Escherichia coli possesses four initiator tRNA (i-tRNA) genes, three of which are present together as metZWV and the fourth one as metY. In E. coli B, all four genes (metZWV and metY) encode i-tRNAfMet1, in which the G at position 46 is modified to m7G46 by TrmB (m7G methyltransferase). However, in E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of m7G46. We generated E. coli strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on metYA46 (metY of E. coli K origin encoding i-tRNAfMet2) or its derivative metYG46 (encoding i-tRNAfMet1) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. The growth fitness advantages are more pronounced for the strains sustained on i-tRNAfMet1 in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs in vivo. Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNAfMet1 than that of i-tRNAfMet2. The stability of i-tRNAfMet1 remains unaffected upon the deletion of TrmB. These studies highlight how metYG46 and metYA46 alleles might influence the growth fitness of E. coli under certain nutrient-limiting conditions.
Importance: Escherichia coli harbors four initiator tRNA (i-tRNA) genes: three of these at metZWV and the fourth one at metY loci. In E. coli B, all four genes encode i-tRNAfMet1. In E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNAfMet1. The strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. Strains harboring metYG46 (B mimic) or metYA46 (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.
{"title":"Physiological significance of the two isoforms of initiator tRNAs in <i>Escherichia coli</i>.","authors":"Amit Kumar Sahu, Riyaz Ahmad Shah, Divya Nashier, Prafful Sharma, Rajagopal Varada, Kuldeep Lahry, Sudhir Singh, Sunil Shetty, Tanweer Hussain, Umesh Varshney","doi":"10.1128/jb.00251-24","DOIUrl":"10.1128/jb.00251-24","url":null,"abstract":"<p><p><i>Escherichia coli</i> possesses four initiator tRNA (i-tRNA) genes, three of which are present together as <i>metZWV</i> and the fourth one as <i>metY</i>. In <i>E. coli</i> B, all four genes (<i>metZWV</i> and <i>metY</i>) encode i-tRNA<sup>fMet1</sup>, in which the G at position 46 is modified to m<sup>7</sup>G46 by TrmB (m<sup>7</sup>G methyltransferase). However, in <i>E. coli</i> K, because of a single-nucleotide polymorphism, <i>metY</i> encodes a variant, i-tRNA<sup>fMet2</sup>, having an A in place of m<sup>7</sup>G46. We generated <i>E. coli</i> strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on <i>metY</i><sub>A46</sub> (<i>metY</i> of <i>E. coli</i> K origin encoding i-tRNA<sup>fMet2</sup>) or its derivative <i>metY</i><sub>G46</sub> (encoding i-tRNA<sup>fMet1</sup>) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNA<sup>fMet1</sup> have a growth fitness advantage over those sustained on i-tRNA<sup>fMet2</sup>. The growth fitness advantages are more pronounced for the strains sustained on i-tRNA<sup>fMet1</sup> in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs <i>in vivo</i>. Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNA<sup>fMet1</sup> than that of i-tRNA<sup>fMet2</sup>. The stability of i-tRNA<sup>fMet1</sup> remains unaffected upon the deletion of TrmB. These studies highlight how <i>metY</i><sub>G46</sub> and <i>metY</i><sub>A46</sub> alleles might influence the growth fitness of <i>E. coli</i> under certain nutrient-limiting conditions.</p><p><strong>Importance: </strong><i>Escherichia coli</i> harbors four initiator tRNA (i-tRNA) genes: three of these at <i>metZWV</i> and the fourth one at <i>metY</i> loci. In <i>E. coli</i> B, all four genes encode i-tRNA<sup>fMet1</sup>. In <i>E. coli</i> K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNA<sup>fMet2</sup>, having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNA<sup>fMet1</sup>. The strains sustained on i-tRNA<sup>fMet1</sup> have a growth fitness advantage over those sustained on i-tRNA<sup>fMet2</sup>. Strains harboring <i>metY</i><sub>G46</sub> (B mimic) or <i>metY</i><sub>A46</sub> (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19Epub Date: 2024-08-19DOI: 10.1128/jb.00228-24
Brett J Baker, Emily Hyde, Pedro Leão
Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.
