We investigated the molecular basis of switches between the relatively phage sensitive S. Typhimurium DT8 and phage resistant DT30 strains that are present in the same phylogenetic clade. DT30 strains emerged from DT8 strains predominantly by deletion of a genomic region affecting the wzy locus encoding an O-antigen polymerase. The deletion site was flanked by two perfect direct repeats designated attL and attR. During broth culture in the presence of a typing phage that used O-antigen as primary receptor the Deltawzy genotype increased in frequency compared with culture in the absence of phage and removal of attL prevented deletion of the wzy locus. Co-culture of S. Typhimurium DT8 with a strain lacking wzy resulted in reversion of the latter to wild type. We propose a model in which reversible deletion of the wzy locus enables recovery of S. Typhimurium DT8 following predation by phage that use O-antigen as their primary receptor. This was consistent with ancestral state reconstruction of DT8 and DT30 phylogeny that supported a model of reversible transition from DT8 to DT30 in natural populations.
{"title":"Reversible excision of the wzy locus in Salmonella Typhimurium may aid recovery following phage predation","authors":"Oliver JD Charity, Gaetan Thilliez, Haider Al-Khanaq, Luke Acton, Rafal Kolenda, Matt Bawn, Liljana Petrovska, Robert A Kingsley","doi":"10.1101/2024.09.17.613263","DOIUrl":"https://doi.org/10.1101/2024.09.17.613263","url":null,"abstract":"Bacteriophage (phage) are promising novel antimicrobials but a key challenge to their effective implementation is the rapid emergence of phage resistance. An improved understanding of phage-host interactions is therefore needed. The Anderson phage typing scheme differentiates closely related strains of Salmonella enterica serovar Typhimurium (S. Typhimurium) based on sensitivity to a panel of phage preparations. Switches in phage type are indicative of changes in phage sensitivity and inform on the dynamics of phage interaction with their host bacteria. We investigated the molecular basis of switches between the relatively phage sensitive S. Typhimurium DT8 and phage resistant DT30 strains that are present in the same phylogenetic clade. DT30 strains emerged from DT8 strains predominantly by deletion of a genomic region affecting the wzy locus encoding an O-antigen polymerase. The deletion site was flanked by two perfect direct repeats designated attL and attR. During broth culture in the presence of a typing phage that used O-antigen as primary receptor the Deltawzy genotype increased in frequency compared with culture in the absence of phage and removal of attL prevented deletion of the wzy locus. Co-culture of S. Typhimurium DT8 with a strain lacking wzy resulted in reversion of the latter to wild type. We propose a model in which reversible deletion of the wzy locus enables recovery of S. Typhimurium DT8 following predation by phage that use O-antigen as their primary receptor. This was consistent with ancestral state reconstruction of DT8 and DT30 phylogeny that supported a model of reversible transition from DT8 to DT30 in natural populations.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259443","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}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.17.613384
Robert Knop, Simon Keweloh, Silvia Dittmann, Daniela Zuehlke, Susanne Sievers
As an intestinal human pathogen, Clostridioides difficile is the main cause of antibiotic-associated diarrhoea. Endospores of this gram-positive bacterium enter the intestinal tract via faecal-oral transmission, germinate into vegetative and toxin-producing cells and can trigger a Clostridioides difficile infection. The microaerophilic conditions (0.1 to 0.4 % O2) of the large intestine represent a challenge for the strictly anaerobic organism, which protects itself by a variety of oxidative stress proteins. Four of these are encoded in an operon that is assumed to be involved in the detoxification of H2O2 and O2●-. This operon encodes a rubrerythrin (rbr), its own transcriptional repressor PerR (perR), a desulfoferrodoxin (rbo) and a putative glutamate dehydrogenase (CD630_08280) with an N-terminal rubredoxin domain, which is only expressed under high oxidative stress conditions. In this study, the enzyme activity of Rbr, Rbo and CD630_08280 was tested in-vitro. Recombinant proteins were overexpressed in C. difficile and purified anaerobically by affinity chromatography. A H2O2 reduction potential was demonstrated for Rbr, Rbo and glutamate dehydrogenase. Rbr and glutamate dehydrogenase proved to synergistically detoxify H2O2 very efficiently. Furthermore, Rbo was verified as a O2●- reductase and its activity compared to the superoxide dismutase of E. coli. The investigated gene locus codes for an oxidative stress operon whose members are able to completely neutralize O2●- and H2O2 to water and could thus be vital for C. difficile to establish an infection in the host.
