Armando Alibrandi, Rolando di Primio, Alexander Bartholomäus, Jens Kallmeyer
Abstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 10 1 –10 3 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.
来自油藏的微生物通过生物降解或酸化等过程形成石油成分。这些工艺被认为对经济有害，并可能对健康和安全造成危害。因此，了解储层微生物群落的组成及其代谢能力至关重要。然而，这种分析受到从原油等复杂液体中提取DNA的困难的阻碍。在这里，我们提出了一种新的DNA提取方法，从石油具有广泛的美国石油协会(API)的重力(密度)范围。我们研究了不同溶剂和表面活性剂(非离子型和离子型)从油脂中提取细胞的能力。此外，我们评估了三种DNA提取方法。总的来说，使用异辛烷作为溶剂，然后使用十二烷基硫酸钠进行离子表面活性剂处理，使用PowerSoil Pro Kit (Qiagen)进行DNA提取，获得了最佳的DNA产量和最高的16S rRNA读取数。然后将最后的方法应用于在无菌条件下从油藏中收集的各种油。尽管预期的低细胞密度为10 1 -10 3个细胞/ml，但新方法获得了可靠的结果，平均16S rRNA测序读数为41431(±8860)个样本。在所有样品中都发现了嗜热、嗜盐和厌氧分类群，这些分类群最有可能是油藏的土生性。原料药重力和DNA产率，尽管获得了足够的DNA，没有显示出相关性。
{"title":"A modified isooctane‐based DNA extraction method from crude oil","authors":"Armando Alibrandi, Rolando di Primio, Alexander Bartholomäus, Jens Kallmeyer","doi":"10.1002/mlf2.12081","DOIUrl":"https://doi.org/10.1002/mlf2.12081","url":null,"abstract":"Abstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 10 1 –10 3 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135588201","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}
Gong Li, Ling Jia, Lei Wan, Lijuan Xia, Ang Gao, Runshi Yang, Ruanyang Sun, Minge Wang, Juan Du, Xinlei Lian, Rongmin Zhang, Liangxing Fang, Xiaoping Liao, Yahong Liu, Bao‐Tao Liu, Jian Sun
Abstract The co‐occurrence of plasmid‐mediated multidrug resistance and hypervirulence in epidemic carbapenem‐resistant Klebsiella pneumoniae has emerged as a global public health issue. In this study, an ST23 carbapenem‐resistant hypervirulent K. pneumoniae (CR‐HvKP) strain VH1‐2 was identified from cucumber in China and harbored a novel hybrid plasmid pVH1‐2‐VIR. The plasmid pVH1‐2‐VIR carrying both virulence and multidrug‐resistance (MDR) genes was likely generated through the recombination of a virulence plasmid and an IncFIIK conjugative MDR plasmid in clinical ST23 18622 isolated from a sputum sample. The plasmid pVH1‐2‐VIR exhibited the capacity for transfer to the clinical ST11 carbapenem‐resistant K. pneumoniae (CRKP) strain via conjugation assay. Acquisition of pVH1‐2‐VIR plasmid directly converted a CRKP into CR‐HvKP strain characterized by hypermucoviscosity, heightened virulence for Galleria mellonella larvae, and increased colonization ability in the mouse intestine. The emergence of such a hybrid plasmid may expedite the spread of CR‐HvKP strains, posing a significant risk to human health.