{"title":"Nature should be the model for microbial sciences.","authors":"Brett J Baker, Emily Hyde, Pedro Leão","doi":"10.1128/jb.00228-24","DOIUrl":"10.1128/jb.00228-24","url":null,"abstract":"<p><p>Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10<sup>28</sup> cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (<i>Nitrosopumilus maritimus</i>), SAR11 (<i>Pelagibacter ubique</i>), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like <i>Buchnera</i>, <i>Aliivibrio</i>, and <i>Rhizobium</i>, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of <i>in situ</i> techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19Epub Date: 2024-09-04DOI: 10.1128/jb.00143-24
Jasper B Gomez, Christopher M Waters
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in V. cholerae given the low diversity of phages that have been isolated, which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16-kB region of the Vibrio pathogenicity island-2, which we name TgvA and TgvB (Type I-embedded gmrSD-like system of VPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modifications are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff, becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We also show that the Type I restriction-modification system that embeds the tgvAB genes protects against phage T3, secΦ18, secΦ27, and λ, suggesting that this region is a phage defense island. Our study uncovers a novel Type IV restriction system in V. cholerae, increasing our understanding of the evolution and ecology of V. cholerae, while highlighting the evolutionary interplay between restriction systems and phage genome modification.IMPORTANCEBacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. In this study, we discover a Type IV restriction system encoded in V. cholerae, which we name TgvAB, and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution of V. cholerae and more broadly how bacteria evade phage predation.
霍乱弧菌面临的一个主要挑战是在水生水库和感染人类宿主期间不断遭到噬菌体的捕食。为了克服噬菌体的捕食,霍乱弧菌获得和/或进化出了无数的噬菌体防御系统。虽然已经发现了几种新的防御系统,但鉴于已分离出的感染霍乱弧菌的噬菌体的多样性较低,我们假设霍乱弧菌中编码了更多的防御系统。利用霍乱弧菌基因组文库,我们在弧菌致病性岛-2 的 16 kB 区域内发现了一个由两个基因组成的 IV 型限制系统,我们将其命名为 TgvA 和 TgvB(VPI-2 的 I 型嵌入式 gmrSD-like 系统)。我们发现,TgvA 和 TgvB 都需要通过靶向葡萄糖基化的 5-羟甲基胞嘧啶(5hmC)来防御 T2、T4 和 T6。失去葡萄糖修饰的 T2 或 T4 噬菌体能抵御 TgvAB 的防御,但在进化过程中会出现明显的折衷,变得容易受到其他针对未葡萄糖化 5hmC 的 IV 型限制系统的攻击。我们还发现,嵌入 tgvAB 基因的 I 型限制修饰系统能抵御噬菌体 T3、secΦ18、secΦ27 和 λ,这表明该区域是一个噬菌体防御岛。我们的研究在霍乱弧菌中发现了一种新的 IV 型限制系统,加深了我们对霍乱弧菌进化和生态学的了解,同时强调了限制系统与噬菌体基因组改造之间的进化相互作用。为了抵御这种捕食,细菌进化出了无数种防御系统。其中一些系统通过识别噬菌体 DNA 上独特的碱基修饰来消化感染的噬菌体。在这项研究中,我们发现了霍乱弧菌中编码的一种 IV 型限制系统,并将其命名为 TgvAB,证明它能识别并限制具有 5-hydroxymethylcytosine 葡萄糖基化 DNA 的噬菌体。此外,对 TgvAB 的抗性进化使噬菌体易受其他 IV 型限制系统的影响,这表明进化过程中存在重大的权衡。这些结果加深了我们对霍乱弧菌进化的理解,更广泛地说,加深了我们对细菌如何躲避噬菌体捕食的理解。
{"title":"A <i>Vibrio cholerae</i> Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection.","authors":"Jasper B Gomez, Christopher M Waters","doi":"10.1128/jb.00143-24","DOIUrl":"10.1128/jb.00143-24","url":null,"abstract":"<p><p>A major challenge faced by <i>Vibrio cholerae</i> is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, <i>V. cholerae</i> has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in <i>V. cholerae</i> given the low diversity of phages that have been isolated, which infect this species. Using a <i>V. cholerae</i> genomic library, we identified a Type IV restriction system consisting of two genes within a 16-kB region of the <i>Vibrio</i> pathogenicity island-2, which we name TgvA and TgvB (<b><u>T</u></b>ype I-embedded <b><i><u>g</u></i></b><i>mrSD</i>-like system of <b><u>V</u></b>PI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modifications are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff, becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We also show that the Type I restriction-modification system that embeds the <i>tgvAB</i> genes protects against phage T3, secΦ18, secΦ27, and λ, suggesting that this region is a phage defense island. Our study uncovers a novel Type IV restriction system in <i>V. cholerae</i>, increasing our understanding of the evolution and ecology of <i>V. cholerae,</i> while highlighting the evolutionary interplay between restriction systems and phage genome modification.IMPORTANCEBacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. In this study, we discover a Type IV restriction system encoded in <i>V. cholerae,</i> which we name TgvAB, and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution of <i>V. cholerae</i> and more broadly how bacteria evade phage predation.