{"title":"A rubrerythrin locus of Clostridioides difficile efficiently detoxifies reactive oxygen species","authors":"Robert Knop, Simon Keweloh, Silvia Dittmann, Daniela Zuehlke, Susanne Sievers","doi":"10.1101/2024.09.17.613384","DOIUrl":"https://doi.org/10.1101/2024.09.17.613384","url":null,"abstract":"As an intestinal human pathogen, <em>Clostridioides difficile</em> is the main cause of antibiotic-associated diarrhoea. Endospores of this gram-positive bacterium enter the intestinal tract via faecal-oral transmission, germinate into vegetative and toxin-producing cells and can trigger a <em>Clostridioides difficile</em> infection. The microaerophilic conditions (0.1 to 0.4 % O<sub>2</sub>) of the large intestine represent a challenge for the strictly anaerobic organism, which protects itself by a variety of oxidative stress proteins. Four of these are encoded in an operon that is assumed to be involved in the detoxification of H<sub>2</sub>O<sub>2</sub> and O<sub>2</sub><sup>●-</sup>. This operon encodes a rubrerythrin (<em>rbr</em>), its own transcriptional repressor PerR (<em>perR</em>), a desulfoferrodoxin (<em>rbo</em>) and a putative glutamate dehydrogenase (<em>CD630_08280</em>) with an N-terminal rubredoxin domain, which is only expressed under high oxidative stress conditions. In this study, the enzyme activity of Rbr, Rbo and CD630_08280 was tested <em>in-vitro</em>. Recombinant proteins were overexpressed in <em>C. difficile</em> and purified anaerobically by affinity chromatography. A H<sub>2</sub>O<sub>2</sub> reduction potential was demonstrated for Rbr, Rbo and glutamate dehydrogenase. Rbr and glutamate dehydrogenase proved to synergistically detoxify H<sub>2</sub>O<sub>2</sub> very efficiently. Furthermore, Rbo was verified as a O<sub>2</sub><sup>●-</sup> reductase and its activity compared to the superoxide dismutase of <em>E. coli</em>. The investigated gene locus codes for an oxidative stress operon whose members are able to completely neutralize O<sub>2</sub><sup>●-</sup> and H<sub>2</sub>O<sub>2</sub> to water and could thus be vital for <em>C. difficile</em> to establish an infection in the host.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259445","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}
The signal transduction ATPases with numerous domains (STAND) superfamily encompasses widely distributed immune systems across bacteria, eukaryotes and archaea. The bacterial antiviral STAND type 5 (Avs5) contains an N-terminal Sirtuin (SIR2) domain, which protects against phage invasion. Despite the established roles of SIR2 and STAND in prokaryotic and eukaryotic immunity, the mechanism underlying their collaboration remains unclear. Here we present cryo-EM structures of Escherichia fergusonii Avs5 (EfAvs5) filaments, elucidating the mechanisms of dimerization, filamentation, filament clustering, ATP binding and NAD+ hydrolysis, all of which are crucial for anti-phage defense. The SIR2 domains and nucleotide-binding oligomerization domains (NOD) engage in the intra- and inter-dimer interaction to form an individual filament, while the outward C-terminal domains contribute to bundle formation. Filamentation potentially stabilizes the dimeric SIR2 configuration, thereby activating the NADase activity of EfAvs5. EfAvs5 is deficient in the ATPase activity, but elevated ATP concentrations can impede its NADase activity. Together, we uncover the filament assembly of Avs5 as a unique mechanism to switch enzyme activities and perform anti-phage defenses.
