1
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Rakibova Y, Dunham DT, Seed KD, Freddolino L. Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. mSphere 2024; 9:e0001124. [PMID: 38920383 PMCID: PMC11288032 DOI: 10.1128/msphere.00011-24] [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: 01/08/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs. IMPORTANCE New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.
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Affiliation(s)
- Yulduz Rakibova
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Drew T. Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Kimberley D. Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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2
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Wan Q, Zhai S, Chen M, Xu M, Guo S. Comparative phenotype and transcriptome analysis revealed the role of ferric uptake regulator (Fur) in the virulence of Vibrio harveyi isolated from diseased American eel (Anguilla rostrata). JOURNAL OF FISH DISEASES 2024; 47:e13931. [PMID: 38373044 DOI: 10.1111/jfd.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/20/2024]
Abstract
Vibrio harveyi is commonly found in salt and brackish water and is recognized as a serious bacterial pathogen in aquaculture worldwide. In this study, we cloned the ferric uptake regulator (fur) gene from V. harveyi wild-type strain HA_1, which was isolated from diseased American eels (Anguilla rostrata) and has a length of 450 bp, encoding 149 amino acids. Then, a mutant strain, HA_1-Δfur, was constructed through homologous recombination of a suicide plasmid (pCVD442). The HA_1-Δfur mutant exhibited weaker biofilm formation and swarming motility, and 18-fold decrease (5.5%) in virulence to the American eels; compared to the wild-type strain, the mutant strain showed time and diameter differences in growth and haemolysis, respectively. Additionally, the adhesion ability of the mutant strain was significantly decreased. Moreover, there were 15 different biochemical indicators observed between the two strains. Transcriptome analysis revealed that 875 genes were differentially expressed in the Δfur mutant, with 385 up-regulated and 490 down-regulated DEGs. GO and KEGG enrichment analysis revealed that, compared to the wild-type strain, the type II and type VI secretion systems (T2SS and T6SS), amino acid synthesis and transport and energy metabolism pathways were significantly down-regulated, but the ABC transporters and biosynthesis of siderophore group non-ribosomal peptides pathways were up-regulated in the Δfur strain. The qRT-PCR results further confirmed that DEGs responsible for amino acid transport and energy metabolism were positively regulated, but DEGs involved in iron acquisition were negatively regulated in the Δfur strain. These findings suggest that the virulence of the Δfur strain was significantly decreased, which is closely related to phenotype changing and gene transcript regulation.
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Affiliation(s)
- Qijuan Wan
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Shaowei Zhai
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Minxia Chen
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Ming Xu
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Songlin Guo
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
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3
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Rakibova Y, Dunham DT, Seed KD, Freddolino PL. Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573743. [PMID: 38260642 PMCID: PMC10802314 DOI: 10.1101/2023.12.30.573743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches it occupies. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified a few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs. Importance New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. Proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.
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Affiliation(s)
- Yulduz Rakibova
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Drew T. Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kimberley D. Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - P. Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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4
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Ferrara S, Bertoni G. Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa. Methods Mol Biol 2024; 2721:183-195. [PMID: 37819523 DOI: 10.1007/978-1-0716-3473-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In recent years, several genome-wide approaches based on RNA sequencing (RNA-seq) have been developed. These methods allow a comprehensive and dynamic view of the structure and function of the multi-layered RNA pathways and networks. Many of these approaches, including the promising one of single-cell transcriptome analysis, have been successfully applied to Pseudomonas aeruginosa. However, we are only at the beginning because only a few surrounding conditions have been considered. Here, we aim to illustrate the different types of approaches based on RNA-seq that will lead us in the future to a better understanding of the dynamics of RNA biology in P. aeruginosa.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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5
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Niu M, Sui Z, Jiang G, Wang L, Yao X, Hu Y. The Mutation of the DNA-Binding Domain of Fur Protein Enhances the Pathogenicity of Edwardsiella piscicida via Inducing Overpowering Pyroptosis. Microorganisms 2023; 12:11. [PMID: 38276180 PMCID: PMC10821184 DOI: 10.3390/microorganisms12010011] [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: 10/20/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Edwardsiella piscicida is an important fish pathogen with a broad host that causes substantial economic losses in the aquaculture industry. Ferric uptake regulator (Fur) is a global transcriptional regulator and contains two typical domains, the DNA-binding domain and dimerization domain. In a previous study, we obtained a mutant strain of full-length fur of E. piscicida, TX01Δfur, which displayed increased siderophore production and stress resistance factors and decreased pathogenicity. To further reveal the regulatory mechanism of Fur, the DNA-binding domain (N-terminal) of Fur was knocked out in this study and the mutant was named TX01Δfur2. We found that TX01Δfur2 displayed increased siderophore production and enhanced adversity tolerance, including a low pH, manganese, and high temperature stress, which was consistent with the phenotype of TX01Δfur. Contrary to TX01Δfur, whose virulence was weakened, TX01Δfur2 displayed an ascended invasion of nonphagocytic cells and enhanced destruction of phagocytes via inducing overpowering or uncontrollable pyroptosis, which was confirmed by the fact that TX01Δfur2 induced higher levels of cytotoxicity, IL-1β, and p10 in macrophages than TX01. More importantly, TX01Δfur2 displayed an increased global virulence to the host, which was confirmed by the result that TX01Δfur2 caused higher lethality outcomes for healthy tilapias than TX01. These results demonstrate that the mutation of the Fur N-terminal domain augments the resistance level against the stress and pathogenicity of E. piscicida, which is not dependent on the bacterial number in host cells or host tissues, although the capabilities of biofilm formation and the motility of TX01Δfur2 decline. These interesting findings provide a new insight into the functional analysis of Fur concerning the regulation of virulence in E. piscicida and prompt us to explore the subtle regulation mechanism of Fur in the future.
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Affiliation(s)
- Mimi Niu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China;
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.J.); (L.W.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Zhihai Sui
- School of Life Science, Linyi University, Linyi 276000, China;
| | - Guoquan Jiang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.J.); (L.W.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.J.); (L.W.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou 571101, China
| | - Xuemei Yao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China;
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China
| | - Yonghua Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.J.); (L.W.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou 571101, China
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6
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Abstract
The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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7
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Wu P, Wang Q, Yang Q, Feng X, Liu X, Sun H, Yan J, Kang C, Liu B, Liu Y, Yang B. A Novel Role of the Two-Component System Response Regulator UvrY in Enterohemorrhagic Escherichia coli O157:H7 Pathogenicity Regulation. Int J Mol Sci 2023; 24:ijms24032297. [PMID: 36768620 PMCID: PMC9916836 DOI: 10.3390/ijms24032297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important human pathogen causing severe diseases, such as hemorrhagic colitis and lethal hemolytic uremic syndrome. The signal-sensing capability of EHEC O157:H7 at specific host colonization sites via different two-component systems (TCSs) is closely related to its pathogenicity during infection. However, the types of systems involved and the regulatory mechanisms are not fully understood. Here, we investigated the function of the TCS BarA/UvrY regulator UvrY in the pathogenicity regulation of EHEC O157:H7. Our results showed that UvrY acts as a positive regulator of EHEC O157:H7 for cellular adherence and mouse colonization through the transcriptional activation of the locus for enterocyte effacement (LEE) pathogenic genes. Furthermore, this regulation is mediated by the LEE island master regulator, Ler. Our results highlight the significance of UvrY in EHEC O157:H7 pathogenicity and underline the unknown importance of BarA/UvrY in colonization establishment and intestinal adaptability during infection.
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Affiliation(s)
- Pan Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Qian Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Qian Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xiaohui Feng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xingmei Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
- Nankai International Advanced Research Institute, Nankai University, Shenzhen 518000, China
| | - Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
- Nankai International Advanced Research Institute, Nankai University, Shenzhen 518000, China
- Correspondence: (Y.L.); (B.Y.)
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
- Correspondence: (Y.L.); (B.Y.)
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8
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Elucidation of a complete mechanical signaling and virulence activation pathway in enterohemorrhagic Escherichia coli. Cell Rep 2022; 39:110614. [PMID: 35385749 DOI: 10.1016/j.celrep.2022.110614] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 12/09/2021] [Accepted: 03/13/2022] [Indexed: 12/23/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important extracellular human pathogen. The initial adherence of EHEC to host cells is a major cue for transcriptional induction of the locus of enterocyte effacement (LEE) genes to promote colonization and pathogenesis, but the mechanism through which this adherence is sensed and the LEE is induced remains largely elusive. Here, we report a complete signal transduction pathway for this virulence activation process. In this pathway, the outer-membrane lipoprotein NlpE senses a mechanical cue generated from initial host adherence and activates the BaeSR two-component regulatory system; the response regulator BaeR then directly activates the expression of airA located on O-island-134 and encoding a LEE transcriptional activator. Disruption of this pathway severely attenuates EHEC O157:H7 virulence both in vitro and in vivo. This study provides further insights into the evolution of EHEC pathogenesis and the host-pathogen interaction.