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We identified and characterized genomic regions of Streptococcus agalactiae that are involved in the Leloir and the tagatose-6-phosphate pathways for D-galactose catabolism. The accumulation of mutations in genes coding the Leloir pathway and the absence of these genes in a significant proportion of the strains suggest that this pathway may no longer be necessary for S. agalactiae and is heading toward extinction. In contrast, a genomic region containing genes coding for intermediates of the tagatose-6-phosphate pathway, a Gat family PTS transporter, and a DeoR/GlpR family regulator is present in the vast majority of strains. By deleting genes that code for intermediates of each of these two pathways in three selected strains, we demonstrated that the tagatose-6-phosphate pathway is their sole route for galactose catabolism. Furthermore, we showed that the Gat family PTS transporter acts as the primary importer of galactose in S. agalactiae. Finally, we proved that the DeoR/GlpR family regulator is a repressor of the tagatose-6-phosphate pathway and that galactose triggers the induction of this biochemical mechanism.IMPORTANCES. agalactiae, a significant pathogen for both humans and animals, encounters galactose and galactosylated components within its various ecological niches. We highlighted the capability of this bacterium to metabolize D-galactose and showed the role of the tagatose-6-phosphate pathway and of a PTS importer in this biochemical process. Since S. agalactiae relies on carbohydrate fermentation for energy production, its ability to uptake and metabolize D-galactose could enhance its persistence and its competitiveness within the microbiome.
我们鉴定并描述了无乳链球菌基因组中参与 D-半乳糖分解代谢的 Leloir 和 tagatose-6-phosphate 途径的区域。Leloir 途径编码基因突变的累积以及相当一部分菌株中这些基因的缺失表明,这种途径可能不再是无乳链球菌所必需的,并正在走向消亡。与此相反,绝大多数菌株的基因组区域都含有编码 6-磷酸标签糖途径中间体、Gat 家族 PTS 转运体和 DeoR/GlpR 家族调节器的基因。通过删除三个选定菌株中编码这两条途径中间体的基因,我们证明了6-磷酸标签糖途径是它们分解半乳糖的唯一途径。此外,我们还发现 Gat 家族的 PTS 转运体是 S. agalactiae 中半乳糖的主要输入体。最后,我们证明 DeoR/GlpR 家族调控因子是标签糖-6-磷酸途径的抑制因子,而半乳糖会诱导这一生化机制的产生。我们强调了这种细菌代谢 D-半乳糖的能力,并展示了标签糖-6-磷酸途径和 PTS 导入器在这一生化过程中的作用。由于 S. agalactiae 依靠碳水化合物发酵来产生能量,因此其吸收和代谢 D-半乳糖的能力可增强其在微生物群中的持久性和竞争力。
{"title":"Characterization of galactose catabolic pathways in <i>Streptococcus agalactiae</i> and identification of a major galactose: phosphotransferase importer.","authors":"Aurelia Hiron, Morgane Melet, Capucine Guerry, Ilona Dubois, Vanessa Rong, Philippe Gilot","doi":"10.1128/jb.00155-24","DOIUrl":"https://doi.org/10.1128/jb.00155-24","url":null,"abstract":"<p><p>We identified and characterized genomic regions of <i>Streptococcus agalactiae</i> that are involved in the Leloir and the tagatose-6-phosphate pathways for D-galactose catabolism. The accumulation of mutations in genes coding the Leloir pathway and the absence of these genes in a significant proportion of the strains suggest that this pathway may no longer be necessary for <i>S. agalactiae</i> and is heading toward extinction. In contrast, a genomic region containing genes coding for intermediates of the tagatose-6-phosphate pathway, a Gat family PTS transporter, and a DeoR/GlpR family regulator is present in the vast majority of strains. By deleting genes that code for intermediates of each of these two pathways in three selected strains, we demonstrated that the tagatose-6-phosphate pathway is their sole route for