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Sikora F, Budja LVP, Milojevic O, Ziemniewicz A, Dudys P, Görke B. Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon. Mol Microbiol 2024. [PMID: 38770591 DOI: 10.1111/mmi.15280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
The rpoN operon, an important regulatory hub in Enterobacteriaceae, includes rpoN encoding sigma factor σ54, hpf involved in ribosome hibernation, rapZ regulating glucosamine-6-phosphate levels, and two genes encoding proteins of the nitrogen-related phosphotransferase system. Little is known about regulatory mechanisms controlling the abundance of these proteins. This study employs transposon mutagenesis and chemical screens to dissect the complex expression of the rpoN operon. We find that envelope stress conditions trigger read-through transcription into the rpoN operon from a promoter located upstream of the preceding lptA-lptB locus. This promoter is controlled by the envelope stress sigma factor E and response regulator PhoP is required for its full response to a subset of stress signals. σE also stimulates ptsN-rapZ-npr expression using an element downstream of rpoN, presumably by interfering with mRNA processing by RNase E. Additionally, we identify a novel promoter in the 3' end of rpoN that directs transcription of the distal genes in response to ethanol. Finally, we show that translation of hpf and ptsN is individually regulated by the RNA chaperone Hfq, perhaps involving small RNAs. Collectively, our work demonstrates that the rpoN operon is subject to complex regulation, integrating signals related to envelope stress and carbon source quality.
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Affiliation(s)
- Florian Sikora
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Lara Veronika Perko Budja
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Olja Milojevic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Amelia Ziemniewicz
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Przemyslaw Dudys
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Boris Görke
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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Fan SM, Li ZQ, Zhang SZ, Chen LY, Wei XY, Liang J, Zhao XQ, Su C. Multi-integrated approach for unraveling small open reading frames potentially associated with secondary metabolism in Streptomyces. mSystems 2023; 8:e0024523. [PMID: 37712700 PMCID: PMC10654065 DOI: 10.1128/msystems.00245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023] Open
Abstract
IMPORTANCE Due to their small size and special chemical features, small open reading frame (smORF)-encoding peptides (SEPs) are often neglected. However, they may play critical roles in regulating gene expression, enzyme activity, and metabolite production. Studies on bacterial microproteins have mainly focused on pathogenic bacteria, which are importance to systematically investigate SEPs in streptomycetes and are rich sources of bioactive secondary metabolites. Our study is the first to perform a global identification of smORFs in streptomycetes. We established a peptidogenomic workflow for non-model microbial strains and identified multiple novel smORFs that are potentially linked to secondary metabolism in streptomycetes. Our multi-integrated approach in this study is meaningful to improve the quality and quantity of the detected smORFs. Ultimately, the workflow we established could be extended to other organisms and would benefit the genome mining of microproteins with critical functions for regulation and engineering useful microorganisms.
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Affiliation(s)
- Si-Min Fan
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Ze-Qi Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Shi-Zhe Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Liang-Yu Chen
- ProteinT (Tianjin) biotechnology Co. Ltd., Tianjin, China
| | - Xi-Ying Wei
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Jian Liang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
- College of Biology and Geography, Yili Normal University, Yining, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Jiao, China
| | - Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
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Confirmation of Glucose Transporters through Targeted Mutagenesis and Transcriptional Analysis in Clostridium acetobutylicum. FERMENTATION 2023. [DOI: 10.3390/fermentation9010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The solvent-producing bacterium Clostridium acetobutylicum is able to grow on a variety of carbohydrates. The main hexose transport system is the phosphoenolpyruvate-dependent phosphotransferase system (PTS). When the gene glcG that encodes the glucose transporter was inactivated, the resulting mutant glcG::int(1224) grew as well as the wild type, yet its glucose consumption was reduced by 17% in a batch fermentation. Transcriptomics analysis of the phosphate-limited continuous cultures showed that the cellobiose transporter GlcCE was highly up-regulated in the mutant glcG::int(1224). The glcCE mutation did not affect growth and even consumed slightly more glucose during solventogenesis growth compared to wild type, indicating that GlcG is the primary glucose-specific PTS. Poor growth of the double mutant glcG::int(1224)-glcCE::int(193) further revealed that GlcCE was the secondary glucose PTS and that there must be other PTSs capable of glucose uptake. The observations obtained in this study provided a promising foundation to understand glucose transport in C. acetobutylicum.
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Abstract
Bacteria utilize two-component regulatory systems to sense and respond to their surroundings. Unlike other two-component systems that directly sense through a sensory domain in the histidine kinase (HK), the PhoB/PhoR two-component system requires additional proteins, including the PstSCAB phosphate transporter and the PhoU protein, to sense phosphate levels. Although PhoU is involved in phosphate signaling by connecting the PstSCAB transporter and PhoR histidine kinase, the mechanism by which PhoU controls expression of pho regulon genes has not yet been clearly understood. Here, we identified PhoU residues required for interacting with PhoR histidine kinase from the intracellular pathogen Salmonella enterica serovar Typhimurium. The PhoU Ala147 residue interacts with the PhoR PAS domain and is involved in repressing pho expression in high phosphate. Unexpectedly, the PhoU Arg184 residue interacts with the PhoR histidine kinase domain and is required for activating pho expression in low Mg2+ by increasing PhoR autophosphorylation, revealing its new function. The substitution of the Arg184 to Gly codon decreased Salmonella virulence both in macrophages and in mice, suggesting that PhoU’s role in promoting PhoR autophosphorylation is required during Salmonella infection.
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The PTS
Ntr
-KdpDE-KdpFABC Pathway Contributes to Low Potassium Stress Adaptation and Competitive Nodulation of Sinorhizobium fredii. mBio 2022; 13:e0372121. [PMID: 35491828 PMCID: PMC9239096 DOI: 10.1128/mbio.03721-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In all ecological niches, potassium is actively consumed by diverse prokaryotes and their interacting eukaryote hosts. It is only just emerging that potassium is a key player in host-pathogen interactions, and the role of potassium in mutualistic interactions remains largely unknown.
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Fosfomycin Resistance Evolutionary Pathways of Stenotrophomonas maltophilia in Different Growing Conditions. Int J Mol Sci 2022; 23:ijms23031132. [PMID: 35163052 PMCID: PMC8835530 DOI: 10.3390/ijms23031132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/24/2022] Open
Abstract
The rise of multidrug-resistant Gram-negative pathogens and the lack of novel antibiotics to address this problem has led to the rescue of old antibiotics without a relevant use, such as fosfomycin. Stenotrophomonas maltophilia is a Gram-negative, non-fermenter opportunistic pathogen that presents a characteristic low susceptibility to several antibiotics of common use. Previous work has shown that while the so-far described mechanisms of fosfomycin resistance in most bacteria consist of the inactivation of the target or the transporters of this antibiotic, as well as the production of antibiotic-inactivating enzymes, these mechanisms are not selected in S. maltophilia fosfomycin-resistant mutants. In this microorganism, fosfomycin resistance is caused by the inactivation of enzymes belonging to its central carbon metabolism, hence linking metabolism with antibiotic resistance. Consequently, it is relevant to determine how different growing conditions, including urine and synthetic sputum medium that resemble infection, could impact the evolutionary pathways towards fosfomycin resistance in S. maltophilia. Our results show that S. maltophilia is able to acquire high-level fosfomycin resistance under all tested conditions. However, although some of the genetic changes leading to resistance are common, there are specific mutations that are selected under each of the tested conditions. These results indicate that the pathways of S. maltophilia evolution can vary depending on the infection point and provide information for understanding in more detail the routes of fosfomycin resistance evolution in S. maltophilia.
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Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J. Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res 2021; 49:7088-7102. [PMID: 34157109 PMCID: PMC8266666 DOI: 10.1093/nar/gkab528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
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Affiliation(s)
- Martin Benda
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Simon Woelfel
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Debora Kálalová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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Yoo W, Choi J, Park B, Byndloss MX, Ryu S. A Nitrogen Metabolic Enzyme Provides Salmonella Fitness Advantage by Promoting Utilization of Microbiota-Derived Carbon Source. ACS Infect Dis 2021; 7:1208-1220. [PMID: 33853321 DOI: 10.1021/acsinfecdis.0c00836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microbes support their growth in vertebrate hosts by exploiting a large variety of dietary components as nutrients, which determines the composition of gut microbiota. A pathogen Salmonella expands by utilizing 1,2-propanediol, a microbiota-fermented product, during mucosal inflammation. However, it remains largely unknown how the pathogen decides which nutrient to consume from the complex mixture in the gut. Here, we show that Salmonella enterica serovar Typhimurium utilizes 1,2-propanediol by EIIANtr (a nitrogen-metabolic PTS component implicated in virulence)-mediated regulation of the pdu operon, thereby expanding in the murine intestine. Propionyl-CoA, a metabolic intermediate produced by 1,2-propanediol catabolism, elevates EIIANtr protein amounts, entailing positive feedback, thereby boosting the 1,2-propanediol-utilization process. EIIANtr promotes pdu expression by enhancing glutathione synthesis. CRP (cAMP receptor protein) induces pdu genes by increasing EIIANtr expression in response to glucose availability. Notably, EIIANtr-mediated 1,2-propanediol-utilization conferred a growth benefit even under high glucose conditions which reduces CRP activity. The EIIANtr-mediated activation is likely conserved in pathogenic enterobacteria including Escherichia coli. Collectively, our findings suggest that Salmonella promotes its fitness by precisely modulating the utilization system for microbiota-derived carbon source. They also suggest that Salmonella may integrate signals, processed via EIIANtr, into its metabolic program as well as virulence circuit.