具有多个结构域的信号转导 ATP 酶（STAND）超家族包括广泛分布于细菌、真核生物和古细菌的免疫系统。细菌抗病毒 STAND 5 型（Avs5）含有一个 N 端 Sirtuin（SIR2）结构域，能抵御噬菌体的入侵。尽管 SIR2 和 STAND 在原核和真核免疫中的作用已经确立，但它们之间的合作机制仍不清楚。在这里，我们展示了弗氏埃希氏菌 Avs5（EfAvs5）菌丝的冷冻电子显微镜结构，阐明了二聚化、成丝、菌丝集群、ATP 结合和 NAD+ 水解的机制，所有这些都是抗噬菌体防御的关键。SIR2 结构域和核苷酸结合寡聚化结构域（NOD）参与二聚体内部和二聚体之间的相互作用，以形成单个丝状体，而向外的 C 端结构域则有助于丝束的形成。丝状化可能会稳定二聚体 SIR2 的构型，从而激活 EfAvs5 的 NAD 酶活性。EfAvs5 缺乏 ATP 酶活性，但 ATP 浓度升高会阻碍其 NAD 酶活性。综上所述，我们发现 Avs5 的丝状组装是切换酶活性和执行抗噬菌体防御的一种独特机制。
{"title":"Cryo-EM Structure of an Active Bacterial SIR2-STAND Filament","authors":"Yiqun Wang, Yuqing Tian, Xu Yang, Feng Yu, Jianting Zheng","doi":"10.1101/2024.09.15.613165","DOIUrl":"https://doi.org/10.1101/2024.09.15.613165","url":null,"abstract":"The signal transduction ATPases with numerous domains (STAND) superfamily encompasses widely distributed immune systems across bacteria, eukaryotes and archaea. The bacterial antiviral STAND type 5 (Avs5) contains an N-terminal Sirtuin (SIR2) domain, which protects against phage invasion. Despite the established roles of SIR2 and STAND in prokaryotic and eukaryotic immunity, the mechanism underlying their collaboration remains unclear. Here we present cryo-EM structures of Escherichia fergusonii Avs5 (EfAvs5) filaments, elucidating the mechanisms of dimerization, filamentation, filament clustering, ATP binding and NAD+ hydrolysis, all of which are crucial for anti-phage defense. The SIR2 domains and nucleotide-binding oligomerization domains (NOD) engage in the intra- and inter-dimer interaction to form an individual filament, while the outward C-terminal domains contribute to bundle formation. Filamentation potentially stabilizes the dimeric SIR2 configuration, thereby activating the NADase activity of EfAvs5. EfAvs5 is deficient in the ATPase activity, but elevated ATP concentrations can impede its NADase activity. Together, we uncover the filament assembly of Avs5 as a unique mechanism to switch enzyme activities and perform anti-phage defenses.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259491","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}
Pub Date : 2024-09-16DOI: 10.1101/2024.09.13.612970
Sangeevan Vellappan, Junhong Sun, John Favate, Pranavi Jagadeesan, Debbie Cerda, Premal Shah, Srujana S Yadavalli
Signaling networks in bacteria enable sensing and adaptation to environmental conditions by activating specific genes that help counteract stressors. Small proteins (≥50 amino acids long) are a rising class of bacterial stress response regulators. Escherichia coli encodes over 150 small proteins, most of which lack known phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we investigate small proteins induced in response to stress using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, a majority of which are transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, which underscore the physiological significance of their expression in low magnesium stress. Most remarkably, our study reveals that a small membrane protein YoaI is an unusual connector of the major signaling networks – PhoR-PhoB and EnvZ-OmpR in E. coli, advancing our understanding of small protein regulators of cellular signaling.