galactose catabolism. Furthermore, we showed that the Gat family PTS transporter acts as the primary importer of galactose in <i>S. agalactiae</i>. Finally, we proved that the DeoR/GlpR family regulator is a repressor of the tagatose-6-phosphate pathway and that galactose triggers the induction of this biochemical mechanism.IMPORTANCE<i>S. agalactiae</i>, a significant pathogen for both humans and animals, encounters galactose and galactosylated components within its various ecological niches. We highlighted the capability of this bacterium to metabolize D-galactose and showed the role of the tagatose-6-phosphate pathway and of a PTS importer in this biochemical process. Since <i>S. agalactiae</i> relies on carbohydrate fermentation for energy production, its ability to uptake and metabolize D-galactose could enhance its persistence and its competitiveness within the microbiome.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here, we describe the regulation of potassium uptake systems in the oligotrophic α-proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by mainly using two K+ transporters to maintain potassium homeostasis, the low-affinity Kup and the high-affinity Kdp uptake systems. When K+ is not limiting, we found that the kup gene is essential while kdp inactivation does not impact the growth. In contrast, kdp becomes critical but not essential and kup dispensable for growth in K+-limited environments. However, in the absence of kdp, mutations in kup were selected to improve growth in K+-depleted conditions, likely by increasing the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulates kdpABCDE expression, suggest that the inner membrane sensor regulatory component KdpD mainly works as a phosphatase to limit the growth when cells reach late exponential phase. Our data therefore suggest that KdpE is phosphorylated by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+ transcriptome. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+ availability.IMPORTANCEPotassium (K+) is a key metal ion involved in many essential cellular processes. Here, we show that the oligotroph Caulobacter crescentus can support growth at micromolar concentrations of K+ by mainly using two K+ uptake systems, the low-affinity Kup and the high-affinity Kdp. Using genome-wide approaches, we also determined the entire set of genes required for C. crescentus to survive at low K+ concentration as well as the full K+-dependent regulon. Finally, we found that the transcriptional regulation mediated by the KdpDE two-component system is unconventional since unlike Escherichia coli, the inner membrane sensor regulatory component KdpD seems to work rather as a phosphatase on the phosphorylated response regulator KdpE~P.
{"title":"Regulation of potassium uptake in <i>Caulobacter crescentus</i>.","authors":"Alex Quintero-Yanes, Loïc Léger, Madeline Collignon, Julien Mignon, Aurélie Mayard, Catherine Michaux, Régis Hallez","doi":"10.1128/jb.00107-24","DOIUrl":"10.1128/jb.00107-24","url":null,"abstract":"<p><p>Potassium (K<sup>+</sup>) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here, we describe the regulation of potassium uptake systems in the oligotrophic α-proteobacterium <i>Caulobacter crescentus</i> known as a model for asymmetric cell division. We show that <i>C. crescentus</i> can grow in concentrations from the micromolar to the millimolar range by mainly using two K<sup>+</sup> transporters to maintain potassium homeostasis, the low-affinity Kup and the high-affinity Kdp uptake systems. When K<sup>+</sup> is not limiting, we found that the <i>kup</i> gene is essential while <i>kdp</i> inactivation does not impact the growth. In contrast, <i>kdp</i> becomes critical but not essential and <i>kup</i> dispensable for growth in K<sup>+</sup>-limited environments. However, in the absence of <i>kdp</i>, mutations in <i>kup</i> were selected to improve growth in K<sup>+</sup>-depleted conditions, likely by increasing the affinity of Kup for K<sup>+</sup>. In addition, mutations in the KdpDE two-component system, which regulates <i>kdpABCDE</i> expression, suggest that the inner membrane sensor regulatory component KdpD mainly works as a phosphatase to limit the growth when cells reach late exponential phase. Our data therefore suggest that KdpE is phosphorylated by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K<sup>+</sup> transcriptome. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K<sup>+</sup> availability.IMPORTANCEPotassium (K<sup>+</sup>) is a key metal ion involved in many essential cellular processes. Here, we show that the oligotroph <i>Caulobacter crescentus</i> can support growth at micromolar concentrations of K<sup>+</sup> by mainly using two K<sup>+</sup> uptake systems, the low-affinity Kup and the high-affinity Kdp. Using genome-wide approaches, we also determined the entire set of genes required for <i>C. crescentus</i> to survive at low K<sup>+</sup> concentration as well as the full K<sup>+</sup>-dependent regulon. Finally, we found that the transcriptional regulation mediated by the KdpDE two-component system is unconventional since unlike <i>Escherichia coli</i>, the inner membrane sensor regulatory component KdpD seems to work rather as a phosphatase on the phosphorylated response regulator KdpE~P.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19Epub Date: 2024-08-28DOI: 10.1128/jb.00246-24
Erik J Kopping, P Todd Benziger, David G Thanassi
Francisella spp. are Gram-negative, facultative intracellular pathogens. Francisella tularensis causes the human disease tularemia and is considered a biological threat agent due to its high infectivity and virulence. A central aspect of Francisella virulence is its ability to dampen host immune responses. We previously identified the outer membrane channel (OMC) protein TolC as a critical F. tularensis virulence factor required for suppression of apoptotic and proinflammatory responses during macrophage infection. TolC functions as part of multidrug efflux systems and the type I secretion pathway that exports bacterial effector proteins. In these systems, TolC forms tripartite complexes together with an inner membrane transporter and periplasmic membrane fusion protein (MFP). To advance understanding of TolC function in Francisella, we analyzed OMC and MFP homologs in Francisella novicida, a widely used model species that causes a tularemia-like disease in mice. In agreement with the previous F. tularensis studies, all three OMCs present in F. novicida contributed to multidrug resistance, but only TolC was important for suppressing macrophage cell death. In addition, we identified the EmrA1 MFP as important for resisting antimicrobial compounds and dampening host cell death. In contrast to results obtained with F. tularensis, the cell death triggered during infection with the F. novicida tolC and emrA1 mutants was dominated by pyroptosis rather than apoptosis. These data expand our understanding of TolC function in Francisella and underscore both conserved and differential aspects of F. novicida and F. tularensis.
Importance: Francisella tularensis is a Gram-negative intracellular bacterial pathogen and causative agent of tularemia. We previously identified the outer membrane channel protein TolC as contributing to antimicrobial resistance and subversion of host responses by F. tularensis. To advance understanding of TolC function in Francisella and to identify components that might work together with TolC, we took advantage of a transposon mutant library in F. novicida, a model species that causes a tularemia-like disease in mice. Our findings identify TolC and the membrane fusion protein EmrA1 as important for both antimicrobial resistance and suppression of macrophage cell death. This study also revealed differences in cell death pathways triggered by F. novicida versus F. tularensis infection that may relate to differences in virulence.