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Affiliation(s)
- Woongjae Yoo
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeongjoon Choi
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Bookyung Park
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Vanderbilt Institute for Infection, Immunology, and Inflammation and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States of America
| | - Mariana X. Byndloss
- Vanderbilt Institute for Infection, Immunology, and Inflammation and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States of America
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
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Krüger L, Herzberg C, Wicke D, Bähre H, Heidemann JL, Dickmanns A, Schmitt K, Ficner R, Stülke J. A meet-up of two second messengers: the c-di-AMP receptor DarB controls (p)ppGpp synthesis in Bacillus subtilis. Nat Commun 2021; 12:1210. [PMID: 33619274 PMCID: PMC7900238 DOI: 10.1038/s41467-021-21306-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/19/2021] [Indexed: 12/23/2022] Open
Abstract
Many bacteria use cyclic di-AMP as a second messenger to control potassium and osmotic homeostasis. In Bacillus subtilis, several c-di-AMP binding proteins and RNA molecules have been identified. Most of these targets play a role in controlling potassium uptake and export. In addition, c-di-AMP binds to two conserved target proteins of unknown function, DarA and DarB, that exclusively consist of the c-di-AMP binding domain. Here, we investigate the function of the c-di-AMP-binding protein DarB in B. subtilis, which consists of two cystathionine-beta synthase (CBS) domains. We use an unbiased search for DarB interaction partners and identify the (p)ppGpp synthetase/hydrolase Rel as a major interaction partner of DarB. (p)ppGpp is another second messenger that is formed upon amino acid starvation and under other stress conditions to stop translation and active metabolism. The interaction between DarB and Rel only takes place if the bacteria grow at very low potassium concentrations and intracellular levels of c-di-AMP are low. We show that c-di-AMP inhibits the binding of DarB to Rel and the DarB–Rel interaction results in the Rel-dependent accumulation of pppGpp. These results link potassium and c-di-AMP signaling to the stringent response and thus to the global control of cellular physiology. In several bacteria, cyclic di-AMP mediates potassium (K+) and osmotic homeostasis. Here, the authors show that DarB, a Bacillus subtilis protein previously reported to bind cyclic di-AMP, interacts with the (p)ppGpp synthetase/hydrolase Rel in a K+-dependent manner in turn leading to Rel-dependent accumulation of pppGpp under conditions of K+ starvation.
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Affiliation(s)
- Larissa Krüger
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Dennis Wicke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Jana L Heidemann
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Service Unit LCMS Protein Analytics, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.
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The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense. mSystems 2020; 5:5/6/e00817-20. [PMID: 33144311 PMCID: PMC7646526 DOI: 10.1128/msystems.00817-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors. The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status. IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
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12
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Global control of bacterial nitrogen and carbon metabolism by a PTS Ntr-regulated switch. Proc Natl Acad Sci U S A 2020; 117:10234-10245. [PMID: 32341157 DOI: 10.1073/pnas.1917471117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance.
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Abstract
Phosphorus is required for many biological molecules and essential functions, including DNA replication, transcription of RNA, protein translation, posttranslational modifications, and numerous facets of metabolism. In order to maintain the proper level of phosphate for these processes, many bacteria adapt to changes in environmental phosphate levels. The mechanisms for sensing phosphate levels and adapting to changes have been extensively studied for multiple organisms. The phosphate response of Escherichia coli alters the expression of numerous genes, many of which are involved in the acquisition and scavenging of phosphate more efficiently. This review shares findings on the mechanisms by which E. coli cells sense and respond to changes in environmental inorganic phosphate concentrations by reviewing the genes and proteins that regulate this response. The PhoR/PhoB two-component signal transduction system is central to this process and works in association with the high-affinity phosphate transporter encoded by the pstSCAB genes and the PhoU protein. Multiple models to explain how this process is regulated are discussed.
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15
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Kale S, Strickland M, Peterkofsky A, Liu J, Tjandra N. Model of a Kinetically Driven Crosstalk between Paralogous Protein Encounter Complexes. Biophys J 2019; 117:1655-1665. [PMID: 31623885 DOI: 10.1016/j.bpj.2019.09.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 10/25/2022] Open
Abstract
Proteins interact with one another across a broad spectrum of affinities. Our understanding of the low end of this spectrum, as characterized by millimolar dissociation constants, relies on a handful of cases in which weak encounters have experimentally been identified. These weak interactions away from the specific target binding site can lead toward a higher-affinity complex. Recently, we detected weak encounters between two paralogous phosphotransferase pathways of Escherichia coli, which regulate various metabolic processes and stress responses. In addition to encounters that are known to occur between cognate proteins, i.e., those that can exchange phosphate groups with each other, surprisingly, encounters involving noncognates were also observed. It is not clear whether these "futile" encounters have a cooperative or competitive role. Using agent-based simulations, we find that the encounter complexes can be cooperative or competitive so as to increase or lower the effective binding affinity of the specific complex under different circumstances. This finding invites further questions into how organisms might exploit such low affinities to connect their signaling components.
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Affiliation(s)
- Seyit Kale
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland; National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland.
| | - Madeleine Strickland
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Alan Peterkofsky
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Jian Liu
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, John Hopkins University, Baltimore, Maryland
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland.
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16
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Park S, Yoon J, Lee CR, Lee JY, Kim YR, Jang KS, Lee KH, Seok YJ. Polar landmark protein HubP recruits flagella assembly protein FapA under glucose limitation in Vibrio vulnificus. Mol Microbiol 2019; 112:266-279. [PMID: 31058375 DOI: 10.1111/mmi.14268] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
How motile bacteria recognize their environment and decide whether to stay or navigate toward more favorable location is a fundamental issue in survival. The flagellum is an elaborate molecular device responsible for bacterial locomotion, and the flagellum-driven motility allows bacteria to move themselves to the appropriate location at the right time. Here, we identify the polar landmark protein HubP as a modulator of polar flagellation that recruits the flagellar assembly protein FapA to the old cell pole, thereby controlling its activity for the early events of flagellar assembly in Vibrio vulnificus. We show that dephosphorylated EIIAGlc of the PEP-dependent sugar transporting phosphotransferase system sequesters FapA from HubP in response to glucose and hence inhibits FapA-mediated flagellation. Thus, flagellar assembly and motility is governed by spatiotemporal control of FapA, which is orchestrated by the competition between dephosphorylated EIIAGlc and HubP, in the human pathogen V. vulnificus.
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Affiliation(s)
- Soyoung Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jihee Yoon
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Yeon-Ran Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Kyu-Ho Lee
- Department of Biological Sciences, Sogang University, Seoul, 04107, Republic of Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea
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17
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Regulation of Iron Uptake by Fine-Tuning the Iron Responsiveness of the Iron Sensor Fur. Appl Environ Microbiol 2019; 85:AEM.03026-18. [PMID: 30824449 DOI: 10.1128/aem.03026-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/23/2019] [Indexed: 02/07/2023] Open
Abstract
Iron is one of most abundant environmental metal ions but is highly limited in organisms. It is an important metal ion as it facilitates various biological processes, including catalysis of metabolic enzymes and DNA biogenesis. In bacteria, the ferric uptake regulator (Fur) protein controls iron uptake by regulating genes coding for iron transporters in response to iron concentration. This iron response is ascribed to Fur's intrinsic affinity for iron because its binding to iron dictates its regulatory function. However, we now report that the pathogen Salmonella achieves a proper response of Fur to changes in environmental iron concentrations via EIIANtr (a nitrogen metabolic phosphotransferase system component). We establish that EIIANtr increases expression of iron transporter-coding genes under low-iron conditions (i.e., nanomolar ranges) in a Fur-dependent manner, which promotes Salmonella growth under such conditions. EIIANtr directly hampers Fur binding to DNA, thereby inducing expression of those genes. This regulation allows Salmonella to express Fur-regulated genes under low-iron conditions. Our findings reveal a potentially widespread control mechanism of bacterial iron uptake systems operating in response to iron availability.IMPORTANCE Iron is a fundamental metal ion for living organisms as it facilitates various biological processes. The ferric uptake regulator (Fur) protein controls iron homeostasis in various bacterial species. It is believed that Fur's iron-dependent regulatory action is sufficient for it to function as an iron sensor. However, we now establish that the bacterial pathogen Salmonella enables Fur to properly reflect changes in surrounding iron availability by fine-tuning its responsiveness to iron. This process requires a protein that hampers Fur DNA binding at low iron concentrations. In this way, Salmonella broadens the range of iron concentrations that Fur responds to. Our findings reveal a potentially widespread control mechanism of bacterial iron homeostasis.