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Murtha AN, Kazi MI, Schargel RD, Cross T, Fihn C, Cattoir V, Carlson EE, Boll JM, Dörr T. High-level carbapenem tolerance requires antibiotic-induced outer membrane modifications. PLoS Pathog 2022; 18:e1010307. [PMID: 35130322 PMCID: PMC8853513 DOI: 10.1371/journal.ppat.1010307] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/17/2022] [Accepted: 01/26/2022] [Indexed: 12/22/2022] Open
Abstract
Antibiotic tolerance is an understudied potential contributor to antibiotic treatment failure and the emergence of multidrug-resistant bacteria. The molecular mechanisms governing tolerance remain poorly understood. A prominent type of β-lactam tolerance relies on the formation of cell wall-deficient spheroplasts, which maintain structural integrity via their outer membrane (OM), an asymmetric lipid bilayer consisting of phospholipids on the inner leaflet and a lipid-linked polysaccharide (lipopolysaccharide, LPS) enriched in the outer monolayer on the cell surface. How a membrane structure like LPS, with its reliance on mere electrostatic interactions to maintain stability, is capable of countering internal turgor pressure is unknown. Here, we have uncovered a novel role for the PhoPQ two-component system in tolerance to the β-lactam antibiotic meropenem in Enterobacterales. We found that PhoPQ is induced by meropenem treatment and promotes an increase in 4-amino-4-deoxy-L-aminoarabinose [L-Ara4N] modification of lipid A, the membrane anchor of LPS. L-Ara4N modifications likely enhance structural integrity, and consequently tolerance to meropenem, in several Enterobacterales species. Importantly, mutational inactivation of the negative PhoPQ regulator mgrB (commonly selected for during clinical therapy with the last-resort antibiotic colistin, an antimicrobial peptide [AMP]) results in dramatically enhanced tolerance, suggesting that AMPs can collaterally select for meropenem tolerance via stable overactivation of PhoPQ. Lastly, we identify histidine kinase inhibitors (including an FDA-approved drug) that inhibit PhoPQ-dependent LPS modifications and consequently potentiate meropenem to enhance lysis of tolerant cells. In summary, our results suggest that PhoPQ-mediated LPS modifications play a significant role in stabilizing the OM, promoting survival when the primary integrity maintenance structure, the cell wall, is removed. Treating an infection with an antibiotic often fails, resulting in a tremendous public health burden. One understudied likely reason for treatment failure is the development of “antibiotic tolerance”, the ability of bacteria to survive normally lethal exposure to an antibiotic. Here, we describe a molecular mechanism promoting tolerance. A bacterial stress sensor (PhoPQ) is activated in response to antibiotic (meropenem) treatment and consequently strengthens a bacterial protective “shell” to enhance survival. We also identify inhibitors of this mechanism, opening the door to developing compounds that help antibiotics work better against tolerant bacteria.
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Affiliation(s)
- Andrew N. Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Misha I. Kazi
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Richard D. Schargel
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Trevor Cross
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Conrad Fihn
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Vincent Cattoir
- Department of Clinical Microbiology and National Reference Center for Antimicrobial Resistance (Lab Enterococci), Rennes University Hospital, Rennes, France; Inserm Unit U1230, University of Rennes 1, Rennes, France
| | - Erin E. Carlson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joseph M. Boll
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
- * E-mail: (JMB); (TD)
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, United States of America
- * E-mail: (JMB); (TD)
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10
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Muranishi K, Ishimori K, Uchida T. Regulation of the expression of the nickel uptake system in Vibrio cholerae by iron and heme via ferric uptake regulator (Fur). J Inorg Biochem 2022; 228:111713. [PMID: 35032924 DOI: 10.1016/j.jinorgbio.2022.111713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/30/2022]
Abstract
Fur (ferric uptake regulator) is a transcription factor that regulates expression of downstream genes containing a specific Fe2+-binding sequence called the Fur box. In Vibrio cholerae, a Fur box is located upstream of the nik operon, which is responsible for nickel uptake, suggesting that its expression is regulated by Fur. However, there are no reports that Ni2+ induces expression of Fur box genes. Accordingly, we here investigated whether Ni2+ or Fe2+ binds to Fur to regulate expression of the nik operon. We found that Fur binds to the Fur box in the presence of Fe2+ with a dissociation constant (Kd) of 1.2 μM, whereas only non-specific binding was observed in the presence of Ni2+. Thus, Fur-mediated expression of the nik operon is dependent on Fe2+, but not Ni2+. Since most iron in cells exists as heme, we examined the effect of heme on the Fur box binding activity of V. cholerae Fur (VcFur). Addition of heme to the VcFur-Fur box complex induced dissociation of VcFur from the Fur box, indicating that expression of the V. cholerae nik operon is regulated by both iron and heme. Furthermore, VCA1098, a nik operon-encoded protein, bound heme with a Kd of 1.3 μM. Collectively, our results suggest that the V. cholerae nik operon is involved not only in nickel uptake but also in heme uptake, and depends on iron and heme concentrations within bacteria.
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Affiliation(s)
- Kazuyoshi Muranishi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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11
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Butt AT, Banyard CD, Haldipurkar SS, Agnoli K, Mohsin M, Vitovski S, Paleja A, Tang Y, Lomax R, Ye F, Green J, Thomas M. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3709-3726. [PMID: 35234897 PMCID: PMC9023288 DOI: 10.1093/nar/gkac137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board ‘anti-σ factor’ in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.
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Affiliation(s)
- Aaron T Butt
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Christopher D Banyard
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Sayali S Haldipurkar
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Kirsty Agnoli
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Muslim I Mohsin
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Srdjan Vitovski
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Ameya Paleja
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Yingzhi Tang
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Rebecca Lomax
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Fuzhou Ye
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Jeffrey Green
- Correspondence may also be addressed to Jeffrey Green. Tel: +44 114 222 4403; Fax: +44 114 222 2800;
| | - Mark S Thomas
- To whom correspondence should be addressed. Tel: +44 114 215 9557; Fax: +44 114 271 1863;
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12
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Lang M, Krin E, Korlowski C, Sismeiro O, Varet H, Coppée JY, Mazel D, Baharoglu Z. Sleeping ribosomes: Bacterial signaling triggers RaiA mediated persistence to aminoglycosides. iScience 2021; 24:103128. [PMID: 34611612 PMCID: PMC8476650 DOI: 10.1016/j.isci.2021.103128] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
Indole is a molecule proposed to be involved in bacterial signaling. We find that indole secretion is induced by sublethal tobramycin concentrations and increases persistence to aminoglycosides in V. cholerae. Indole transcriptomics showed increased expression of raiA, a ribosome associated factor. Deletion of raiA abolishes the appearance of indole dependent persisters to aminoglycosides, although its overexpression leads to 100-fold increase of persisters, and a reduction in lag phase, evocative of increased active 70S ribosome content, confirmed by sucrose gradient analysis. We propose that, under stress conditions, RaiA-bound inactive 70S ribosomes are stored as “sleeping ribosomes”, and are rapidly reactivated upon stress relief. Our results point to an active process of persister formation through ribosome protection during translational stress (e.g., aminoglycoside treatment) and reactivation upon antibiotic removal. Translation is a universal process, and these results could help elucidate a mechanism of persistence formation in a controlled, thus inducible way. Indole is produced under sub-MIC tobramycin stress in V. cholerae and upregulates raiA RaiA is involved in indole-dependent formation of aminoglycoside specific persisters RaiA overexpression allows faster growth restart and increases 70S ribosome content RaiA-bound inactive 70S ribosomes form intact and reactivable sleeping ribosome pools
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Affiliation(s)
- Manon Lang
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Evelyne Krin
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Chloé Korlowski
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Odile Sismeiro
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Hugo Varet
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Jean-Yves Coppée
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Didier Mazel
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Corresponding author
| | - Zeynep Baharoglu
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Corresponding author
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13