{"title":"Acquisition of a novel conjugative multidrug‐resistant hypervirulent plasmid leads to hypervirulence in clinical carbapenem‐resistant <i>Klebsiella pneumoniae</i> strains","authors":"Gong Li, Ling Jia, Lei Wan, Lijuan Xia, Ang Gao, Runshi Yang, Ruanyang Sun, Minge Wang, Juan Du, Xinlei Lian, Rongmin Zhang, Liangxing Fang, Xiaoping Liao, Yahong Liu, Bao‐Tao Liu, Jian Sun","doi":"10.1002/mlf2.12086","DOIUrl":"https://doi.org/10.1002/mlf2.12086","url":null,"abstract":"Abstract The co‐occurrence of plasmid‐mediated multidrug resistance and hypervirulence in epidemic carbapenem‐resistant Klebsiella pneumoniae has emerged as a global public health issue. In this study, an ST23 carbapenem‐resistant hypervirulent K. pneumoniae (CR‐HvKP) strain VH1‐2 was identified from cucumber in China and harbored a novel hybrid plasmid pVH1‐2‐VIR. The plasmid pVH1‐2‐VIR carrying both virulence and multidrug‐resistance (MDR) genes was likely generated through the recombination of a virulence plasmid and an IncFIIK conjugative MDR plasmid in clinical ST23 18622 isolated from a sputum sample. The plasmid pVH1‐2‐VIR exhibited the capacity for transfer to the clinical ST11 carbapenem‐resistant K. pneumoniae (CRKP) strain via conjugation assay. Acquisition of pVH1‐2‐VIR plasmid directly converted a CRKP into CR‐HvKP strain characterized by hypermucoviscosity, heightened virulence for Galleria mellonella larvae, and increased colonization ability in the mouse intestine. The emergence of such a hybrid plasmid may expedite the spread of CR‐HvKP strains, posing a significant risk to human health.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135587902","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 recounting Dr. James M. Tiedje's outstanding research achievements spanning the past 55 years, it is easy to overlook his early and mid-career endeavors. Specifically, his contribution to the aerobic degradation of pesticides and other chemicals, as well as methanogenic degradation of those compounds retains their brilliance. Many researchers in environmental microbiology have gained invaluable knowledge from these studies, which have been applied to the elucidation of previously uncultivated microorganisms. Dr. Tiedje embarked on his career in soil microbiology at Cornell University in 1964 under the guidance of Martin Alexander. Motivated by Rachel Carson's Silent Spring published in 1962, he developed a keen interest in studying the degradation of 2,4-dichlorophenoxy acetic acid (2,4-D), widely used as a broad-leaf herbicide. Dr. Tiedje found that an Arthrobacter species converts 2,4-D into chlorocatechols, facilitated by a soluble ether linkage-cleaving enzyme1, 2. Subsequently, extensive investigations into the 2,4-D degradation by aerobic microorganisms were conducted, leading to the identification of α-ketoglutarate-dependent dioxygenase, the enzyme involved in the first step of 2,4-D metabolism3 (Figure 1). The story starts with my involvement in the “2,4-D project.” The project took place at the Center for Microbial Ecology, Michigan State University (MSU), where we focused on microbial evolution. 2,4-D, being an anthropogenic chemical with no analogous compounds found in nature, provided an excellent opportunity to explore how enzymes with different original functions were recruited and evolved to adapt to 2,4-D degradation. The project was initiated by Profs. James M. Tiedje and Keiji Yano (followed by Prof. Koki Horikoshi) in 1991 and received funding from Japan Science and Technology Agency (JST, formerly JRDC) and National Science Foundation USA. It involved numerous scientists and over 10 postdocs from various parts of the world. It was the mid-1990s, a time before high-throughput genome sequencing became available, and molecular biological studies were conducted using classical methods such as DNA sequencing using big gel plates. During this period, I had been working on methanogenic Archaea till I joined the project. To begin, we initiated genetic analysis of known 2,4-D-degraders, as well as search for previously unknown 2,4-D-degrading microbes4, 5. Meanwhile, Dr. Tiedje, who was supposed to lead the project, was on sabbatical, enjoying the warmer climate of Hawaii (quite different from Michigan) and collaborating with Hawaiian researchers. He learned that there were soils in Hawaii that had not been exposed to 2,4-D, and he brought those untouched soils back to Michigan. The underlying idea was to investigate whether the microorganisms capable of breaking down this widely used chemical, which was artificially synthesized and sprayed in large quantities, were absent in the Hawaiian soils, or there were microbes possessing th