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18
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Abstract
Signal transduction systems dictate various cellular behaviors in response to environmental changes. To operate cellular programs appropriately, organisms have sophisticated regulatory factors to optimize the signal response. The PhoP/PhoQ master virulence regulatory system of the intracellular pathogen Salmonella enterica is activated inside acidic macrophage phagosomes. Here we report that Salmonella delays the activation of this system inside macrophages using an inhibitory protein, EIIANtr (a component of the nitrogen-metabolic phosphotransferase system). We establish that EIIANtr directly restrains PhoP binding to its target promoter, thereby negatively controlling the expression of PhoP-activated genes. PhoP furthers its activation by promoting Lon-mediated degradation of EIIANtr at acidic pH. These results suggest that Salmonella ensures robust activation of its virulence system by suspending the activation of PhoP until a sufficient level of active PhoP is present to overcome the inhibitory effect of EIIANtr Our findings reveal how a pathogen precisely and efficiently operates its virulence program during infection.IMPORTANCE To accomplish successful infection, pathogens must operate their virulence programs in a precise, time-sensitive, and coordinated manner. A major question is how pathogens control the timing of virulence gene expression during infection. Here we report that the intracellular pathogen Salmonella controls the timing and level of virulence gene expression by using an inhibitory protein, EIIANtr A DNA binding master virulence regulator, PhoP, controls various virulence genes inside acidic phagosomes. Salmonella decreases EIIANtr amounts at acidic pH in a Lon- and PhoP-dependent manner. This, in turn, promotes expression of the PhoP-activated virulence program because EIIANtr hampers activation of PhoP-regulated genes by interfering with PhoP binding to DNA. EIIANtr enables Salmonella to impede the activation of PhoP-regulated gene expression inside macrophages. Our findings suggest that Salmonella achieves programmed delay of virulence gene activation by adjusting levels of an inhibitory factor.
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Engineering of phosphoenolpyruvate: carbohydrate phosphotransferase system increased acetate assimilation in Escherichia coli. 3 Biotech 2019; 9:77. [PMID: 30800588 DOI: 10.1007/s13205-019-1600-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/31/2019] [Indexed: 12/27/2022] Open
Abstract
Acetate is a potential low-cost carbon source and can be used for microbial production of valuable chemicals in Escherichia coli. In this study, separate and simultaneous inactivation of the ptsG, ptsI, and ptsP genes involved in the phosphoenolpyruvate:carbohydrate phosphotransferase system was performed in E. coli and the effects on cell growth and acetate assimilation were evaluated. The mutant strain with double deletion of ptsG and ptsP exhibited faster acetate use than the other mutants. Inactivation of ptsI seriously reduced acetate consumption. This work provides a novel engineering target for improving acetate use rates.
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Abstract
SixA, a well-conserved protein found in proteobacteria, actinobacteria, and cyanobacteria, is the only reported example of a bacterial phosphohistidine phosphatase. A single protein target of SixA has been reported to date: the Escherichia coli histidine kinase ArcB. The present work analyzes an ArcB-independent growth defect of a sixA deletion in E. coli A screen for suppressors, analysis of various mutants, and phosphorylation assays indicate that SixA modulates phosphorylation of the nitrogen-related phosphotransferase system (PTSNtr). The PTSNtr is a widely conserved bacterial pathway that regulates diverse metabolic processes through the phosphorylation states of its protein components, EINtr, NPr, and EIIANtr, which receive phosphoryl groups on histidine residues. However, a mechanism for dephosphorylating this system has not been reported. The results presented here suggest a model in which SixA removes phosphoryl groups from the PTSNtr by acting on NPr. This work uncovers a new role for the phosphohistidine phosphatase SixA and, through factors that affect SixA expression or activity, may point to additional inputs that regulate the PTSNtr IMPORTANCE One common means to regulate protein activity is through phosphorylation. Protein phosphatases exist to reverse this process, returning the protein to the unphosphorylated form. The vast majority of protein phosphatases that have been identified target phosphoserine, phosphotheronine, and phosphotyrosine. A widely conserved phosphohistidine phosphatase was identified in Escherichia coli 20 years ago but remains relatively understudied. The present work shows that this phosphatase modulates the nitrogen-related phosphotransferase system, a pathway that is regulated by nitrogen and carbon metabolism and affects diverse aspects of bacterial physiology. Until now, there was no known mechanism for removing phosphoryl groups from this pathway.
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Abstract
σN (also σ54) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σN is encoded as the first gene of a five-gene operon including rpoN (σN), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σN has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors. For most pathogens how this is achieved is unknown. In enterohemorrhagic Escherichia coli (EHEC) O157, Salmonella enterica, and Borrelia burgdorferi, regulation of virulence by σN requires another alternative sigma factor, σS, yet the model by which σN-σS virulence regulation is predicted to occur is varied in each of these pathogens. In this review, the importance of σN to bacterial pathogenesis is introduced, and common features of σN-dependent virulence regulation discussed. Emphasis is placed on the molecular mechanisms underlying σN virulence regulation in E. coli O157. This includes a review of the structure and function of regulatory pathways connecting σN to virulence expression, predicted input signals for pathway stimulation, and the role for cognate σN activators in initiation of gene systems determining pathogenic behavior.
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22
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Rsd balances (p)ppGpp level by stimulating the hydrolase activity of SpoT during carbon source downshift in Escherichia coli. Proc Natl Acad Sci U S A 2018; 115:E6845-E6854. [PMID: 29915072 PMCID: PMC6055147 DOI: 10.1073/pnas.1722514115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most bacteria accumulate the molecular alarmone (p)ppGpp to divert resources away from growth and division toward biosynthesis under various nutrient limitations. Despite its crucial role, uncontrolled accumulation of this alarmone causes severe growth inhibition and cell death. Thus, fine-tuning the cellular (p)ppGpp level is required to ensure survival and adaptation under harsh nutritional conditions. Here, we identify Rsd as a stimulator of the (p)ppGpp-degrading activity of SpoT during carbon source downshift in Escherichia coli, and this regulation is controlled by the phosphorylation state of HPr, a general component of the PEP-dependent sugar transport system. This study establishes a direct link between sugar signaling and the bacterial stringent response. Bacteria respond to nutritional stresses by changing the cellular concentration of the alarmone (p)ppGpp. This control mechanism, called the stringent response, depends on two enzymes, the (p)ppGpp synthetase RelA and the bifunctional (p)ppGpp synthetase/hydrolase SpoT in Escherichia coli and related bacteria. Because SpoT is the only enzyme responsible for (p)ppGpp hydrolysis in these bacteria, SpoT activity needs to be tightly regulated to prevent the uncontrolled accumulation of (p)ppGpp, which is lethal. To date, however, no such regulation of SpoT (p)ppGpp hydrolase activity has been documented in E. coli. In this study, we show that Rsd directly interacts with SpoT and stimulates its (p)ppGpp hydrolase activity. Dephosphorylated HPr, but not phosphorylated HPr, of the phosphoenolpyruvate-dependent sugar phosphotransferase system could antagonize the stimulatory effect of Rsd on SpoT (p)ppGpp hydrolase activity. Thus, we suggest that Rsd is a carbon source-dependent regulator of the stringent response in E. coli.
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23
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Gravina F, Sanchuki HS, Rodrigues TE, Gerhardt ECM, Pedrosa FO, Souza EM, Valdameri G, de Souza GA, Huergo LF. Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes. J Proteomics 2017; 174:28-35. [PMID: 29274402 DOI: 10.1016/j.jprot.2017.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/29/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022]
Abstract
The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTSNtr (nitrogen related PTS). PTSNtr is composed of EINtr (ptsP), NPr (ptsO), and EIIANtr (ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EINtr, NPr and them to EIIANtr. PTSNtr is not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EINtr is regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTSNtr is designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed. SIGNIFICANCE The nitrogen related PTSNtr phosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTSNtr phosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.
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Affiliation(s)
- Fernanda Gravina
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Heloisa S Sanchuki
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Thiago E Rodrigues
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | | | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Gláucio Valdameri
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Departamento de Análises Clínicas, UFPR, Curitiba, PR, Brazil
| | - Gustavo A de Souza
- Oslo University Hospital, The Proteomics Core Facility, Rikshospitalet, Oslo, Norway; Instituto do Cérebro, UFRN, Natal, RN, Brazil
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Setor Litoral, UFPR, Matinhos, PR, Brazil.