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Gao H, Wang H, Qin Q, Gao Y, Qiu Y, Zhang J, Li J, Lou J, Diao B, Zhang Y, Kan B. Transcriptional regulation of the mannitol phosphotransferase system operon by the ferric uptake regulator (Fur) in Vibrio cholerae El Tor serogroup O1. Res Microbiol 2021; 172:103848. [PMID: 34089838 DOI: 10.1016/j.resmic.2021.103848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 04/22/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022]
Abstract
The phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) allows bacteria to use various carbohydrates as energy resources including mannitol. The mannitol-specific PTS transporter in Vibrio cholerae is encoded by the mtlADR operon. Expression of the mtl operon has been shown to be strictly regulated by CRP, MtlS, and MtlR. In the present study, we investigated the regulation of mtlADR by the ferric uptake regulator (Fur). The results showed that Fur binds to the promoter-proximal DNA region of mtlADR to repress its transcription independent of iron, in mannitol-containing growth medium. The capacity for mannitol fermentation was significantly increased in Δfur relative to that of WT for normal and iron-replete growth media. The level of organic acids produced by Δfur was significantly enhanced relative to that produced by the WT strain in the normal and iron-replete media but not in an iron-starved medium. The results provided for a deeper understanding of the regulation of mtlADR in V. cholerae.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Han Wang
- Department of Clinical Diagnostic Centre, The Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Qin Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yue Gao
- First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yue Qiu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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14
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Bradley JM, Svistunenko DA, Wilson MT, Hemmings AM, Moore GR, Le Brun NE. Bacterial iron detoxification at the molecular level. J Biol Chem 2021; 295:17602-17623. [PMID: 33454001 PMCID: PMC7762939 DOI: 10.1074/jbc.rev120.007746] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Indexed: 01/18/2023] Open
Abstract
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
| | | | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom; Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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15
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Shin J, Choe D, Ransegnola B, Hong H, Onyekwere I, Cross T, Shi Q, Cho B, Westblade LF, Brito IL, Dörr T. A multifaceted cellular damage repair and prevention pathway promotes high-level tolerance to β-lactam antibiotics. EMBO Rep 2021; 22:e51790. [PMID: 33463026 PMCID: PMC7857431 DOI: 10.15252/embr.202051790] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/17/2020] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
Bactericidal antibiotics are powerful agents due to their ability to convert essential bacterial functions into lethal processes. However, many important bacterial pathogens are remarkably tolerant against bactericidal antibiotics due to inducible damage repair responses. The cell wall damage response two-component system VxrAB of the gastrointestinal pathogen Vibrio cholerae promotes high-level β-lactam tolerance and controls a gene network encoding highly diverse functions, including negative control over multiple iron uptake systems. How this system contributes to tolerance is poorly understood. Here, we show that β-lactam antibiotics cause an increase in intracellular free iron levels and collateral oxidative damage, which is exacerbated in the ∆vxrAB mutant. Mutating major iron uptake systems dramatically increases ∆vxrAB tolerance to β-lactams. We propose that VxrAB reduces antibiotic-induced toxic iron and concomitant metabolic perturbations by downregulating iron uptake transporters and show that iron sequestration enhances tolerance against β-lactam therapy in a mouse model of cholera infection. Our results suggest that a microorganism's ability to counteract diverse antibiotic-induced stresses promotes high-level antibiotic tolerance and highlights the complex secondary responses elicited by antibiotics.
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Affiliation(s)
- Jung‐Ho Shin
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Donghui Choe
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Brett Ransegnola
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Hye‐Rim Hong
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Ikenna Onyekwere
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Trevor Cross
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Qiaojuan Shi
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Byung‐Kwan Cho
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
- Intelligent Synthetic Biology CenterDaejeonKorea
| | - Lars F Westblade
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkNYUSA
- Division of Infectious DiseasesDepartment of MedicineWeill Cornell MedicineNew YorkNYUSA
| | - Ilana L Brito
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
- Cornell Institute of Host‐Microbe Interactions and DiseaseCornell UniversityIthacaNYUSA
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16
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Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Peschek N, Herzog R, Singh PK, Sprenger M, Meyer F, Fröhlich KS, Schröger L, Bramkamp M, Drescher K, Papenfort K. RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae. Nat Commun 2020; 11:6067. [PMID: 33247102 PMCID: PMC7695739 DOI: 10.1038/s41467-020-19890-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrio cholerae, the cause of cholera disease, exhibits a characteristic curved rod morphology, which promotes infectivity and motility in dense hydrogels. Periplasmic protein CrvA determines cell curvature in V. cholerae, yet the regulatory factors controlling CrvA are unknown. Here, we discover the VadR small RNA (sRNA) as a post-transcriptional inhibitor of the crvA mRNA. Mutation of vadR increases cell curvature, whereas overexpression has the inverse effect. We show that vadR transcription is activated by the VxrAB two-component system and triggered by cell-wall-targeting antibiotics. V. cholerae cells failing to repress crvA by VadR display decreased survival upon challenge with penicillin G indicating that cell shape maintenance by the sRNA is critical for antibiotic resistance. VadR also blocks the expression of various key biofilm genes and thereby inhibits biofilm formation in V. cholerae. Thus, VadR is an important regulator for synchronizing peptidoglycan integrity, cell shape, and biofilm formation in V. cholerae.
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Affiliation(s)
- Nikolai Peschek
- Institute of Microbiology, Friedrich Schiller University, 07745, Jena, Germany
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
| | - Roman Herzog
- Institute of Microbiology, Friedrich Schiller University, 07745, Jena, Germany
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Marcel Sprenger
- Institute of Microbiology, Friedrich Schiller University, 07745, Jena, Germany
| | - Fabian Meyer
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Kathrin S Fröhlich
- Institute of Microbiology, Friedrich Schiller University, 07745, Jena, Germany
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Luise Schröger
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
| | - Marc Bramkamp
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, 07745, Jena, Germany.
- Faculty of Biology, Ludwig-Maximilians-University of Munich, 82152, Martinsried, Germany.
- Microverse Cluster, Friedrich Schiller University Jena, 07743, Jena, Germany.
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18
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Abstract
Sensing specific gut metabolites is an important strategy for inducing crucial virulence programs by enterohemorrhagic Escherichia coli (EHEC) O157:H7 during colonization and infection. Here, we identified a virulence-regulating pathway wherein the PhoQ/PhoP two-component regulatory system signals to the O island 119-encoded low magnesium-induced regulator A (LmiA), which, in turn, activates locus of enterocyte effacement (LEE) genes to promote EHEC O157:H7 adherence in the low-magnesium conditions of the large intestine. This regulatory pathway is widely present in a range of EHEC and enteropathogenic E. coli (EPEC) serotypes. Disruption of this pathway significantly decreased EHEC O157:H7 adherence in the mouse intestinal tract. Moreover, mice fed a magnesium-rich diet showed significantly reduced EHEC O157:H7 adherence in vivo, indicating that magnesium may help in preventing EHEC and EPEC infection in humans. The large intestinal pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7 detects host cues to regulate virulence gene expression during colonization and infection. However, virulence regulatory mechanisms of EHEC O157:H7 in the human large intestine are not fully understood. Herein, we identified a virulence-regulating pathway where the PhoQ/PhoP two-component regulatory system senses low magnesium levels and signals to the O island 119-encoded Z4267 (LmiA; low magnesium-induced regulator A), directly activating loci of enterocyte effacement genes to promote EHEC O157:H7 adherence in the large intestine. Disruption of this pathway significantly decreased EHEC O157:H7 adherence in the mouse intestinal tract. Moreover, feeding mice a magnesium-rich diet significantly reduced EHEC O157:H7 adherence in vivo. This LmiA-mediated virulence regulatory pathway is also conserved among several EHEC and enteropathogenic E. coli serotypes; therefore, our findings support the use of magnesium as a dietary supplement and provide greater insights into the dietary cues that can prevent enteric infections.