{"title":"Cultivating the unseen: Lessons from James Tiedje","authors":"Yoichi Kamagata","doi":"10.1002/mlf2.12083","DOIUrl":"https://doi.org/10.1002/mlf2.12083","url":null,"abstract":"In recounting Dr. James M. Tiedje's outstanding research achievements spanning the past 55 years, it is easy to overlook his early and mid-career endeavors. Specifically, his contribution to the aerobic degradation of pesticides and other chemicals, as well as methanogenic degradation of those compounds retains their brilliance. Many researchers in environmental microbiology have gained invaluable knowledge from these studies, which have been applied to the elucidation of previously uncultivated microorganisms. Dr. Tiedje embarked on his career in soil microbiology at Cornell University in 1964 under the guidance of Martin Alexander. Motivated by Rachel Carson's Silent Spring published in 1962, he developed a keen interest in studying the degradation of 2,4-dichlorophenoxy acetic acid (2,4-D), widely used as a broad-leaf herbicide. Dr. Tiedje found that an Arthrobacter species converts 2,4-D into chlorocatechols, facilitated by a soluble ether linkage-cleaving enzyme1, 2. Subsequently, extensive investigations into the 2,4-D degradation by aerobic microorganisms were conducted, leading to the identification of α-ketoglutarate-dependent dioxygenase, the enzyme involved in the first step of 2,4-D metabolism3 (Figure 1). The story starts with my involvement in the “2,4-D project.” The project took place at the Center for Microbial Ecology, Michigan State University (MSU), where we focused on microbial evolution. 2,4-D, being an anthropogenic chemical with no analogous compounds found in nature, provided an excellent opportunity to explore how enzymes with different original functions were recruited and evolved to adapt to 2,4-D degradation. The project was initiated by Profs. James M. Tiedje and Keiji Yano (followed by Prof. Koki Horikoshi) in 1991 and received funding from Japan Science and Technology Agency (JST, formerly JRDC) and National Science Foundation USA. It involved numerous scientists and over 10 postdocs from various parts of the world. It was the mid-1990s, a time before high-throughput genome sequencing became available, and molecular biological studies were conducted using classical methods such as DNA sequencing using big gel plates. During this period, I had been working on methanogenic Archaea till I joined the project. To begin, we initiated genetic analysis of known 2,4-D-degraders, as well as search for previously unknown 2,4-D-degrading microbes4, 5. Meanwhile, Dr. Tiedje, who was supposed to lead the project, was on sabbatical, enjoying the warmer climate of Hawaii (quite different from Michigan) and collaborating with Hawaiian researchers. He learned that there were soils in Hawaii that had not been exposed to 2,4-D, and he brought those untouched soils back to Michigan. The underlying idea was to investigate whether the microorganisms capable of breaking down this widely used chemical, which was artificially synthesized and sprayed in large quantities, were absent in the Hawaiian soils, or there were microbes possessing th","PeriodicalId":94145,"journal":{"name":"mLife","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915610","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}
Tiantian Yu, Haining Hu, Xianhong Zeng, Yinzhao Wang, Donald Pan, Longhui Deng, Lewen Liang, Jialin Hou, Fengping Wang
Abstract Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia , which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of Bathyarchaeia , named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 ( Ca . B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. Ca . B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, mtgB ) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the mtgB gene confirmed O ‐demethylation activity. The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that Bathyarchaeia , capable of O ‐demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.