{"title":"Translational profiling of stress-induced small proteins uncovers an unexpected connection among distinct signaling systems","authors":"Sangeevan Vellappan, Junhong Sun, John Favate, Pranavi Jagadeesan, Debbie Cerda, Premal Shah, Srujana S Yadavalli","doi":"10.1101/2024.09.13.612970","DOIUrl":"https://doi.org/10.1101/2024.09.13.612970","url":null,"abstract":"Signaling networks in bacteria enable sensing and adaptation to environmental conditions by activating specific genes that help counteract stressors. Small proteins (≥50 amino acids long) are a rising class of bacterial stress response regulators. <em>Escherichia coli</em> encodes over 150 small proteins, most of which lack known phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we investigate small proteins induced in response to stress using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, a majority of which are transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, which underscore the physiological significance of their expression in low magnesium stress. Most remarkably, our study reveals that a small membrane protein YoaI is an unusual connector of the major signaling networks – PhoR-PhoB and EnvZ-OmpR in <em>E. coli</em>, advancing our understanding of small protein regulators of cellular signaling.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259499","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}
Pub Date : 2024-09-16DOI: 10.1101/2024.09.12.612785
Samson Ali, Adrian Koh, David Popp, Kotaro Tanaka, Yoshihito Kitaoku, Noriyuki Miyazaki, Kenji Iwasaki, Kaoru Mitsuoka, Robert C Robinson, Akihiro Narita
ParMs generally exist on low copy number plasmids where they contribute to plasmid segregation and stable inheritance. We carried out bioinformatics analysis, which indicated that ParM genes are not only confined to plasmids but are also occasionally found on genomes. Here we report the discovery and characterization of two chromosome encoded ParMs (cParMs) from the genomes of Desulfitobacterium hafniense (Dh-cParM1) and Clostridium botulinum (Cb-cParM). Both cParMs form filaments, exhibit nucleotide hydrolysis, and possess characteristic ParM subunit structures. Dh-cParM1 forms single and tightly coupled double filaments and is highly conserved on the chromosomes of five of six Desulfitobacterium species. Interestingly, these bacteria have not been reported to harbour plasmids. Cb-cParM possesses unique properties. Its filaments were stable after nucleotide hydrolysis and Pi release, and its ParR, (Cb-cParR) did not affect the initial stage of Cb-cParM polymerization but displayed properties of a depolymerization factor for mature filaments. These results indicate functional, polymerizing ParMs can be encoded on genomes, suggesting that ParM roles may extend to other functions beyond plasmid segregation.
{"title":"Bacterial genome encoded ParMs","authors":"Samson Ali, Adrian Koh, David Popp, Kotaro Tanaka, Yoshihito Kitaoku, Noriyuki Miyazaki, Kenji Iwasaki, Kaoru Mitsuoka, Robert C Robinson, Akihiro Narita","doi":"10.1101/2024.09.12.612785","DOIUrl":"https://doi.org/10.1101/2024.09.12.612785","url":null,"abstract":"ParMs generally exist on low copy number plasmids where they contribute to plasmid segregation and stable inheritance. We carried out bioinformatics analysis, which indicated that ParM genes are not only confined to plasmids but are also occasionally found on genomes. Here we report the discovery and characterization of two chromosome encoded ParMs (cParMs) from the genomes of Desulfitobacterium hafniense (Dh-cParM1) and Clostridium botulinum (Cb-cParM). Both cParMs form filaments, exhibit nucleotide hydrolysis, and possess characteristic ParM subunit structures. Dh-cParM1 forms single and tightly coupled double filaments and is highly conserved on the chromosomes of five of six Desulfitobacterium species. Interestingly, these bacteria have not been reported to harbour plasmids. Cb-cParM possesses unique properties. Its filaments were stable after nucleotide hydrolysis and Pi release, and its ParR, (Cb-cParR) did not affect the initial stage of Cb-cParM polymerization but displayed properties of a depolymerization factor for mature filaments. These results indicate functional, polymerizing ParMs can be encoded on genomes, suggesting that ParM roles may extend to other functions beyond plasmid segregation.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259496","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：