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19
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Gao H, Ma L, Qin Q, Qiu Y, Zhang J, Li J, Lou J, Diao B, Zhao H, Shi Q, Zhang Y, Kan B. Fur Represses Vibrio cholerae Biofilm Formation via Direct Regulation of vieSAB, cdgD, vpsU, and vpsA-K Transcription. Front Microbiol 2020; 11:587159. [PMID: 33193241 PMCID: PMC7641913 DOI: 10.3389/fmicb.2020.587159] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Attached Vibrio cholerae biofilms are essential for environmental persistence and infectivity. The vps loci (vpsU, vpsA-K, and vpsL-Q) are required for mature biofilm formation and are responsible for the synthesis of exopolysaccharide. Transcription of vps genes is activated by the signaling molecule bis-(3'-5')-cyclic di-GMP (c-di-GMP), whose metabolism is controlled by the proteins containing the GGDEF and/or EAL domains. The ferric uptake regulator (Fur) plays key roles in the transcription of many genes involved in iron metabolism and non-iron functions. However, roles for Fur in Vibrio biofilm production have not been documented. In this study, phenotypic assays demonstrated that Fur, independent of iron, decreases in vivo c-di-GMP levels and inhibits in vitro biofilm formation by Vibrio cholerae. The Fur box-like sequences were detected within the promoter-proximal DNA regions of vpsU, vpsA-K, vieSAB, and cdgD, suggesting that transcription of these genes may be under the direct control of Fur. Indeed, the results of luminescence, quantitative PCR (qPCR), electrophoretic mobility shift assay (EMSA), and DNase I footprinting assays demonstrated Fur to bind to the promoter-proximal DNA regions of vpsU, vpsA-K, and cdgD to repress their transcription. In contrast, Fur activates the transcription of vieSAB in a direct manner. The cdgD and vieSAB encode proteins with GGDEF and EAL domains, respectively. Thus, data presented here highlight a new physiological role for Fur wherein it acts as a repressor of V. cholerae biofilm formation mediated by decreasing the production of exopolysaccharide and the intracellular levels of c-di-GMP.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lizhi Ma
- Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qin Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yue Qiu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China.,Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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20
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Ferric Uptake Regulator Fur Coordinates Siderophore Production and Defense against Iron Toxicity and Oxidative Stress and Contributes to Virulence in Chromobacterium violaceum. Appl Environ Microbiol 2020; 86:AEM.01620-20. [PMID: 32859594 DOI: 10.1128/aem.01620-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022] Open
Abstract
Iron is a highly reactive metal that participates in several processes in prokaryotic and eukaryotic cells. Hosts and pathogens compete for iron in the context of infection. Chromobacterium violaceum, an environmental Gram-negative bacterial pathogen, relies on siderophores to overcome iron limitation in the host. In this work, we studied the role of the ferric uptake regulator Fur in the physiology and virulence of C. violaceum A Δfur mutant strain showed decreased growth and fitness under regular in vitro growth conditions and presented high sensitivity to iron and oxidative stresses. Furthermore, the absence of fur caused derepression of siderophore production and reduction in swimming motility and biofilm formation. Consistent with these results, the C. violaceum Δfur mutant was highly attenuated for virulence and liver colonization in mice. In contrast, a manganese-selected spontaneous fur mutant showed only siderophore overproduction and sensitivity to oxidative stress, indicating that Fur remained partially functional in this strain. We found that mutations in genes related to siderophore biosynthesis and a putative CRISPR-Cas locus rescued the Δfur mutant growth defects, indicating that multiple Fur-regulated processes contribute to maintaining bacterial cell fitness. Overall, our data indicated that Fur is conditionally essential in C. violaceum mainly by protecting cells from iron overload and oxidative damage. The requirement of Fur for virulence highlights the importance of iron in the pathogenesis of C. violaceum IMPORTANCE Maintenance of iron homeostasis, i.e., avoiding both deficiency and toxicity of this metal, is vital to bacteria and their hosts. Iron sequestration by host proteins is a crucial strategy to combat bacterial infections. In bacteria, the ferric uptake regulator Fur coordinates the expression of several iron-related genes. Sometimes, Fur can also regulate several other processes. In this work, we performed an in-depth phenotypic characterization of fur mutants in the human opportunistic pathogen Chromobacterium violaceum We determined that fur is a conditionally essential gene necessary for proper growth under regular conditions and is fully required for survival under iron and oxidative stresses. Fur also controlled several virulence-associated traits, such as swimming motility, biofilm formation, and siderophore production. Consistent with these results, a C. violaceum fur null mutant showed attenuation of virulence. Therefore, our data established Fur as a major player required for C. violaceum to manage iron, including during infection in the host.
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Gao H, Zhang J, Lou J, Li J, Qin Q, Shi Q, Zhang Y, Kan B. Direct Binding and Regulation by Fur and HapR of the Intermediate Regulator and Virulence Factor Genes Within the ToxR Virulence Regulon in Vibrio cholerae. Front Microbiol 2020; 11:709. [PMID: 32362889 PMCID: PMC7181404 DOI: 10.3389/fmicb.2020.00709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/26/2020] [Indexed: 01/30/2023] Open
Abstract
Cholera toxin (CT) and toxin coregulated pilus (TCP, TcpA is the major subunit) are two major virulence factors of Vibrio cholerae, both of which play critical roles in developing severe diarrhea in human. Expression of CT and TCP is under the tight control of the regulatory cascade known as the ToxR virulence regulon, which is composed of three regulators ToxR, TcpP, and ToxT. Besides, their expression is also regulated by the quorum sensing (QS) master regulator HapR and the regulatory protein Fur. Though transcription of tcpP, toxT, and/or tcpA are reported to be regulated by HapR and Fur, to date there are no studies to verify their direct regulations. In the present study, we showed that HapR directly repress the transcription of tcpP and tcpA by binding to their promoter regions, and possibly repress toxT transcription in an indirect manner. Fur directly activated the transcription of tcpP, toxT, and tcpA by binding to their promoters. Taking account of the sequential expression of hapR, fur, tcpP, toxT, and tcpA in the different growth phases of V. cholerae, we deduce that at the early mid-logarithmic growth phase, Fur binds to the promoters of tcpP, toxT, and tcpA to activate their transcription; while at the later mid-logarithmic growth phase, HapR can bind to the promoters of tcpP and tcpA to repress their transcription. Our study reveals the new recognition in the virulence regulatory pathways in V. cholerae and suggests the complicated and subtle regulation network with the growth density dependence.
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Affiliation(s)
- He Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qin Qin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Morabe ML, McCarter LL. Vibrio parahaemolyticus FcrX, a Fur-controlled regulator that inhibits repression by Fur. Mol Microbiol 2020; 114:77-92. [PMID: 32096286 DOI: 10.1111/mmi.14497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 02/20/2020] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
Iron is an essential nutrient for most organisms, but its limited availability and inherent toxicity necessitate the strict regulation of iron homeostasis. In bacteria, iron starvation affects a broad range of phenotypes including virulence, motility and biofilm formation. For Vibrio parahaemolyticus, a marine bacterium and pathogen, iron limitation is a signal modulating swarmer cell differentiation. In this work, we show the iron regulation of swarming works through the ferric uptake regulator protein Fur. We identified a new Fur-controlled regulator that is upregulated upon iron starvation. FcrX is a 144-amino acid protein containing a domain of unknown function (DUF2753) with three tetratricopeptide repeats. We found that overexpressing fcrX+ was sufficient to induce swarming, luminescence and iron uptake gene expression in multiple Vibrio species; furthermore, ectopic expression increased the transcription of a Fur-controlled gene in Escherichia coli. FcrX production increased intracellular iron. Thus, the overexpression of fcrX+ phenocopied a fur mutant and may prove a generally useful tool to ectopically derepress the Fur regulon. Both V. parahaemolyticus and E. coli Fur interacted with FcrX, and this interaction was altered by iron availability. These data support a model in which this new regulator of iron homeostasis limits the repressive action of Fur.
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Affiliation(s)
- Maria L Morabe
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Linda L McCarter
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
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Mason C, Liu X, Prabhudeva S, Ouyang Z. The CXXC Motifs Are Essential for the Function of BosR in Borrelia burgdorferi. Front Cell Infect Microbiol 2019; 9:109. [PMID: 31041197 PMCID: PMC6476982 DOI: 10.3389/fcimb.2019.00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/28/2019] [Indexed: 01/07/2023] Open
Abstract
BosR, a Fur family member, is essential for the pathogenesis of the Lyme disease pathogen, Borrelia burgdorferi. Unlike typical Fur proteins in which DNA binding represses gene expression, binding of BosR to the rpoS promoter directly activates rpoS transcription in B. burgdorferi. However, virtually nothing is known concerning potential structural features and amino acid residues of BosR that are important for protein function and virulence regulation in B. burgdorferi. Particularly, it remains unknown what structural motifs or residues of BosR coordinate Zn, although previous analyses have indicated that the function of BosR may depend on Zn. To address these information gaps, we herein introduced mutations into four conserved cysteine residues in two putative CXXC motifs of BosR. Our data showed that the ability of BosR to bind Zn was dramatically reduced when the CXXC motifs were mutated. Moreover, we found that the two CXXC motifs contributed to the ability of BosR to form dimers. By using a trans-complementation genetic approach, we additionally demonstrated that both CXXC motifs of BosR were essential for in vivo gene expression regulation. Mutation of any of the four cysteines abolished the transcriptional activation of rpoS. In contrast to wild type BosR, each mutant protein was incapable of binding the rpoS promoter in electrophoretic mobility shift assays. The combined data strongly support that the two CXXC motifs and four cysteines constitute the structural site essential for Zn-coordination, protein dimerization, and the unique regulatory activity of BosR.