{"title":"Widespread <i>Bathyarchaeia</i> encode a novel methyltransferase utilizing lignin‐derived aromatics","authors":"Tiantian Yu, Haining Hu, Xianhong Zeng, Yinzhao Wang, Donald Pan, Longhui Deng, Lewen Liang, Jialin Hou, Fengping Wang","doi":"10.1002/mlf2.12082","DOIUrl":"https://doi.org/10.1002/mlf2.12082","url":null,"abstract":"Abstract Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia , which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of Bathyarchaeia , named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 ( Ca . B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. Ca . B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, mtgB ) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the mtgB gene confirmed O ‐demethylation activity. The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that Bathyarchaeia , capable of O ‐demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135349559","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}
Yu Zhang, Pramod Bhasme, Dinesh S. Reddy, Dejian Liu, Zhaoxiao Yu, Tianhu Zhao, Yaqian Zheng, Amit Kumar, Haiying Yu, Luyan Z. Ma
Abstract Antibiotic resistance or tolerance of pathogens is one of the most serious global public health threats. Bacteria in biofilms show extreme tolerance to almost all antibiotic classes. Thus, use of antibiofilm drugs without bacterial‐killing effects is one of the strategies to combat antibiotic tolerance. In this study, we discovered a coumarin–chalcone conjugate C9, which can inhibit the biofilm formation of three common pathogens that cause nosocomial infections, namely, Pseudomonas aeruginosa , Staphylococcus aureus , and Escherichia coli , with the best antibiofilm activity against P. aeruginosa . Further investigations indicate that C9 decreases the synthesis of the key biofilm matrix exopolysaccharide Psl and bacterial second messenger cyclic‐di‐GMP. Meanwhile, C9 can interfere with the regulation of the quorum sensing (QS) system to reduce the virulence of P. aeruginosa . C9 treatment enhances the sensitivity of biofilm to several antibiotics and reduces the survival rate of P. aeruginosa under starvation or oxidative stress conditions, indicating its excellent potential for use as an antibiofilm‐forming and anti‐QS drug.
{"title":"Dual functions: A coumarin–chalcone conjugate inhibits cyclic‐di‐GMP and quorum‐sensing signaling to reduce biofilm formation and virulence of pathogens","authors":"Yu Zhang, Pramod Bhasme, Dinesh S. Reddy, Dejian Liu, Zhaoxiao Yu, Tianhu Zhao, Yaqian Zheng, Amit Kumar, Haiying Yu, Luyan Z. Ma","doi":"10.1002/mlf2.12087","DOIUrl":"https://doi.org/10.1002/mlf2.12087","url":null,"abstract":"Abstract Antibiotic resistance or tolerance of pathogens is one of the most serious global public health threats. Bacteria in biofilms show extreme tolerance to almost all antibiotic classes. Thus, use of antibiofilm drugs without bacterial‐killing effects is one of the strategies to combat antibiotic tolerance. In this study, we discovered a coumarin–chalcone conjugate C9, which can inhibit the biofilm formation of three common pathogens that cause nosocomial infections, namely, Pseudomonas aeruginosa , Staphylococcus aureus , and Escherichia coli , with the best antibiofilm activity against P. aeruginosa . Further investigations indicate that C9 decreases the synthesis of the key biofilm matrix exopolysaccharide Psl and bacterial second messenger cyclic‐di‐GMP. Meanwhile, C9 can interfere with the regulation of the quorum sensing (QS) system to reduce the virulence of P. aeruginosa . C9 treatment enhances the sensitivity of biofilm to several antibiotics and reduces the survival rate of P. aeruginosa under starvation or oxidative stress conditions, indicating its excellent potential for use as an antibiofilm‐forming and anti‐QS drug.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915613","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}
Xi Shen, Zixiang Yang, Zihan Li, Dan Xiong, Jinxing Liao, Weimei He, Danyu Shen, Xiaolong Shao, Ben Niu, Yongxing He, Yong‐Gui Gao, Guoliang Qian
Abstract To remain competitive, proteobacteria use various contact‐dependent weapon systems to defend against microbial competitors. The bacterial‐killing type IV secretion system (T4SS) is one such powerful weapon. It commonly controls the killing/competition between species by secreting the lethal T4 SS e ffector (T4E) proteins carrying conserved XVIPCD domains into competing cells. In this study, we sought knowledge to understand whether the bacterial‐killing T4SS‐producing bacteria encode T4E‐like proteins and further explore their biological functions. To achieve this, we designed a T4E‐guided approach to discover T4E‐like proteins that are designated as atypical T4Es. Initially, this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS‐producing bacteria. These homologous genes were then screened in Escherichia coli to identify antibacterial candidates (atypical T4Es) and their neighboring detoxification proteins, followed by testing their gene cotranscription and validating their physical interactions. Using this approach, we did discover two atypical T4E proteins from the plant‐beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri . We also provided substantial evidence to show that the atypical T4E protein Le1637‐mediated bacterial defense in interspecies interactions between L. enzymogenes and its competitors. Therefore, the newly designed T4E‐guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.