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A Novel Regulatory Pathway for K + Uptake in the Legume Symbiont Azorhizobium caulinodans in Which TrkJ Represses the kdpFABC Operon at High Extracellular K + Concentrations. Appl Environ Microbiol 2017; 83:AEM.01197-17. [PMID: 28778893 DOI: 10.1128/aem.01197-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 07/28/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria have multiple K+ uptake systems. Escherichia coli, for example, has three types of K+ uptake systems, which include the low-K+-inducible KdpFABC system and two constitutive systems, Trk (TrkAG and TrkAH) and Kup. Azorhizobium caulinodans ORS571, a rhizobium that forms nitrogen-fixing nodules on the stems and roots of Sesbania rostrata, also has three types of K+ uptake systems. Through phylogenetic analysis, we found that A. caulinodans has two genes homologous to trkG and trkH, designated trkI and trkJ We also found that trkI is adjacent to trkA in the genome and these two genes are transcribed as an operon; however, trkJ is present at a distinct locus. Our results demonstrated that trkAI, trkJ, and kup were expressed in the wild-type stem nodules, whereas kdpFABC was not. Interestingly, Δkup and Δkup ΔkdpA mutants formed Fix- nodules, while the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant formed Fix+ nodules, suggesting that with the additional deletion of Trk system genes in the Δkup mutant, Fix+ nodule phenotypes were recovered. kdpFABC of the Δkup ΔtrkJ mutant was expressed in stem nodules, but not in the free-living state, under high-K+ conditions. However, kdpFABC of the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant was highly expressed even under high-K+ conditions. The cytoplasmic K+ levels in the Δkup ΔtrkA ΔtrkI mutant, which did not express kdpFABC under high-K+ conditions, were markedly lower than those in the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant. Taking all these results into consideration, we propose that TrkJ is involved in the repression of kdpFABC in response to high external K+ concentrations and that the TrkAI system is unable to function in stem nodules.IMPORTANCE K+ is a major cytoplasmic cation in prokaryotic and eukaryotic cells. Bacteria have multiple K+ uptake systems to control the cytoplasmic K+ levels. In many bacteria, the K+ uptake system KdpFABC is expressed under low-K+ conditions. For years, many researchers have argued over how bacteria sense K+ concentrations. Although KdpD of Escherichia coli is known to sense both cytoplasmic and extracellular K+ concentrations, the detailed mechanism of K+ sensing is still unclear. In this study, we propose that the transmembrane TrkJ protein of Azorhizobium caulinodans acts as a sensor for the extracellular K+ concentration and that high extracellular K+ concentrations repress the expression of KdpFABC via TrkJ.
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25
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Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM. Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry. Front Cell Infect Microbiol 2017; 7:354. [PMID: 28848714 PMCID: PMC5554493 DOI: 10.3389/fcimb.2017.00354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 07/21/2017] [Indexed: 01/31/2023] Open
Abstract
The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver.
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Affiliation(s)
- Liljana Petrovska
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Yue Tang
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Melissa J Jansen van Rensburg
- Department of Zoology, University of OxfordOxford, United Kingdom.,NIHR Health Protection Research Unit in Gastrointestinal Infections, University of OxfordOxford, United Kingdom
| | - Shaun Cawthraw
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Javier Nunez
- Veterinary Surveillance, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Samuel K Sheppard
- Department of Biology and Biotechnology, The Milner Centre for Evolution, University of BathBath, United Kingdom
| | - Richard J Ellis
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Adrian M Whatmore
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Tim R Crawshaw
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Richard M Irvine
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
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26
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Mörk-Mörkenstein M, Heermann R, Göpel Y, Jung K, Görke B. Non-canonical activation of histidine kinase KdpD by phosphotransferase protein PtsN through interaction with the transmitter domain. Mol Microbiol 2017; 106:54-73. [PMID: 28714556 DOI: 10.1111/mmi.13751] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 02/02/2023]
Abstract
The two-component system KdpD/KdpE governs K+ homeostasis by controlling synthesis of the high affinity K+ transporter KdpFABC. When sensing low environmental K+ concentrations, the dimeric kinase KdpD autophosphorylates in trans and transfers the phosphoryl-group to the response regulator KdpE, which subsequently activates kdpFABC transcription. In Escherichia coli, KdpD can also be activated by interaction with the non-phosphorylated form of the accessory protein PtsN. PtsN stimulates KdpD kinase activity thereby increasing phospho-KdpE levels. Here, we analyzed the interplay between KdpD/KdpE and PtsN. PtsN binds specifically to the catalytic DHp domain of KdpD, which is also contacted by KdpE. Accordingly, PtsN and KdpE compete for binding, providing a paradox. Low levels of non-phosphorylated PtsN stimulate, whereas high amounts reduce kdpFABC expression by blocking access of KdpE to KdpD. Ligand fishing experiments provided insight as they revealed ternary complex formation of PtsN/KdpD2 /KdpE in vivo demonstrating that PtsN and KdpE bind different protomers in the KdpD dimer. PtsN may bind one protomer to stimulate phosphorylation of the second KdpD protomer, which then phosphorylates bound KdpE. Phosphorylation of PtsN prevents its incorporation in ternary complexes. Interaction with the conserved DHp domain enables PtsN to regulate additional kinases such as PhoR.
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Affiliation(s)
- Markus Mörk-Mörkenstein
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ralf Heermann
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried/München, Germany
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried/München, Germany
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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27
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Binepal G, Wenderska IB, Crowley P, Besingi RN, Senadheera DB, Jeannine Brady L, Cvitkovitch DG. K+ modulates genetic competence and the stress regulon of Streptococcus mutans. MICROBIOLOGY-SGM 2017; 163:719-730. [PMID: 28530170 DOI: 10.1099/mic.0.000458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Potassium (K+) is the most abundant cation in dental plaque fluid. Previously, we reported the link between K+ transport via Trk2 in Streptococcus mutans and its two critical virulence attributes: acid tolerance and surface adhesion. Herein, we build further on the intimate link between K+ levels and S. mutans biology. High (>25 mM) versus low (≤5 mM) K+ concentrations in the growth medium affected conformational epitopes of cell surface-localized adhesin P1. At low K+, the expression of stress response elements gcrR and codY, cell-adhesion-associated genes such as spaP and metabolism-associated genes such as bglP was induced at stationary phase (P<0.05), suggesting that K+-mediated regulation is growth phase-dependent and stress-sensitive. Production of the newly discovered secretory protein encoded by SMU_63c was strongly dependent on the availability of K+ and growth phase. This protein is a newly discovered regulator of genetic competence and biofilm cell density. Thus, the influence of K+ on DNA transformation efficiency was also examined. Compared with 25 mM K+ concentration, the presence of low K+ reduced the transformation frequency by 100-fold. Genetic transformation was abolished in a strain lacking a Trk2 system under all K+ concentrations tested. Consistent with these findings, repression of competence-associated genes, comS and comX, was observed under low environmental K+ conditions and in the strain lacking Trk2. Taken together, these results highlight a pivotal role for environmental K+ as a regulatory cation that modulates stress responses and genetic transformation in S. mutans.
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Affiliation(s)
- Gursonika Binepal
- Department of Oral Microbiology, Faculty of Dentistry, University of Toronto, ON M5G 1G6, Toronto, Canada
| | - Iwona B Wenderska
- Department of Oral Microbiology, Faculty of Dentistry, University of Toronto, ON M5G 1G6, Toronto, Canada
| | - Paula Crowley
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Richard N Besingi
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Dilani B Senadheera
- Department of Oral Microbiology, Faculty of Dentistry, University of Toronto, ON M5G 1G6, Toronto, Canada
| | - L Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Dennis G Cvitkovitch
- Department of Oral Microbiology, Faculty of Dentistry, University of Toronto, ON M5G 1G6, Toronto, Canada
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Barbier T, Zúñiga-Ripa A, Moussa S, Plovier H, Sternon JF, Lázaro-Antón L, Conde-Álvarez R, De Bolle X, Iriarte M, Moriyón I, Letesson JJ. Brucella central carbon metabolism: an update. Crit Rev Microbiol 2017; 44:182-211. [PMID: 28604247 DOI: 10.1080/1040841x.2017.1332002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The brucellae are facultative intracellular pathogens causing brucellosis, an important zoonosis. Here, we review the nutritional, genetic, proteomic and transcriptomic studies on Brucella carbon uptake and central metabolism, information that is needed for a better understanding of Brucella virulence. There is no uniform picture across species but the studies suggest primary and/or secondary transporters for unknown carbohydrates, lactate, glycerol phosphate, erythritol, xylose, ribose, glucose and glucose/galactose, and routes for their incorporation to central metabolism, including an erythritol pathway feeding the pentose phosphate cycle. Significantly, all brucellae lack phosphoenolpyruvate synthase and phosphofructokinase genes, which confirms previous evidence on glycolysis absence, but carry all Entner-Doudoroff (ED) pathway and Krebs cycle (and glyoxylate pathway) genes. However, glucose catabolism proceeds through the pentose phosphate cycle in the classical species, and the ED pathway operates in some rodent-associated brucellae, suggesting an ancestral character for this pathway in this group. Gluconeogenesis is functional but does not rely exclusively on classical fructose bisphosphatases. Evidence obtained using infection models is fragmentary but suggests the combined or sequential use of hexoses/pentoses, amino acids and gluconeogenic substrates. We also discuss the role of the phosphotransferase system, stringent reponse, quorum sensing, BvrR/S and sRNAs in metabolism control, an essential aspect of the life style of facultative intracellular parasites.