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Affiliation(s)
- Charlotte Mason
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| | - Xiaoyan Liu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Spoorthy Prabhudeva
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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Genome-Wide Characterization of the Fur Regulatory Network Reveals a Link between Catechol Degradation and Bacillibactin Metabolism in Bacillus subtilis. mBio 2018; 9:mBio.01451-18. [PMID: 30377275 PMCID: PMC6212828 DOI: 10.1128/mbio.01451-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many bacteria synthesize high-affinity iron chelators (siderophores). Siderophore-mediated iron acquisition is an efficient and widely utilized strategy for bacteria to meet their cellular iron requirements. One prominent class of siderophores uses catecholate groups to chelate iron. B. subtilis bacillibactin, structurally similar to enterobactin (made by enteric bacteria), is a triscatecholate siderophore that is hydrolyzed to monomeric units after import to release iron. However, the ultimate fates of these catechol compounds and their potential toxicities have not been defined previously. We performed genome-wide identification of Fur binding sites in vivo and uncovered a connection between catechol degradation and bacillibactin metabolism in B. subtilis. Besides its role in the detoxification of environmental catechols, the catechol 2,3-dioxygenase encoded by catDE also protects cells from intoxication by endogenous bacillibactin-derived catechol metabolites under iron-limited conditions. These findings shed light on the degradation pathway and precursor recycling of the catecholate siderophores. The ferric uptake regulator (Fur) is the global iron biosensor in many bacteria. Fur functions as an iron-dependent transcriptional repressor for most of its regulated genes. There are a few examples where holo-Fur activates transcription, either directly or indirectly. Recent studies suggest that apo-Fur might also act as a positive regulator and that, besides iron metabolism, the Fur regulon might encompass other biological processes such as DNA synthesis, energy metabolism, and biofilm formation. Here, we obtained a genomic view of the Fur regulatory network in Bacillus subtilis using chromatin immunoprecipitation sequencing (ChIP-seq). Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron-sufficient conditions. Among the new sites detected, a Fur binding site in the promoter region of the catDE operon is of particular interest. This operon, encoding catechol 2,3-dioxygenase, is critical for catechol degradation and is under negative regulation of CatR and YodB. These three repressors (Fur, CatR, and YodB) function cooperatively to regulate the transcription of catDE, with Fur functioning as a sensor of iron limitation and CatR as the major sensor of catechol stress. Genetic analysis suggests that CatDE is involved in metabolism of the catecholate siderophore bacillibactin, particularly when bacillibactin is constitutively produced and accumulates intracellularly, potentially generating endogenous toxic catechol derivatives. This study documents a role for catechol degradation in bacillibactin metabolism and provides evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants.
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Gao H, Xu J, Lu X, Li J, Lou J, Zhao H, Diao B, Shi Q, Zhang Y, Kan B. Expression of Hemolysin Is Regulated Under the Collective Actions of HapR, Fur, and HlyU in Vibrio cholerae El Tor Serogroup O1. Front Microbiol 2018; 9:1310. [PMID: 29971055 PMCID: PMC6018088 DOI: 10.3389/fmicb.2018.01310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
The biotype El Tor of serogroup O1 and most of the non-O1/non-O139 strains of Vibrio cholerae can produce an extracellular pore-forming toxin known as cholera hemolysin (HlyA). Expression of HlyA has been previously reported to be regulated by the quorum sensing (QS) and the regulatory proteins HlyU and Fur, but lacks the direct evidence for their binding to the promoter of hlyA. In the present work, we showed that the QS regulator HapR, along with Fur and HlyU, regulates the transcription of hlyA in V. cholerae El Tor biotype. At the late mid-logarithmic growth phase, HapR binds to the three promoters of fur, hlyU, and hlyA to repress their transcription. At the early mid-logarithmic growth phase, Fur binds to the promoters of hlyU and hlyA to repress their transcription; meanwhile, HlyU binds to the promoter of hlyA to activate its transcription, but it manifests direct inhibition of its own gene. The highest transcriptional level of hlyA occurs at an OD600 value of around 0.6–0.7, which may be due to the subtle regulation of HapR, Fur, and HlyU. The complex regulation of HapR, Fur, and HlyU on hlyA would be beneficial to the invasion and pathogenesis of V. cholerae during the different infection stages.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Xu
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Kim HY, Go J, Lee KM, Oh YT, Yoon SS. Guanosine tetra- and pentaphosphate increase antibiotic tolerance by reducing reactive oxygen species production in Vibrio cholerae. J Biol Chem 2018; 293:5679-5694. [PMID: 29475943 PMCID: PMC5900777 DOI: 10.1074/jbc.ra117.000383] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/16/2018] [Indexed: 02/06/2023] Open
Abstract
The pathogen Vibrio cholerae is the causative agent of cholera. Emergence of antibiotic-resistant V. cholerae strains is increasing, but the underlying mechanisms remain unclear. Herein, we report that the stringent response regulator and stress alarmone guanosine tetra- and pentaphosphate ((p)ppGpp) significantly contributes to antibiotic tolerance in V. cholerae We found that N16961, a pandemic V. cholerae strain, and its isogenic (p)ppGpp-overexpressing mutant ΔrelAΔspoT are both more antibiotic-resistant than (p)ppGpp0 (ΔrelAΔrelVΔspoT) and ΔdksA mutants, which cannot produce or utilize (p)ppGpp, respectively. We also found that additional disruption of the aconitase B-encoding and tricarboxylic acid (TCA) cycle gene acnB in the (p)ppGpp0 mutant increases its antibiotic tolerance. Moreover, expression of TCA cycle genes, including acnB, was increased in (p)ppGpp0, but not in the antibiotic-resistant ΔrelAΔspoT mutant, suggesting that (p)ppGpp suppresses TCA cycle activity, thereby entailing antibiotic resistance. Importantly, when grown anaerobically or incubated with an iron chelator, the (p)ppGpp0 mutant became antibiotic-tolerant, suggesting that reactive oxygen species (ROS) are involved in antibiotic-mediated bacterial killing. Consistent with that hypothesis, tetracycline treatment markedly increased ROS production in the antibiotic-susceptible mutants. Interestingly, expression of the Fe(III) ABC transporter substrate-binding protein FbpA was increased 10-fold in (p)ppGpp0, and fbpA gene deletion restored viability of tetracycline-exposed (p)ppGpp0 cells. Of note, FbpA expression was repressed in the (p)ppGpp-accumulating mutant, resulting in a reduction of intracellular free iron, required for the ROS-generating Fenton reaction. Our results indicate that (p)ppGpp-mediated suppression of central metabolism and iron uptake reduces antibiotic-induced oxidative stress in V. cholerae.
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Affiliation(s)
- Hwa Young Kim
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, and ,the Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea and
| | - Junhyeok Go
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, and ,the Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea and
| | - Kang-Mu Lee
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, and ,the Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea and
| | - Young Taek Oh
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, and ,the Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, SangJu 37242, Korea, To whom correspondence may be addressed:
Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, SangJu-si 37242, Korea. Tel.:
82-54-530-0932; Fax:
82-54-530-0949; E-mail:
| | - Sang Sun Yoon
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, and ,the Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea and , To whom correspondence may be addressed:
Dept. of Microbiology and Immunology, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-gu Seoul 120-752, Korea. Tel.:
82-2-2228-1824; Fax:
82-2-392-7088; E-mail:
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Yang B, Wang S, Huang J, Yin Z, Jiang L, Hou W, Li X, Feng L. Transcriptional Activator GmrA, Encoded in Genomic Island OI-29, Controls the Motility of Enterohemorrhagic Escherichia coli O157:H7. Front Microbiol 2018. [PMID: 29520261 PMCID: PMC5826968 DOI: 10.3389/fmicb.2018.00338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Enterohemorrhagic Escherichia coli O157:H7 is a major human enteric pathogen capable of causing large outbreaks of severe infections that induce bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Its genome contains 177 unique O islands (OIs) including those carrying the main virulence elements, Shiga toxin-converting phages (OI-45 and OI-93) and locus for enterocyte effacement (OI-148). However, many of these islands harbor only genes of unknown function. Here, we demonstrate that OI-29 encodes a newly discovered transcriptional activator, Z0639 (named GmrA), that is required for motility and flagellar synthesis in O157:H7. GmrA directly binds to the promoter of fliA, an RNA polymerase sigma factor, and thereby regulates flagellar genes controlled by FliA. Expression of gmrA is maximal under host conditions (37°C, neutral pH, and physiological osmolarity), and in the presence of host epithelial cells, indicative of a role of this gene in infection by promoting motility. Finally, GmrA was found to be a widespread regulator of bacterial motility and flagellar synthesis in different pathotypes of E. coli. Our work largely enriches our understanding of bacterial motility control, and provides another example of regulators acquired laterally that mediate flagellar synthesis.