为了保持竞争力，变形菌使用各种接触依赖武器系统来防御微生物竞争者。杀灭细菌的IV型分泌系统(T4SS)就是这样一种强大的武器。它通常通过分泌携带保守XVIPCD结构域的致死性T4 SS e效应蛋白(T4E)进入竞争细胞来控制物种之间的杀伤/竞争。在这项研究中，我们寻求知识，以了解细菌杀灭T4SS -产生细菌是否编码T4E -样蛋白，并进一步探索其生物学功能。为了实现这一目标，我们设计了一种T4E引导的方法来发现被指定为非典型T4E的T4E样蛋白。最初，这种方法需要科学家进行简单的BlastP搜索，以确定T4SS产生细菌基因组中缺乏XVIPCD结构域的T4E同源物。然后在大肠杆菌中筛选这些同源基因，以确定抗菌候选基因(非典型T4Es)及其邻近的解毒蛋白，随后测试它们的基因共转录并验证它们的物理相互作用。使用这种方法，我们确实从植物有益的溶酶杆菌和植物病原体黄单胞菌中发现了两种非典型T4E蛋白。我们还提供了大量证据表明，非典型T4E蛋白Le1637‐介导了酵素乳杆菌及其竞争对手种间相互作用中的细菌防御。因此，新设计的T4E引导方法有望检测细菌细胞中的功能性非典型T4E蛋白。
{"title":"Identification of atypical T4SS effector proteins mediating bacterial defense","authors":"Xi Shen, Zixiang Yang, Zihan Li, Dan Xiong, Jinxing Liao, Weimei He, Danyu Shen, Xiaolong Shao, Ben Niu, Yongxing He, Yong‐Gui Gao, Guoliang Qian","doi":"10.1002/mlf2.12084","DOIUrl":"https://doi.org/10.1002/mlf2.12084","url":null,"abstract":"Abstract To remain competitive, proteobacteria use various contact‐dependent weapon systems to defend against microbial competitors. The bacterial‐killing type IV secretion system (T4SS) is one such powerful weapon. It commonly controls the killing/competition between species by secreting the lethal T4 SS e ffector (T4E) proteins carrying conserved XVIPCD domains into competing cells. In this study, we sought knowledge to understand whether the bacterial‐killing T4SS‐producing bacteria encode T4E‐like proteins and further explore their biological functions. To achieve this, we designed a T4E‐guided approach to discover T4E‐like proteins that are designated as atypical T4Es. Initially, this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS‐producing bacteria. These homologous genes were then screened in Escherichia coli to identify antibacterial candidates (atypical T4Es) and their neighboring detoxification proteins, followed by testing their gene cotranscription and validating their physical interactions. Using this approach, we did discover two atypical T4E proteins from the plant‐beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri . We also provided substantial evidence to show that the atypical T4E protein Le1637‐mediated bacterial defense in interspecies interactions between L. enzymogenes and its competitors. Therefore, the newly designed T4E‐guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915609","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}
Impact statement Gut microbiota‐derived trimethylamine (TMA) is associated with cardiometabolic disorders and exemplifies a microbial involvement in the etiology of emerging, noncommunicable diseases, the leading causes of death worldwide. Three biochemical pathways taking dietary compounds as intake have been described with distinct taxa involved that are all present at low relative abundances. A recently discovered pathway is now considered to be the main route for TMA synthesis from l ‐carnitine involving γ‐butyrobetaine as an intermediate product. By comprehensive (meta) genomic screening of publicly available data, namely, genomes of the UHGG catalog ( n > 200,000) and 10 metagenomic (transcriptomic) data sets, we revealed bacteria synthesizing TMA via this pathway and specified their ecophysiology. Results will contribute to stratification of individuals based on their gut microbiota's potential to synthesize TMA and might aid in the development of strategies restricting TMA formation.