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Affiliation(s)
- T Barbier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - A Zúñiga-Ripa
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - S Moussa
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - H Plovier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - J F Sternon
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - L Lázaro-Antón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - R Conde-Álvarez
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - X De Bolle
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - M Iriarte
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - I Moriyón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - J J Letesson
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
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The Legionella pneumophila Incomplete Phosphotransferase System Is Required for Optimal Intracellular Growth and Maximal Expression of PmrA-Regulated Effectors. Infect Immun 2017; 85:IAI.00121-17. [PMID: 28373357 DOI: 10.1128/iai.00121-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/30/2017] [Indexed: 11/20/2022] Open
Abstract
The nitrogen phosphotransferase system (PTSNtr) is a regulatory cascade present in many bacteria, where it controls different functions. This system is usually composed of three basic components: enzyme INtr (EINtr), NPr, and EIIANtr (encoded by the ptsP, ptsO, and ptsN genes, respectively). In Legionella pneumophila, as well as in many other Legionella species, the EIIANtr component is missing. However, we found that deletion mutations in both ptsP and ptsO are partially attenuated for intracellular growth. Furthermore, these two PTSNtr components were found to be required for maximal expression of effector-encoding genes regulated by the transcriptional activator PmrA. Genetic analyses which include the construction of single and double deletion mutants and overexpression of wild-type and mutated forms of EINtr, NPr, and PmrA indicated that the PTSNtr components affect the expression of PmrA-regulated genes via PmrA and independently from PmrB and that EINtr and NPr are part of the same cascade and require their conserved histidine residues in order to function. Furthermore, expression of the Legionella micdadei EIINtr component in L. pneumophila resulted in a reduction in the levels of expression of PmrA-regulated genes which was completely dependent on the L. pneumophila PTS components and the L. micdadei EIINtr conserved histidine residue. Moreover, reconstruction of the L. pneumophila PTS in vitro indicated that EINtr is phosphorylated by phosphoenolpyruvate (PEP) and transfers its phosphate to NPr. Our results demonstrate that the L. pneumophila incomplete PTSNtr is functional and involved in the expression of effector-encoding genes regulated by PmrA.
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Enzyme IIA Ntr Regulates Salmonella Invasion Via 1,2-Propanediol And Propionate Catabolism. Sci Rep 2017; 7:44827. [PMID: 28333132 PMCID: PMC5363084 DOI: 10.1038/srep44827] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/15/2017] [Indexed: 11/08/2022] Open
Abstract
Many Proteobacteria possess a nitrogen-metabolic phosphotransferase system (PTSNtr) consisting of EINtr, NPr, and EIIANtr (encoded by ptsP, ptsO, and ptsN, respectively). The PTSNtr plays diverse regulatory roles, but the substrate phosphorylated by EIIANtr and its primary functions have not yet been identified. To comprehensively understand the roles of PTSNtr in Salmonella Typhimurium, we compared the whole transcriptomes of wild-type and a ΔptsN mutant. Genome-wide RNA sequencing revealed that 3.5% of the annotated genes were up- or down-regulated by three-fold or more in the absence of EIIANtr. The ΔptsN mutant significantly down-regulated the expression of genes involved in vitamin B12 synthesis, 1,2-propanediol utilization, and propionate catabolism. Moreover, the invasiveness of the ΔptsN mutant increased about 5-fold when 1,2-propanediol or propionate was added, which was attributable to the increased stability of HilD, the transcriptional regulator of Salmonella pathogenicity island-1. Interestingly, an abundance of 1,2-propanediol or propionate promoted the production of EIIANtr, suggesting the possibility of a positive feedback loop between EIIANtr and two catabolic pathways. These results demonstrate that EIIANtr is a key factor for the utilization of 1,2-propanediol and propionate as carbon and energy sources, and thereby modulates the invasiveness of Salmonella via 1,2-propanediol or propionate catabolism.
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Hawkins JP, Oresnik IJ. Characterisation of a gene encoding a membrane protein that affects exopolysaccharide production and intracellular Mg2+ concentrations in Ensifer meliloti. FEMS Microbiol Lett 2017; 364:3072829. [DOI: 10.1093/femsle/fnx061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
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The general PTS component HPr determines the preference for glucose over mannitol. Sci Rep 2017; 7:43431. [PMID: 28225088 PMCID: PMC5320558 DOI: 10.1038/srep43431] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/24/2017] [Indexed: 11/08/2022] Open
Abstract
Preferential sugar utilization is a widespread phenomenon in biological systems. Glucose is usually the most preferred carbon source in various organisms, especially in bacteria where it is taken up via the phosphoenolpyruvate:sugar phosphotransferase system (PTS). The currently proposed model for glucose preference over non-PTS sugars in enteric bacteria including E. coli is strictly dependent on the phosphorylation state of the glucose-specific PTS component, enzyme IIAGlc (EIIAGlc). However, the mechanism of the preference among PTS sugars is largely unknown in Gram-negative bacteria. Here, we show that glucose preference over another PTS sugar, mannitol, is absolutely dependent on the general PTS component HPr, but not on EIIAGlc, in E. coli. Dephosphorylated HPr accumulates during the transport of glucose and interacts with the mannitol operon regulator, MtlR, to augment its repressor activity. This interaction blocks the inductive effect of mannitol on the mannitol operon expression and results in the inhibition of mannitol utilization.
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Galinier A, Deutscher J. Sophisticated Regulation of Transcriptional Factors by the Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System. J Mol Biol 2017; 429:773-789. [PMID: 28202392 DOI: 10.1016/j.jmb.2017.02.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/04/2017] [Indexed: 11/16/2022]
Abstract
The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is a carbohydrate transport and phosphorylation system present in bacteria of all different phyla and in archaea. It is usually composed of three proteins or protein complexes, enzyme I, HPr, and enzyme II, which are phosphorylated at histidine or cysteine residues. However, in many bacteria, HPr can also be phosphorylated at a serine residue. The PTS not only functions as a carbohydrate transporter but also regulates numerous cellular processes either by phosphorylating its target proteins or by interacting with them in a phosphorylation-dependent manner. The target proteins can be catabolic enzymes, transporters, and signal transduction proteins but are most frequently transcriptional regulators. In this review, we will describe how PTS components interact with or phosphorylate proteins to regulate directly or indirectly the activity of transcriptional repressors, activators, or antiterminators. We will briefly summarize the well-studied mechanism of carbon catabolite repression in firmicutes, where the transcriptional regulator catabolite control protein A needs to interact with seryl-phosphorylated HPr in order to be functional. We will present new results related to transcriptional activators and antiterminators containing specific PTS regulation domains, which are the phosphorylation targets for three different types of PTS components. Moreover, we will discuss how the phosphorylation level of the PTS components precisely regulates the activity of target transcriptional regulators or antiterminators, with or without PTS regulation domain, and how the availability of PTS substrates and thus the metabolic status of the cell are connected with various cellular processes, such as biofilm formation or virulence of certain pathogens.