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Affiliation(s)
- Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Shaomeng Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
| | - Jianxiao Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
| | - Zhiqiu Yin
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
| | - Lingyan Jiang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Wenqi Hou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
| | - Xiaomin Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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BosR Is A Novel Fur Family Member Responsive to Copper and Regulating Copper Homeostasis in Borrelia burgdorferi. J Bacteriol 2017; 199:JB.00276-17. [PMID: 28583949 DOI: 10.1128/jb.00276-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/01/2017] [Indexed: 12/17/2022] Open
Abstract
The ferric uptake regulator (Fur) family of DNA-binding proteins represses and/or activates gene transcription via divalent metal ion-dependent signal sensing. The Borrelia burgdorferi Fur homologue, also known as Borrelia oxidative stress regulator (BosR), promotes spirochetal adaptation to the mammalian host by directly repressing the lipoproteins required for tick colonization and indirectly activating those required for establishing infection in the mammal. Here, we examined whether the DNA-binding activity of BosR was regulated by any of the four most prevalent transition metal ions in B. burgdorferi, Mn, Fe, Cu, and Zn. Our data indicated that in addition to a structural site occupied by Zn(II), BosR had two regulatory sites that could be occupied by Zn(II), Fe(II), or Cu(II) but not by Mn(II). While Fe(II) had no effect, Cu(II) and Zn(II) had a dose-dependent inhibitory effect on the BosR DNA-binding activity. Competition experiments indicated that Cu(II) had a higher affinity for BosR than Zn(II) or Fe(II). A BosR deficiency in B. burgdorferi resulted in a significant increase in the Cu level but no significant change in the levels of Mn, Fe, or Zn. These data suggest that Cu regulates BosR activity, and BosR in turn regulates Cu homeostasis in B. burgdorferi While this regulatory paradigm is characteristic of the Fur family, BosR is the first one shown to be responsive to Cu(II), which may be an adaptation to the potentially high level of Cu present in the Lyme disease spirochete.IMPORTANCE Transition metal ions serve an essential role in the metabolism of all living organisms. Members of the ferric uptake regulator (Fur) family play critical roles in regulating the cellular homeostasis of transition metals in diverse bacteria, and their DNA-binding activity is often regulated by coordination of the cognate divalent metal ions. To date, regulators with metal ion specificity to Fe(II), Mn(II), Zn(II), and Ni(II) have all been described. In this study, we demonstrate that BosR, the sole Fur homologue in Borrelia burgdorferi, is responsive to Cu(II) and regulates Cu homeostasis in this bacterium, which may be an adaption to potentially Cu-rich milieu in the Lyme disease spirochete. This study has expanded the repertoire of the Fur family's metal ion specificity.
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Thode SK, Bækkedal C, Söderberg JJ, Hjerde E, Hansen H, Haugen P. Construction of a fur null mutant and RNA-sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon. PeerJ 2017; 5:e3461. [PMID: 28717590 PMCID: PMC5511505 DOI: 10.7717/peerj.3461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur. To provide a more accurate and deeper global understanding of the biological role of Fur we have now generated an A. salmonicida fur knock-out strain and used RNA-sequencing to compare gene expression between the wild-type and fur null mutant strains. RESULTS An A. salmonicida fur null mutant strain was constructed. Biological assays demonstrate that deletion of fur results in loss of fitness, with reduced growth rates, and reduced abilities to withstand low-iron conditions, and oxidative stress. When comparing expression levels in the wild-type and the fur null mutant we retrieved 296 differentially expressed genes distributed among 18 of 21 functional classes of genes. A gene cluster encoding biosynthesis of the siderophore bisucaberin represented the highest up-regulated genes in the fur null mutant. Other highly up-regulated genes all encode proteins important for iron acquisition. Potential targets for the RyhB sRNA was predicted from the list of down-regulated genes, and significant complementarities were found between RyhB and mRNAs of the fur, sodB, cysN and VSAL_I0422 genes. Other sRNAs with potential functions in iron homeostasis were identified. CONCLUSION The present work provides by far the most comprehensive and deepest understanding of the Fur regulon in A. salmonicida to date. Our data also contribute to a better understanding of how Fur plays a key role in iron homeostasis in bacteria in general, and help to show how Fur orchestrates iron uptake when iron levels are extremely low.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Cecilie Bækkedal
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Jenny Johansson Söderberg
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
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The Vibrio cholerae VexGH RND Efflux System Maintains Cellular Homeostasis by Effluxing Vibriobactin. mBio 2017; 8:mBio.00126-17. [PMID: 28512090 PMCID: PMC5433094 DOI: 10.1128/mbio.00126-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Resistance-nodulation-division (RND) superfamily efflux systems have been widely studied for their role in antibiotic resistance, but their native biological functions remain poorly understood. We previously showed that loss of RND-mediated efflux in Vibrio cholerae resulted in activation of the Cpx two-component regulatory system, which mediates adaptation to stress resulting from misfolded membrane proteins. Here, we investigated the mechanism linking RND-mediated efflux to the Cpx response. We performed transposon mutagenesis screening of RND-deficient V. cholerae to identify Cpx suppressors. Suppressor mutations mapped to genes involved in the biosynthesis of the catechol siderophore vibriobactin. We subsequently demonstrated that vibriobactin secretion is impaired in mutants lacking the VexGH RND efflux system and that impaired vibriobactin secretion is responsible for Cpx system activation, suggesting that VexGH secretes vibriobactin. This conclusion was bolstered by results showing that vexGH expression is induced by iron limitation and that vexH-deficient cells exhibit reduced fitness during growth under iron-limiting conditions. Our results support a model where VexGH contributes to cellular homeostasis by effluxing vibriobactin. In the absence of vexGH, retained vibriobactin appears to chelate iron from iron-rich components of the respiratory chain, with the deferrated proteins functioning to activate the Cpx response. Our collective results demonstrate that a native function of the V. cholerae VexGH RND efflux system is in vibriobactin secretion and that vibriobactin efflux is critical for maintenance of cellular homeostasis.IMPORTANCE RND efflux systems are ubiquitous Gram-negative transporters that play critical roles in antimicrobial resistance. In addition to antimicrobial resistance, RND transporters also affect the expression of diverse phenotypes, including virulence, cell metabolism, and stress responses. The latter observations suggest that RND transporters fulfill unknown physiological functions in the cell independently of their role in antimicrobial resistance. Vibrio cholerae is representative of many Gram-negative bacteria in encoding multiple RND transporters that are redundant in antimicrobial resistance and affect multiple phenotypes. Here we describe a novel function of the V. cholerae VexGH RND transporter in vibriobactin secretion. We show that vibriobactin production in VexGH-deficient cells impacts cell homeostasis, leading to activation of the Cpx stress response and reduced fitness under iron-limiting conditions. Our results highlight a native physiological function of an RND transporter and provide insight into the selective forces that maintain what was thought to be a redundant multidrug transporter.
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Han R, Xu L, Wang T, Liu B, Wang L. A Small Regulatory RNA Contributes to the Preferential Colonization of Escherichia coli O157:H7 in the Large Intestine in Response to a Low DNA Concentration. Front Microbiol 2017; 8:274. [PMID: 28289405 PMCID: PMC5326754 DOI: 10.3389/fmicb.2017.00274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/09/2017] [Indexed: 11/13/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 (O157) is one of the most notorious human pathogens, causing severe disease in humans worldwide. O157 specifically colonizes the large intestine of mammals after passing through the small intestine, and this process is influenced by differential signals between the two regions. Small regulatory RNAs (sRNAs) are able to sense and respond to environmental changes and regulate diverse physiological processes in pathogenic bacteria. Although some sRNAs of O157 have been extensively investigated, whether these molecules can sense differences between the small and large intestine and influence the preferential colonization in the large intestine by O157 remains unknown. In this study, we identified a new sRNA, Esr055, in O157 which senses the low DNA concentration in the large intestine and contributes to the preferential colonization of the bacteria in this region. The number of O157 wild-type that adhered to the colon is 30.18 times higher than the number that adhered to the ileum of mice, while the number of the ΔEsr055 mutant that adhered to the colon decreased to 13.27 times higher than the number adhered to the ileum. Furthermore, we found that the expression of Esr055 is directly activated by the regulator, DeoR, and its expression is positively affected by DNA, which is significantly more abundant in the ileum than in the colon of mice. Additionally, combining the results of informatics predictions and transcriptomic analysis, we found that several virulence genes are up-regulated in the ΔEsr055 mutant and five candidate genes (z0568, z0974, z1356, z1926, and z5187) may be its direct targets.