{"title":"A small, polyphyletic group of <i>Firmicutes</i> synthesizes trimethylamine from <scp>l</scp>‐carnitine","authors":"Marius Vital, Ylenia Heinrich‐Sanchez","doi":"10.1002/mlf2.12079","DOIUrl":"https://doi.org/10.1002/mlf2.12079","url":null,"abstract":"Impact statement Gut microbiota‐derived trimethylamine (TMA) is associated with cardiometabolic disorders and exemplifies a microbial involvement in the etiology of emerging, noncommunicable diseases, the leading causes of death worldwide. Three biochemical pathways taking dietary compounds as intake have been described with distinct taxa involved that are all present at low relative abundances. A recently discovered pathway is now considered to be the main route for TMA synthesis from l ‐carnitine involving γ‐butyrobetaine as an intermediate product. By comprehensive (meta) genomic screening of publicly available data, namely, genomes of the UHGG catalog ( n > 200,000) and 10 metagenomic (transcriptomic) data sets, we revealed bacteria synthesizing TMA via this pathway and specified their ecophysiology. Results will contribute to stratification of individuals based on their gut microbiota's potential to synthesize TMA and might aid in the development of strategies restricting TMA formation.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135304857","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}
Kun Meng, Jin Yang, Juan Xue, Jun Lv, Ping Zhu, Liuliu Shi, Shan Li
Abstract Salmonella Typhimurium creates an intracellular niche for its replication by utilizing a large cohort of effectors, including several that function to interfere with host ubiquitin signaling. Although the mechanism of action of many such effectors has been elucidated, how the interplay between the host ubiquitin network and bacterial virulence factors dictates the outcome of infection largely remains undefined. In this study, we found that the SPI‐2 effector SseK3 inhibits SNARE pairing to promote the formation of a Salmonella ‐induced filament by Arg‐GlcNAcylation of SNARE proteins, including SNAP25, VAMP8, and Syntaxin. Further study reveals that host cells counteract the activity of SseK3 by inducing the expression of the E3 ubiquitin ligase TRIM32, which catalyzes K48‐linked ubiquitination on SseK3 and targets its membrane‐associated portion for degradation. Hence, TRIM32 antagonizes SNAP25 Arg‐GlcNAcylation induced by SseK3 to restrict Salmonella ‐induced filament biogenesis and Salmonella replication. Our study reveals a mechanism by which host cells inhibit bacterial replication by eliminating specific virulence factors.
{"title":"A host E3 ubiquitin ligase regulates <i>Salmonella</i> virulence by targeting an SPI‐2 effector involved in SIF biogenesis","authors":"Kun Meng, Jin Yang, Juan Xue, Jun Lv, Ping Zhu, Liuliu Shi, Shan Li","doi":"10.1002/mlf2.12063","DOIUrl":"https://doi.org/10.1002/mlf2.12063","url":null,"abstract":"Abstract Salmonella Typhimurium creates an intracellular niche for its replication by utilizing a large cohort of effectors, including several that function to interfere with host ubiquitin signaling. Although the mechanism of action of many such effectors has been elucidated, how the interplay between the host ubiquitin network and bacterial virulence factors dictates the outcome of infection largely remains undefined. In this study, we found that the SPI‐2 effector SseK3 inhibits SNARE pairing to promote the formation of a Salmonella ‐induced filament by Arg‐GlcNAcylation of SNARE proteins, including SNAP25, VAMP8, and Syntaxin. Further study reveals that host cells counteract the activity of SseK3 by inducing the expression of the E3 ubiquitin ligase TRIM32, which catalyzes K48‐linked ubiquitination on SseK3 and targets its membrane‐associated portion for degradation. Hence, TRIM32 antagonizes SNAP25 Arg‐GlcNAcylation induced by SseK3 to restrict Salmonella ‐induced filament biogenesis and Salmonella replication. Our study reveals a mechanism by which host cells inhibit bacterial replication by eliminating specific virulence factors.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136108096","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}