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Affiliation(s)
- Anne Galinier
- Laboratoire de Chimie Bactérienne, UPR 9043, CNRS, Aix Marseille Université, IMM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Centre National de la Recherche Scientifique, UMR8261 (affiliated with the Univ. Paris Diderot, Sorbonne, Paris Cité), Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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34
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Muriel-Millán LF, Moreno S, Gallegos-Monterrosa R, Espín G. Unphosphorylated EIIA Ntr induces ClpAP-mediated degradation of RpoS in Azotobacter vinelandii. Mol Microbiol 2017; 104:197-211. [PMID: 28097724 DOI: 10.1111/mmi.13621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2017] [Indexed: 02/02/2023]
Abstract
The nitrogen-related phosphotransferase system (PTSNtr ) is composed of the EINtr , NPr and EIIANtr proteins that form a phosphorylation cascade from phosphoenolpyruvate. PTSNtr is a global regulatory system present in most Gram-negative bacteria that controls some pivotal processes such as potassium and phosphate homeostasis, virulence, nitrogen fixation and ABC transport activation. In the soil bacterium Azotobacter vinelandii, unphosphorylated EIIANtr negatively regulates the expression of genes related to the synthesis of the bioplastic polyester poly-β-hydroxybutyrate (PHB) and cyst-specific lipids alkylresorcinols (ARs). The mechanism by which EIIANtr controls gene expression in A. vinelandii is not known. Here, we show that, in presence of unphosphorylated EIIANtr , the stability of the stationary phase sigma factor RpoS, which is necessary for transcriptional activation of PHB and ARs synthesis related genes, is reduced, and that the inactivation of genes coding for ClpAP protease complex in strains that carry unphosphorylated EIIANtr , restored the levels and in vivo stability of RpoS, as well as the synthesis of PHB and ARs. Taken together, our results reveal a novel mechanism, by which EIIANtr globally controls gene expression in A. vinelandii, where the unphosphorylated EIIANtr induces the degradation of RpoS by the proteolytic complex ClpAP.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Ramsés Gallegos-Monterrosa
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
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Strickland M, Stanley AM, Wang G, Botos I, Schwieters CD, Buchanan SK, Peterkofsky A, Tjandra N. Structure of the NPr:EIN Ntr Complex: Mechanism for Specificity in Paralogous Phosphotransferase Systems. Structure 2016; 24:2127-2137. [PMID: 27839951 PMCID: PMC5143221 DOI: 10.1016/j.str.2016.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 10/03/2016] [Accepted: 10/12/2016] [Indexed: 12/13/2022]
Abstract
Paralogous enzymes arise from gene duplication events that confer a novel function, although it is unclear how cross-reaction between the original and duplicate protein interaction network is minimized. We investigated HPr:EIsugar and NPr:EINtr, the initial complexes of paralogous phosphorylation cascades involved in sugar import and nitrogen regulation in bacteria, respectively. Although the HPr:EIsugar interaction has been well characterized, involving multiple complexes and transient interactions, the exact nature of the NPr:EINtr complex was unknown. We set out to identify the key features of the interaction by performing binding assays and elucidating the structure of NPr in complex with the phosphorylation domain of EINtr (EINNtr), using a hybrid approach involving X-ray, homology, and sparse nuclear magnetic resonance. We found that the overall fold and active-site structure of the two complexes are conserved in order to maintain productive phosphorylation, however, the interface surface potential differs between the two complexes, which prevents cross-reaction.
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Affiliation(s)
- Madeleine Strickland
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Marie Stanley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guangshun Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan Peterkofsky
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Radolf JD, Deka RK, Anand A, Šmajs D, Norgard MV, Yang XF. Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen. Nat Rev Microbiol 2016; 14:744-759. [PMID: 27721440 DOI: 10.1038/nrmicro.2016.141] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The past two decades have seen a worldwide resurgence in infections caused by Treponema pallidum subsp. pallidum, the syphilis spirochete. The well-recognized capacity of the syphilis spirochete for early dissemination and immune evasion has earned it the designation 'the stealth pathogen'. Despite the many hurdles to studying syphilis pathogenesis, most notably the inability to culture and to genetically manipulate T. pallidum, in recent years, considerable progress has been made in elucidating the structural, physiological, and regulatory facets of T. pallidum pathogenicity. In this Review, we integrate this eclectic body of information to garner fresh insights into the highly successful parasitic lifestyles of the syphilis spirochete and related pathogenic treponemes.
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Affiliation(s)
- Justin D Radolf
- Departments of Medicine, Pediatrics, Genetics and Genomic Science, Molecular Biology and Biophysics, and Immunology, UConn Health, 263 Farmington Avenue, Farmington, Connecticut 06030-3715, USA
| | - Ranjit K Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9048, USA
| | - Arvind Anand
- Department of Medicine, UConn Health, 263 Farmington Avenue, Farmington, Connecticut 06030-3715, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Michael V Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9048, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Yoo W, Yoon H, Seok YJ, Lee CR, Lee HH, Ryu S. Fine-tuning of amino sugar homeostasis by EIIA(Ntr) in Salmonella Typhimurium. Sci Rep 2016; 6:33055. [PMID: 27628932 PMCID: PMC5024086 DOI: 10.1038/srep33055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/17/2016] [Indexed: 11/08/2022] Open
Abstract
The nitrogen-metabolic phosphotransferase system, PTS(Ntr), consists of the enzymes I(Ntr), NPr and IIA(Ntr) that are encoded by ptsP, ptsO, and ptsN, respectively. Due to the proximity of ptsO and ptsN to rpoN, the PTS(Ntr) system has been postulated to be closely related with nitrogen metabolism. To define the correlation between PTS(Ntr) and nitrogen metabolism, we performed ligand fishing with EIIA(Ntr) as a bait and revealed that D-glucosamine-6-phosphate synthase (GlmS) directly interacted with EIIA(Ntr). GlmS, which converts D-fructose-6-phosphate (Fru6P) into D-glucosamine-6-phosphate (GlcN6P), is a key enzyme producing amino sugars through glutamine hydrolysis. Amino sugar is an essential structural building block for bacterial peptidoglycan and LPS. We further verified that EIIA(Ntr) inhibited GlmS activity by direct interaction in a phosphorylation-state-dependent manner. EIIA(Ntr) was dephosphorylated in response to excessive nitrogen sources and was rapidly degraded by Lon protease upon amino sugar depletion. The regulation of GlmS activity by EIIA(Ntr) and the modulation of glmS translation by RapZ suggest that the genes comprising the rpoN operon play a key role in maintaining amino sugar homeostasis in response to nitrogen availability and the amino sugar concentration in the bacterial cytoplasm.
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Affiliation(s)
- Woongjae Yoo
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 17058, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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Ouyang J, Guo W, Li B, Gu L, Zhang H, Xinhua Chen H. Erratum to “Proteomic analysis of differential protein expression in Acidithiobacillus ferrooxidans cultivated in high potassium concentration” [Microbiol. Res. 168 (7) (2013) 455–460]. Microbiol Res 2016; 182:163-8. [PMID: 27062771 DOI: 10.1016/j.micres.2015.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile that oxidizes ferrous iron or sulfur compounds to obtain energy in the presence of various ions. To investigate the potassium ion response of A. ferrooxidans, we conducted a proteomics analysis. We identified eight proteins that were differentially expressed in the presence of high potassium concentration, including four up-regulated and four down-regulated proteins. Transcription levels of the genes encoding differential expressed proteins were subsequently analyzed by Northern blot in the presence of high potassium concentration. Among the up-regulated proteins, GDP-mannose 4,6-dehydratase, ribose 5-phosphate isomerase A and ribose-phosphate pyrophosphokinase were known to be implicated in the synthesis of glycocalyx, suggesting that the formation of glycocalyx might be involved in the A. ferrooxidans response to high potassium concentration. Thickening of the glycocalyx layer was also observed in cells cultivated under high potassium concentration via transmission electronic microscopy (TEM) analysis. Among the down-regulated proteins, ATP synthase F1 delta subunit and ATP synthase F1 beta subunit were two important components of ATP synthase. ATP synthase (P-ATPase) is directly linked to the transport of potassium into the cell, thus Acidithiobacillus ferrooxidans might just reduce the quantity of ATP synthase to offset the high potassium level in the culture medium. Therefore, the results obtained here provide some new clues to improve our understanding of the response of A. ferrooxidans to high potassium concentration.
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Growth Inhibition by External Potassium of Escherichia coli Lacking PtsN (EIIANtr) Is Caused by Potassium Limitation Mediated by YcgO. J Bacteriol 2016; 198:1868-1882. [PMID: 27137496 DOI: 10.1128/jb.01029-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED The absence of PtsN, the terminal phosphoacceptor of the phosphotransferase system comprising PtsP-PtsO-PtsN, in Escherichia coli confers a potassium-sensitive (K(s)) phenotype as the external K(+) concentration ([K(+)]e) is increased above 5 mM. A growth-inhibitory increase in intracellular K(+) content, resulting from hyperactivated Trk-mediated K(+) uptake, is thought to cause this K(s) We provide evidence that the K(s) of the ΔptsN mutant is associated with K(+) limitation. Accordingly, the moderate K(s) displayed by the ΔptsN mutant was exacerbated in the absence of the Trk and Kup K(+) uptake transporters and was associated with reduced cellular K(+) content. Conversely, overproduction of multiple K(+) uptake proteins suppressed the K(s) Expression of PtsN variants bearing the H73A, H73D, and H73E substitutions of the phosphorylation site histidine of PtsN complemented the K(s) Absence of the predicted inner membrane protein YcgO (also called CvrA) suppressed the K(s), which was correlated with elevated cellular K(+) content in the ΔptsN mutant, but the ΔptsN mutation did not alter YcgO levels. Heterologous overexpression of ycgO also led to K(s) that was associated with reduced cellular K(+) content, exacerbated by the absence of Trk and Kup and alleviated by overproduction of Kup. Our findings are compatible with a model that postulates that K(s) in the ΔptsN mutant occurs due to K(+) limitation resulting from activation of K(+) efflux mediated by YcgO, which may be additionally stimulated by [K(+)]e, implicating a role for PtsN (possibly its dephosphorylated form) as an inhibitor of YcgO activity. IMPORTANCE This study examines the physiological link between the phosphotransferase system comprising PtsP-PtsO-PtsN and K(+) ion metabolism in E. coli Studies on the physiological defect that renders an E. coli mutant lacking PtsN to be growth inhibited by external K(+) indicate that growth impairment results from cellular K(+) limitation that is mediated by YcgO, a predicted inner membrane protein. Additional observations suggest that dephospho-PtsN may inhibit and external K(+) may stimulate K(+) limitation mediated by YcgO. It is speculated that YcgO-mediated K(+) limitation may be an output of a response to certain stresses, which by modulating the phosphotransfer capacity of the PtsP-PtsO-PtsN phosphorelay leads to growth cessation and stress tolerance.