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Affiliation(s)
- Runhua Han
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China
| | - Letian Xu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China
| | - Ting Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China; State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
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Stacy A, Abraham N, Jorth P, Whiteley M. Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection. PLoS Pathog 2016; 12:e1006084. [PMID: 27973608 PMCID: PMC5156373 DOI: 10.1371/journal.ppat.1006084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Iron is an essential nutrient for bacterial pathogenesis, but in the host, iron is tightly sequestered, limiting its availability for bacterial growth. Although this is an important arm of host immunity, most studies examine how bacteria respond to iron restriction in laboratory rather than host settings, where the microbiome can potentially alter pathogen strategies for acquiring iron. One of the most important transcriptional regulators controlling bacterial iron homeostasis is Fur. Here we used a combination of RNA-seq and chromatin immunoprecipitation (ChIP)-seq to characterize the iron-restricted and Fur regulons of the biofilm-forming opportunistic pathogen Aggregatibacter actinomycetemcomitans. We discovered that iron restriction and Fur regulate 4% and 3.5% of the genome, respectively. While most genes in these regulons were related to iron uptake and metabolism, we found that Fur also directly regulates the biofilm-dispersing enzyme Dispersin B, allowing A. actinomycetemcomitans to escape from iron-scarce environments. We then leveraged these datasets to assess the availability of iron to A. actinomycetemcomitans in its primary infection sites, abscesses and the oral cavity. We found that A. actinomycetemcomitans is not restricted for iron in a murine abscess mono-infection, but becomes restricted for iron upon co-infection with the oral commensal Streptococcus gordonii. Furthermore, in the transition from health to disease in human gum infection, A. actinomycetemcomitans also becomes restricted for iron. These results suggest that host iron availability is heterogeneous and dependent on the infecting bacterial community. One of the most well-studied phenomena in microbiology is nutritional immunity, or how the host withholds nutrients such as iron to combat infection. As part of this, researchers have characterized how many pathogens respond to iron restriction. However, these studies are often conducted in laboratory media rather than the host. As a result, they overlook how the host environment, such as its microbiome, might alter pathogen behavior regarding iron during infection. To address this gap, we used an opportunistic pathogen that causes abscess and oral cavity infections. We defined how it responds to iron restriction in vitro and then used this data to assess its iron status in vivo. Our results show that in mono-culture abscesses the pathogen is not starved for iron but in co-culture abscesses and multispecies gum disease it is starved for iron. Therefore, host environments are not uniformly restricted for iron, and the microbiome can modulate iron availability to pathogens.
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Affiliation(s)
- Apollo Stacy
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Nader Abraham
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Peter Jorth
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
- * E-mail:
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Identification and Characterization of a Putative Manganese Export Protein in Vibrio cholerae. J Bacteriol 2016; 198:2810-7. [PMID: 27481926 DOI: 10.1128/jb.00215-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Manganese plays an important role in the cellular physiology and metabolism of bacterial species, including the human pathogen Vibrio cholerae The intracellular level of manganese ions is controlled through coordinated regulation of the import and export of this element. We have identified a putative manganese exporter (VC0022), named mneA (manganese exporter A), which is highly conserved among Vibrio spp. An mneA mutant exhibited sensitivity to manganese but not to other cations. Under high-manganese conditions, the mneA mutant showed an almost 50-fold increase in intracellular manganese levels and reduced intracellular iron relative to those of its wild-type parent, suggesting that the mutant's manganese sensitivity is due to the accumulation of toxic levels of manganese and reduced iron. Expression of mneA suppressed the manganese-sensitive phenotype of an Escherichia coli strain carrying a mutation in the nonhomologous manganese export gene, mntP, further supporting a manganese export function for V. cholerae MneA. The level of mneA mRNA was induced approximately 2.5-fold after addition of manganese to the medium, indicating regulation of this gene by manganese. This study offers the first insights into understanding manganese homeostasis in this important pathogen. IMPORTANCE Bacterial cells control intracellular metal concentrations by coordinating acquisition in metal-limited environments with export in metal-excess environments. We identified a putative manganese export protein, MneA, in Vibrio cholerae An mneA mutant was sensitive to manganese, and this effect was specific to manganese. The mneA mutant accumulated high levels of intracellular manganese with a concomitant decrease in intracellular iron levels when grown in manganese-supplemented medium. Expression of mneA in trans suppressed the manganese sensitivity of an E. coli mntP mutant. This study is the first to investigate manganese export in V. cholerae.
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Kazi MI, Conrado AR, Mey AR, Payne SM, Davies BW. ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization. PLoS Pathog 2016; 12:e1005570. [PMID: 27070545 PMCID: PMC4829181 DOI: 10.1371/journal.ppat.1005570] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/22/2016] [Indexed: 02/04/2023] Open
Abstract
The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR’s genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters. The transcription factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express essential host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors. Our results suggest that ToxR has gained regulatory control over important acquired elements that not only drive V. cholerae pathogenesis, but also define the major transitions of V. cholerae pandemic lineages. We demonstrate that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS for control of critical colonization functions. This regulatory interaction is the major role of ToxR in V. cholerae colonization, since deletion of hns abrogates the need for ToxR in V. cholerae host colonization. By comparing the genome-wide binding profiles of ToxR and other critical virulence regulators, we show that, despite similar predicted DNA binding requirements, ToxR is unique in its global control of progenitor-encoded and acquired genes. Our results suggest that factors in addition to primary DNA structure determine selection of ToxR binding sites.
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Affiliation(s)
- Misha I. Kazi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Aaron R. Conrado
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alexandra R. Mey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shelley M. Payne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Bryan W. Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Payne SM, Mey AR, Wyckoff EE. Vibrio Iron Transport: Evolutionary Adaptation to Life in Multiple Environments. Microbiol Mol Biol Rev 2016; 80:69-90. [PMID: 26658001 PMCID: PMC4711184 DOI: 10.1128/mmbr.00046-15] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Iron is an essential element for Vibrio spp., but the acquisition of iron is complicated by its tendency to form insoluble ferric complexes in nature and its association with high-affinity iron-binding proteins in the host. Vibrios occupy a variety of different niches, and each of these niches presents particular challenges for acquiring sufficient iron. Vibrio species have evolved a wide array of iron transport systems that allow the bacteria to compete for this essential element in each of its habitats. These systems include the secretion and uptake of high-affinity iron-binding compounds (siderophores) as well as transport systems for iron bound to host complexes. Transporters for ferric and ferrous iron not complexed to siderophores are also common to Vibrio species. Some of the genes encoding these systems show evidence of horizontal transmission, and the ability to acquire and incorporate additional iron transport systems may have allowed Vibrio species to more rapidly adapt to new environmental niches. While too little iron prevents growth of the bacteria, too much can be lethal. The appropriate balance is maintained in vibrios through complex regulatory networks involving transcriptional repressors and activators and small RNAs (sRNAs) that act posttranscriptionally. Examination of the number and variety of iron transport systems found in Vibrio spp. offers insights into how this group of bacteria has adapted to such a wide range of habitats.
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Affiliation(s)
- Shelley M Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Alexandra R Mey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Elizabeth E Wyckoff
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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Nonredundant Roles of Iron Acquisition Systems in Vibrio cholerae. Infect Immun 2015; 84:511-23. [PMID: 26644383 DOI: 10.1128/iai.01301-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/24/2015] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae, the causative agent of the severe diarrheal disease cholera, thrives in both marine environments and the human host. To do so, it must encode the tools necessary to acquire essential nutrients, including iron, under these vastly different conditions. A number of V. cholerae iron acquisition systems have been identified; however, the precise role of each system is not fully understood. To test the roles of individual systems, we generated a series of mutants in which only one of the four systems that support iron acquisition on unsupplemented LB agar, Feo, Fbp, Vct, and Vib, remains functional. Analysis of these mutants under different growth conditions showed that these systems are not redundant. The strain carrying only the ferrous iron transporter Feo grew well at acidic, but not alkaline, pH, whereas the ferric iron transporter Fbp promoted better growth at alkaline than at acidic pH. A strain defective in all four systems (null mutant) had a severe growth defect under aerobic conditions but accumulated iron and grew as well as the wild type in the absence of oxygen, suggesting the presence of an additional, unidentified iron transporter in V. cholerae. In support of this, the null mutant was only moderately attenuated in an infant mouse model of infection. While the null mutant used heme as an iron source in vitro, we demonstrate that heme is not available to V. cholerae in the infant mouse intestine.