Abstract Kinase, putative Endopeptidase, and Other Proteins of Small size (KEOPS) is a multisubunit protein complex conserved in eukaryotes and archaea. It is composed of Pcc1, Kae1, Bud32, Cgi121, and Gon7 in eukaryotes and is primarily involved in N 6 ‐threonylcarbamoyl adenosine (t 6 A) modification of transfer RNAs (tRNAs). Recently, it was reported that KEOPS participates in homologous recombination (HR) repair in yeast. To characterize the KEOPS in archaea (aKEOPS), we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus . We show that aKEOPS also possesses five subunits, Pcc1, Kae1, Bud32, Cgi121, and Pcc1‐like (or Gon7‐like), just like eukaryotic KEOPS. Pcc1‐like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex (Kae1‐Pcc1‐Pcc1‐Kae1), suggesting that Pcc1‐like is a functional homolog of the eukaryotic Gon7 subunit. Strikingly, none of the genes encoding aKEOPS subunits, including Pcc1 and Pcc1‐like, can be deleted in the wild type and in a t 6 A modification complementary strain named TsaKI, implying that the aKEOPS complex is essential for an additional cellular process in this archaeon. Knock‐down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI. These results suggest that aKEOPS plays an essential role independent of the cellular t 6 A modification level. In addition, archaeal Cgi121 possesses dsDNA‐binding activity that relies on its tRNA 3ʹ CCA tail binding module. Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7. The study also reveals a possible link between the function in t 6 A modification and the additional function, presumably HR.
{"title":"The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular t<sup>6</sup>A modification level","authors":"Pengju Wu, Qi Gan, Xuemei Zhang, Yunfeng Yang, Yuanxi Xiao, Qunxin She, Jinfeng Ni, Qihong Huang, Yulong Shen","doi":"10.1002/mlf2.12051","DOIUrl":"https://doi.org/10.1002/mlf2.12051","url":null,"abstract":"Abstract Kinase, putative Endopeptidase, and Other Proteins of Small size (KEOPS) is a multisubunit protein complex conserved in eukaryotes and archaea. It is composed of Pcc1, Kae1, Bud32, Cgi121, and Gon7 in eukaryotes and is primarily involved in N 6 ‐threonylcarbamoyl adenosine (t 6 A) modification of transfer RNAs (tRNAs). Recently, it was reported that KEOPS participates in homologous recombination (HR) repair in yeast. To characterize the KEOPS in archaea (aKEOPS), we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus . We show that aKEOPS also possesses five subunits, Pcc1, Kae1, Bud32, Cgi121, and Pcc1‐like (or Gon7‐like), just like eukaryotic KEOPS. Pcc1‐like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex (Kae1‐Pcc1‐Pcc1‐Kae1), suggesting that Pcc1‐like is a functional homolog of the eukaryotic Gon7 subunit. Strikingly, none of the genes encoding aKEOPS subunits, including Pcc1 and Pcc1‐like, can be deleted in the wild type and in a t 6 A modification complementary strain named TsaKI, implying that the aKEOPS complex is essential for an additional cellular process in this archaeon. Knock‐down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI. These results suggest that aKEOPS plays an essential role independent of the cellular t 6 A modification level. In addition, archaeal Cgi121 possesses dsDNA‐binding activity that relies on its tRNA 3ʹ CCA tail binding module. Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7. The study also reveals a possible link between the function in t 6 A modification and the additional function, presumably HR.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135107313","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}
{"title":"Inspiration and encounters: Carl Woese and my 30‐year research journey","authors":"Y. Ishino","doi":"10.1002/mlf2.12050","DOIUrl":"https://doi.org/10.1002/mlf2.12050","url":null,"abstract":"","PeriodicalId":94145,"journal":{"name":"mLife","volume":"708 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76865341","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}
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