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Park S, Park YH, Lee CR, Kim YR, Seok YJ. Glucose induces delocalization of a flagellar biosynthesis protein from the flagellated pole. Mol Microbiol 2016; 101:795-808. [PMID: 27218601 DOI: 10.1111/mmi.13424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 01/08/2023]
Abstract
To survive in a continuously changing environment, bacteria sense concentration gradients of attractants or repellents, and purposefully migrate until a more favourable habitat is encountered. While glucose is known as the most effective attractant, the flagellar biosynthesis and hence chemotactic motility has been known to be repressed by glucose in some bacteria. To date, the only known regulatory mechanism of the repression of flagellar synthesis by glucose is via downregulation of the cAMP level, as shown in a few members of the family Enterobacteriaceae. Here we show that, in Vibrio vulnificus, the glucose-mediated inhibition of flagellar motility operates by a completely different mechanism. In the presence of glucose, EIIA(Glc) is dephosphorylated and inhibits the polar localization of FapA (flagellar assembly protein A) by sequestering it from the flagellated pole. A loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility. However, when glucose is depleted, EIIA(Glc) is phosphorylated and releases FapA such that free FapA can be localized back to the pole and trigger flagellation. Together, these data provide new insight into a bacterial strategy to reach and stay in the glucose-rich area.
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Affiliation(s)
- Soyoung Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, 17058, Republic of Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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Søndberg E, Jelsbak L. Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice. BMC Microbiol 2016; 16:30. [PMID: 26955808 PMCID: PMC4784465 DOI: 10.1186/s12866-016-0646-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/25/2016] [Indexed: 01/27/2023] Open
Abstract
Background Typhoid fever caused by Salmonella enterica serovar Typhi (S. Typhi) is a severe systemic human disease and endemic in regions of the world with poor drinking water quality and sewage treatment facilities. A significant number of patients become asymptomatic life-long carriers of S. Typhi and serve as the reservoir for the disease. The specific mechanisms and adaptive strategies enabling S. Typhi to survive inside the host for extended periods are incompletely understood. Yet, elucidation of these processes is of major importance for improvement of therapeutic strategies. In the current study genetic adaptation during experimental chronic S. Typhimurium infections of mice, an established model of chronic typhoid fever, was probed as an approach for studying the molecular mechanisms of host-adaptation during long-term host-association. Results Individually sequence-tagged wild type strains of S. Typhimurium 4/74 were used to establish chronic infections of 129X1/SvJ mice. Over the course of infections, S. Typhimurium bacteria were isolated from feces and from livers and spleens upon termination of the experiment. In all samples dominant clones were identified and select clones were subjected to whole genome sequencing. Dominant clones isolated from either systemic organs or fecal samples exhibited distinct single nucleotide polymorphisms (SNPs). One mouse appeared to have distinct adapted clones in the spleen and liver, respectively. Three mice were colonized in the intestines by the same clone containing the same non-synonymous SNP in a transcriptional regulator, kdgR, of metabolic genes. This likely indicates transmission of this clone between mice. The mutation was tracked to have occurred prior to 2 weeks post infection in one of the three mice and had subsequently been transmitted to the other two mice. Re-infection with this clone confirmed that it is superior to the wild type for intestinal colonization. Conclusions During 4 to 6 weeks of chronic infections, S. Typhimurium acquired distinct SNPs in known regulators of metabolic and virulence genes. One SNP, the kdgR-SNP was confirmed to confer selective advantage during chronic infections and constitute a true patho-adaptive mutation. Together, the results provide evidence for rapid genetic adaptation to the host of S. Typhimurium and validate experimental evolution in the context of host infection as a strategy for elucidating pathogen host interactions at the molecular level. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0646-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emilie Søndberg
- Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
| | - Lotte Jelsbak
- Department of Science, Systems and Models, Roskilde University, Universitetsvej 1, DK-4000, Roskilde, Denmark.
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Li YZ, Wang D, Feng XY, Jiao J, Chen WX, Tian CF. Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants. Appl Environ Microbiol 2016; 82:1305-15. [PMID: 26682851 PMCID: PMC4751829 DOI: 10.1128/aem.03454-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
The nitrogen phosphotransferase system (PTS(Ntr)) consists of EI(Ntr), NPr, and EIIA(Ntr). The active phosphate moiety derived from phosphoenolpyruvate is transferred through EI(Ntr) and NPr to EIIA(Ntr). Sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). In this study, S. fredii strains with mutations in ptsP and ptsO (encoding EI(Ntr) and NPr, respectively) formed ineffective nodules on soybeans, while a strain with a ptsN mutation (encoding EIIA(Ntr)) was not defective in symbiosis with soybeans. Notable reductions in the numbers of bacteroids within each symbiosome and of poly-β-hydroxybutyrate granules in bacteroids were observed in nodules infected by the ptsP or ptsO mutant strains but not in those infected with the ptsN mutant strain. However, these defects of the ptsP and ptsO mutant strains were recovered in ptsP ptsN and ptsO ptsN double-mutant strains, implying a negative role of unphosphorylated EIIA(Ntr) in symbiosis. Moreover, the symbiotic defect of the ptsP mutant was also recovered by expressing EI(Ntr) with or without the GAF domain, indicating that the putative glutamine-sensing domain GAF is dispensable in symbiotic interactions. The critical role of PTS(Ntr) in symbiosis was also observed when related PTS(Ntr) mutant strains of S. fredii were inoculated on pigeonpea plants. Furthermore, nodule occupancy and carbon utilization tests suggested that multiple outputs could be derived from components of PTS(Ntr) in addition to the negative role of unphosphorylated EIIA(Ntr).
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Affiliation(s)
- Yue Zhen Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Dan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Xue Ying Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
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Cabeen MT, Leiman SA, Losick R. Colony-morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen-related phosphotransferase system in biofilm formation. Mol Microbiol 2016; 99:557-70. [PMID: 26483285 PMCID: PMC5130288 DOI: 10.1111/mmi.13250] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2015] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen whose survival is aided by forming communities known as biofilms, in which cells are encased in a self-produced matrix. We devised a mutant screen based on colony morphology to identify additional genes with previously unappreciated roles in biofilm formation. Our screen, which identified most known biofilm-related genes, also uncovered PA14_16550 and PA14_69700, deletions of which abrogated and augmented biofilm formation respectively. We also identified ptsP, which encodes enzyme I of the nitrogen-regulated phosphotransferase (PTS(Ntr)) system, as being important for cyclic-di-GMP production and for biofilm formation. Further experiments showed that biofilm formation is hindered in the absence of phosphotransfer through the PTS(Ntr), but only in the presence of enzyme II (PtsN), the putative regulatory module of the PTS(Ntr). These results implicate unphosphorylated PtsN as a negative regulator of biofilm formation and establish one of the first known roles of the PTS(Ntr) in P. aeruginosa.