{"title":"TolC and EmrA1 contribute to <i>Francisella novicida</i> multidrug resistance and modulation of host cell death.","authors":"Erik J Kopping, P Todd Benziger, David G Thanassi","doi":"10.1128/jb.00246-24","DOIUrl":"10.1128/jb.00246-24","url":null,"abstract":"<p><p><i>Francisella</i> spp. are Gram-negative, facultative intracellular pathogens. <i>Francisella tularensis</i> causes the human disease tularemia and is considered a biological threat agent due to its high infectivity and virulence. A central aspect of <i>Francisella</i> virulence is its ability to dampen host immune responses. We previously identified the outer membrane channel (OMC) protein TolC as a critical <i>F. tularensis</i> virulence factor required for suppression of apoptotic and proinflammatory responses during macrophage infection. TolC functions as part of multidrug efflux systems and the type I secretion pathway that exports bacterial effector proteins. In these systems, TolC forms tripartite complexes together with an inner membrane transporter and periplasmic membrane fusion protein (MFP). To advance understanding of TolC function in <i>Francisella</i>, we analyzed OMC and MFP homologs in <i>Francisella novicida</i>, a widely used model species that causes a tularemia-like disease in mice. In agreement with the previous <i>F. tularensis</i> studies, all three OMCs present in <i>F. novicida</i> contributed to multidrug resistance, but only TolC was important for suppressing macrophage cell death. In addition, we identified the EmrA1 MFP as important for resisting antimicrobial compounds and dampening host cell death. In contrast to results obtained with <i>F. tularensis</i>, the cell death triggered during infection with the <i>F. novicida tolC</i> and <i>emrA1</i> mutants was dominated by pyroptosis rather than apoptosis. These data expand our understanding of TolC function in <i>Francisella</i> and underscore both conserved and differential aspects of <i>F. novicida</i> and <i>F. tularensis</i>.</p><p><strong>Importance: </strong><i>Francisella tularensis</i> is a Gram-negative intracellular bacterial pathogen and causative agent of tularemia. We previously identified the outer membrane channel protein TolC as contributing to antimicrobial resistance and subversion of host responses by <i>F. tularensis</i>. To advance understanding of TolC function in <i>Francisella</i> and to identify components that might work together with TolC, we took advantage of a transposon mutant library in <i>F. novicida</i>, a model species that causes a tularemia-like disease in mice. Our findings identify TolC and the membrane fusion protein EmrA1 as important for both antimicrobial resistance and suppression of macrophage cell death. This study also revealed differences in cell death pathways triggered by <i>F. novicida</i> versus <i>F. tularensis</i> infection that may relate to differences in virulence.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pilar Menendez-GilDiana VelevaMollie VirgoJige ZhangRita RamalheteBrian T. Ho1Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom2Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United KingdomLaurie E. Comstock
Journal of Bacteriology, Ahead of Print.
细菌学杂志》,提前出版。
{"title":"Modulation of Vibrio cholerae gene expression through conjugative delivery of engineered regulatory small RNAs","authors":"Pilar Menendez-GilDiana VelevaMollie VirgoJige ZhangRita RamalheteBrian T. Ho1Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom2Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United KingdomLaurie E. Comstock","doi":"10.1128/jb.00142-24","DOIUrl":"https://doi.org/10.1128/jb.00142-24","url":null,"abstract":"Journal of Bacteriology, Ahead of Print. <br/>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isaac P. PayneBrody AubryJordan M. BarrowsPamela J. B. BrownErin D. Goley1Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA2Division of Biological Sciences, University of Missouri, Columbia, Missouri, USAConrad W. Mullineaux
Journal of Bacteriology, Ahead of Print.
细菌学杂志》,提前出版。
{"title":"The cell division protein FzlA performs a conserved function in diverse alphaproteobacteria","authors":"Isaac P. PayneBrody AubryJordan M. BarrowsPamela J. B. BrownErin D. Goley1Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA2Division of Biological Sciences, University of Missouri, Columbia, Missouri, USAConrad W. Mullineaux","doi":"10.1128/jb.00225-24","DOIUrl":"https://doi.org/10.1128/jb.00225-24","url":null,"abstract":"Journal of Bacteriology, Ahead of Print. <br/>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
George C. NwokochaArpita GhoshAnne Grove1Corteva Agriscience, Johnston, Iowa, USA2Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USAGeorge O'Toole
Journal of Bacteriology, Ahead of Print.
细菌学杂志》,提前出版。
{"title":"Regulation of bacterial virulence genes by PecS family transcription factors","authors":"George C. NwokochaArpita GhoshAnne Grove1Corteva Agriscience, Johnston, Iowa, USA2Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USAGeorge O'Toole","doi":"10.1128/jb.00302-24","DOIUrl":"https://doi.org/10.1128/jb.00302-24","url":null,"abstract":"Journal of Bacteriology, Ahead of Print. <br/>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexis G. SommerfieldMichelle WangJulia MamanaAndrew J. Darwin1Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USAJoseph Bondy-Denomy
Journal of Bacteriology, Ahead of Print.
细菌学杂志》,提前出版。
{"title":"In vivo and in vitro analyses of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa","authors":"Alexis G. SommerfieldMichelle WangJulia MamanaAndrew J. Darwin1Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USAJoseph Bondy-Denomy","doi":"10.1128/jb.00222-24","DOIUrl":"https://doi.org/10.1128/jb.00222-24","url":null,"abstract":"Journal of Bacteriology, Ahead of Print. <br/>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}