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Affiliation(s)
- Matthew T Cabeen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sara A Leiman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
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Liu Y, Yang J, Chen LM. Structure and Function of SLC4 Family [Formula: see text] Transporters. Front Physiol 2015; 6:355. [PMID: 26648873 PMCID: PMC4664831 DOI: 10.3389/fphys.2015.00355] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022] Open
Abstract
The solute carrier SLC4 family consists of 10 members, nine of which are [Formula: see text] transporters, including three Na(+)-independent Cl(-)/[Formula: see text] exchangers AE1, AE2, and AE3, five Na(+)-coupled [Formula: see text] transporters NBCe1, NBCe2, NBCn1, NBCn2, and NDCBE, as well as "AE4" whose Na(+)-dependence remains controversial. The SLC4 [Formula: see text] transporters play critical roles in pH regulation and transepithelial movement of electrolytes with a broad range of demonstrated physiological relevances. Dysfunctions of these transporters are associated with a series of human diseases. During the past decades, tremendous amount of effort has been undertaken to investigate the topological organization of the SLC4 transporters in the plasma membrane. Based upon the proposed topology models, mutational and functional studies have identified important structural elements likely involved in the ion translocation by the SLC4 transporters. In the present article, we review the advances during the past decades in understanding the structure and function of the SLC4 transporters.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biophysics and Molecular Physiology, School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing, China
| | - Li-Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biophysics and Molecular Physiology, School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
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Park YH, Um SH, Song S, Seok YJ, Ha NC. Structural basis for the sequestration of the anti-σ(70) factor Rsd from σ(70) by the histidine-containing phosphocarrier protein HPr. ACTA ACUST UNITED AC 2015; 71:1998-2008. [PMID: 26457424 DOI: 10.1107/s1399004715013759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022]
Abstract
Histidine-containing phosphocarrier protein (HPr) is a general component of the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) involved in the phosphorylation-coupled transport of numerous sugars called PTS sugars. HPr mainly exists in a dephosphorylated form in the presence of PTS sugars in the medium, while its phosphorylation increases in the absence of PTS sugars. A recent study revealed that the dephosphorylated form of HPr binds and antagonizes the function of the antisigma factor Rsd. This anti-sigma factor sequesters the housekeeping sigma factor σ(70) to facilitate switching of the sigma subunit on RNA polymerase from σ(70) to the stress-responsive sigma factor σ(S) in stationary-phase cells. In this study, the structure of the complex of Rsd and HPr was determined at 2.1 Å resolution and revealed that the binding site for HPr on the surface of Rsd partly overlaps with that for σ(70). The localization of the phosphorylation site on HPr at the binding interface for Rsd explains why phosphorylation of HPr abolishes its binding to Rsd. The mutation of crucial residues involved in the HPr-Rsd interaction significantly influenced the competition between HPr and σ(70) for binding to Rsd both in vitro and in vivo. The results provide a structural basis for the linkage of global gene regulation to nutrient availability in the external environment.
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Affiliation(s)
- Young Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Si Hyeon Um
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Saemee Song
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Yeong Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Nam Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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The KdpD Sensor Kinase of Escherichia coli Responds to Several Distinct Signals To Turn on Expression of the Kdp Transport System. J Bacteriol 2015; 198:212-20. [PMID: 26350129 DOI: 10.1128/jb.00602-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/27/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Kdp, one of three saturable K(+) uptake systems in Escherichia coli, is the system with the highest affinity for K(+) and the only one whose expression is strongly controlled by medium K(+) concentration. Expression is controlled by a two-component system of KdpD, the sensor kinase, and KdpE, the response regulator. There is general agreement that expression occurs when the growth rate of cells begins to become limited by K(+) availability. How K(+) limitation results in expression has been controversial. Studying the roles of the major components of the growth medium shows that KdpD senses at least two distinct signals inside the cell, those of Na(+) and NH4 (+), and it probably senses other monovalent cations in the cell. KdpD does not sense turgor. IMPORTANCE The expression of the Kdp K(+) transport system of E. coli occurs when cells become limited in their growth rate by the availability of K(+). Cells sense limited K(+) and try to compensate by taking up other monovalent cations, particularly Na(+) and NH4 (+). These cations are sensed in the cytoplasm by the KdpD response regulator, presumably to stimulate its kinase activity. It is shown that KdpD does not sense turgor, as was suggested earlier.
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Wolf S, Pflüger-Grau K, Kremling A. Modeling the Interplay of Pseudomonas putida EIIA Ntr with the Potassium Transporter KdpFABC. J Mol Microbiol Biotechnol 2015; 25:178-94. [DOI: 10.1159/000381214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nitrogen phosphotransferase system (PTS<sup>Ntr</sup>) of <i>Pseudomonas putida</i> is a key regulatory device that participates in controlling many physiological processes in a posttranscriptional fashion. One of the target functions of the PTS<sup>Ntr</sup> is the regulation of potassium transport. This is mediated by the direct interaction of one of its components with the sensor kinase KdpD of the two-component system controlling transcription of the <i>kdpFABC</i> genes. From a detailed experimental analysis of the activity of the <i>kdpF</i> promoter in <i>P. putida</i> wild-type and <i>pts</i> mutant strains with varying potassium concentrations, we had highly time-resolved data at hand, describing the influence of the PTS<sup>Ntr</sup> on the transcription of the KdpFABC potassium transporter. Here, this data was used to construct a mathematical model based on a black box approach. The model was able to describe the data quantitatively with convincing accuracy. The qualitative interpretation of the model allowed the prediction of two general points describing the interplay between the PTS<sup>Ntr</sup> and the KdpFABC potassium transporter: (1) the influence of cell number on the performance of the <i>kdpF</i> promoter is mainly by dilution by growth and (2) potassium uptake is regulated not only by the activity of the KdpD/KdpE two-component system (in turn influenced by PtsN). An additional controller with integrative behavior is predicted by the model structure. This suggests the presence of a novel physiological mechanism during regulation of potassium uptake with the KdpFABC transporter and may serve as a starting point for further investigations.
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Lüttmann D, Göpel Y, Görke B. Cross-Talk between the Canonical and the Nitrogen-Related Phosphotransferase Systems Modulates Synthesis of the KdpFABC Potassium Transporter in Escherichia coli. J Mol Microbiol Biotechnol 2015; 25:168-77. [DOI: 10.1159/000375497] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Many Proteobacteria possess the regulatory nitrogen-related phosphotransferase system (PTS<sup>Ntr</sup>), which operates in parallel to the transport PTS. PTS<sup>Ntr</sup> is composed of the proteins EI<sup>Ntr</sup> and NPr and the final phosphate acceptor EIIA<sup>Ntr</sup>. Both PTSs can exchange phosphoryl groups among each other. Proteins governing K<sup>+</sup> uptake represent a major target of PTS<sup>Ntr</sup> in <i>Escherichia coli</i>. Nonphosphorylated EIIA<sup>Ntr</sup> binds and stimulates the K<sup>+</sup> sensor KdpD, which activates expression of the <i>kdpFABC</i> operon encoding a K<sup>+</sup> transporter. Here we show that this regulation also operates in an <i>ilvG</i><sup><i>+</i></sup> strain ruling out previous concern about interference with a nonfunctional <i>ilvG</i> allele present in many strains. Furthermore, we analyzed phosphorylation of EIIA<sup>Ntr</sup>. In wild-type cells EIIA<sup>Ntr</sup> is predominantly phosphorylated, regardless of the growth stage and the utilized carbon source. However, cross-phosphorylation of EIIA<sup>Ntr</sup> by the transport PTS becomes apparent in the absence of EI<sup>Ntr</sup>: EIIA<sup>Ntr</sup> is predominantly nonphosphorylated when cells grow on a PTS sugar and phosphorylated when a non-PTS carbohydrate is utilized. These differences in phosphorylation are transduced into corresponding <i>kdpFABC</i> transcription levels. Thus, the transport PTS may affect phosphorylation of EIIA<sup>Ntr</sup> and accordingly modulate processes controlled by EIIA<sup>Ntr</sup>. Our data suggest that this cross-talk becomes most relevant under conditions that would inhibit activity of EI<sup>Ntr</sup>.
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The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions. Microbiol Mol Biol Rev 2015; 78:231-56. [PMID: 24847021 DOI: 10.1128/mmbr.00001-14] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The bacterial phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) carries out both catalytic and regulatory functions. It catalyzes the transport and phosphorylation of a variety of sugars and sugar derivatives but also carries out numerous regulatory functions related to carbon, nitrogen, and phosphate metabolism, to chemotaxis, to potassium transport, and to the virulence of certain pathogens. For these different regulatory processes, the signal is provided by the phosphorylation state of the PTS components, which varies according to the availability of PTS substrates and the metabolic state of the cell. PEP acts as phosphoryl donor for enzyme I (EI), which, together with HPr and one of several EIIA and EIIB pairs, forms a phosphorylation cascade which allows phosphorylation of the cognate carbohydrate bound to the membrane-spanning EIIC. HPr of firmicutes and numerous proteobacteria is also phosphorylated in an ATP-dependent reaction catalyzed by the bifunctional HPr kinase/phosphorylase. PTS-mediated regulatory mechanisms are based either on direct phosphorylation of the target protein or on phosphorylation-dependent interactions. For regulation by PTS-mediated phosphorylation, the target proteins either acquired a PTS domain by fusing it to their N or C termini or integrated a specific, conserved PTS regulation domain (PRD) or, alternatively, developed their own specific sites for PTS-mediated phosphorylation. Protein-protein interactions can occur with either phosphorylated or unphosphorylated PTS components and can either stimulate or inhibit the function of the target proteins. This large variety of signal transduction mechanisms allows the PTS to regulate numerous proteins and to form a vast regulatory network responding to the phosphorylation state of various PTS components.
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