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ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response. PLoS One 2015; 10:e0138466. [PMID: 26389830 PMCID: PMC4577112 DOI: 10.1371/journal.pone.0138466] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
The alternative sigma factor σE functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σE in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σE-binding sites in Salmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σE-binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cell division factor, and a signal transduction modulator. The consensus sequence identified for σE in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σE-binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σE modulates transcription. By dissecting direct and indirect modes of σE-mediated regulation, we found that σE activates gene expression through recognition of both canonical and reversed consensus sequence. New σE regulated genes (greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.
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Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, C Gomes AL, Galagan JE, McDonough KA. Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res 2015; 44:134-51. [PMID: 26358810 PMCID: PMC4705688 DOI: 10.1093/nar/gkv889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/26/2015] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ∼200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.
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Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Anna Lyubetskaya
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Gwendowlyn S Knapp
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | | | - Michaela Gazdik
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | | | - James E Galagan
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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Kong W, Zhao J, Kang H, Zhu M, Zhou T, Deng X, Liang H. ChIP-seq reveals the global regulator AlgR mediating cyclic di-GMP synthesis in Pseudomonas aeruginosa. Nucleic Acids Res 2015. [PMID: 26206672 PMCID: PMC4787818 DOI: 10.1093/nar/gkv747] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
AlgR is a key transcriptional regulator required for the expression of multiple virulence factors, including type IV pili and alginate in Pseudomonas aeruginosa. However, the regulon and molecular regulatory mechanism of AlgR have yet to be fully elucidated. Here, among 157 loci that were identified by a ChIP-seq assay, we characterized a gene, mucR, which encodes an enzyme that synthesizes the intracellular second messenger cyclic diguanylate (c-di-GMP). A ΔalgR strain produced lesser biofilm than did the wild-type strain, which is consistent with a phenotype controlled by c-di-GMP. AlgR positively regulates mucR via direct binding to its promoter. A ΔalgRΔmucR double mutant produced lesser biofilm than did the single ΔalgR mutant, demonstrating that c-di-GMP is a positive regulator of biofilm formation. AlgR controls the levels of c-di-GMP synthesis via direct regulation of mucR. In addition, the cognate sensor of AlgR, FimS/AlgZ, also plays an important role in P. aeruginosa virulence. Taken together, this study provides new insights into the AlgR regulon and reveals the involvement of c-di-GMP in the mechanism underlying AlgR regulation.
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Affiliation(s)
- Weina Kong
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, ShaanXi 710069, China
| | - Jingru Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, ShaanXi 710069, China
| | - Huaping Kang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, ShaanXi 710069, China
| | - Miao Zhu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, ShaanXi 710069, China
| | - Tianhong Zhou
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, Tianjin 300457, China
| | - Xin Deng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, Tianjin 300457, China
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, ShaanXi 710069, China
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Deng Z, Wang Q, Liu Z, Zhang M, Machado ACD, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z. Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Nat Commun 2015; 6:7642. [PMID: 26134419 PMCID: PMC4506495 DOI: 10.1038/ncomms8642] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/27/2015] [Indexed: 01/21/2023] Open
Abstract
Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.
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Affiliation(s)
- Zengqin Deng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Qing Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhao Liu
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Manfeng Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Tsu-Pei Chiu
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Chong Feng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Qi Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Yu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Lei Qi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Jiangge Zheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xu Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - XinMei Huo
- Institute of Apicultural Research, Key Laboratory of Pollinating Insect Biology, Chinese Academy of Agricultural Science, Beijing 100093, China
| | - Xiaoxuan Qi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaorong Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Ying Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
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Myers KS, Park DM, Beauchene NA, Kiley PJ. Defining bacterial regulons using ChIP-seq. Methods 2015; 86:80-8. [PMID: 26032817 DOI: 10.1016/j.ymeth.2015.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/22/2015] [Accepted: 05/23/2015] [Indexed: 11/28/2022] Open
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful method that identifies protein-DNA binding sites in vivo. Recent studies have illustrated the value of ChIP-seq in studying transcription factor binding in various bacterial species under a variety of growth conditions. These results show that in addition to identifying binding sites, correlation of ChIP-seq data with expression data can reveal important information about bacterial regulons and regulatory networks. In this chapter, we provide an overview of the current state of knowledge about ChIP-seq methodology in bacteria, from sample preparation to raw data analysis. We also describe visualization and various bioinformatic analyses of processed ChIP-seq data.
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Affiliation(s)
- Kevin S Myers
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Dan M Park
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Nicole A Beauchene
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA.
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Yang B, Feng L, Wang F, Wang L. Enterohemorrhagic Escherichia coli senses low biotin status in the large intestine for colonization and infection. Nat Commun 2015; 6:6592. [PMID: 25791315 PMCID: PMC4382993 DOI: 10.1038/ncomms7592] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/10/2015] [Indexed: 12/17/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is an important foodborne pathogen that infects humans by colonizing the large intestine. Here we identify a virulence-regulating pathway in which the biotin protein ligase BirA signals to the global regulator Fur, which in turn activates LEE (locus of enterocyte effacement) genes to promote EHEC adherence in the low-biotin large intestine. LEE genes are repressed in the high-biotin small intestine, thus preventing adherence and ensuring selective colonization of the large intestine. The presence of this pathway in all nine EHEC serotypes tested indicates that it is an important evolutionary strategy for EHEC. The pathway is incomplete in closely related small-intestinal enteropathogenic E. coli due to the lack of the Fur response to BirA. Mice fed with a biotin-rich diet show significantly reduced EHEC adherence, indicating that biotin might be useful to prevent EHEC infection in humans. Enterohaemorrhagic Escherichia coli (EHEC) is an important foodborne pathogen that colonizes the large intestine. Here, the authors identify a signalling pathway that controls EHEC adherence to host cells in response to variations in biotin levels, ensuring selective colonization of the large intestine.
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Affiliation(s)
- Bin Yang
- 1] TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Lu Feng
- 1] TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China [3] Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, P.R. China [4] State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P.R. China [5] SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P.R. China
| | - Fang Wang
- 1] TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Lei Wang
- 1] TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China [3] Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, P.R. China [4] State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P.R. China
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Thode SK, Kahlke T, Robertsen EM, Hansen H, Haugen P. The immediate global responses of Aliivibrio salmonicida to iron limitations. BMC Microbiol 2015; 15:9. [PMID: 25649684 PMCID: PMC4324432 DOI: 10.1186/s12866-015-0342-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/09/2015] [Indexed: 01/15/2023] Open
Abstract
Background Iron is an essential micronutrient for all living organisms, and virulence and sequestration of iron in pathogenic bacteria are believed to be correlated. As a defence mechanism, potential hosts therefore keep the level of free iron inside the body to a minimum. In general, iron metabolism is well studied for some bacteria (mostly human or animal pathogens). However, this area is still under-investigated for a number of important bacterial pathogens. Aliivibrio salmonicida is a fish pathogen, and previous studies of this bacterium have shown that production of siderophores is temperature regulated and dependent on low iron conditions. In this work we studied the immediate changes in transcription in response to a sudden decrease in iron levels in cultures of A. salmonicida. In addition, we compared our results to studies performed with Vibrio cholerae and Vibrio vulnificus using a pan-genomic approach. Results Microarray technology was used to monitor global changes in transcriptional levels. Cultures of A. salmonicida were grown to mid log phase before the iron chelator 2,2’-dipyridyl was added and samples were collected after 15 minutes of growth. Using our statistical cut-off values, we retrieved thirty-two differentially expressed genes where the most up-regulated genes belong to an operon encoding proteins responsible for producing the siderophore bisucaberin. A subsequent pan-transcriptome analysis revealed that nine of the up-regulated genes from our dataset were also up-regulated in datasets from similar experiments using V. cholerae and V. vulnificus, thus indicating that these genes are involved in a shared strategy to mitigate low iron conditions. Conclusions The present work highlights the effect of iron limitation on the gene regulatory network of the fish pathogen A. salmonicida, and provides insights into common and unique strategies of Vibrionaceae species to mitigate low iron conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0342-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Tim Kahlke
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway. .,Current address: Environmental Genomics Team, CSIRO Marine and Atmospheric Research, Castray Esplanade, Hobart, 7000, TAS, Australia.
| | - Espen Mikal Robertsen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Hilde Hansen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Peik Haugen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
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The Vibrio cholerae Cpx envelope stress response senses and mediates adaptation to low iron. J Bacteriol 2014; 197:262-76. [PMID: 25368298 DOI: 10.1128/jb.01957-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Cpx pathway, a two-component system that employs the sensor histidine kinase CpxA and the response regulator CpxR, regulates crucial envelope stress responses across bacterial species and affects antibiotic resistance. To characterize the CpxR regulon in Vibrio cholerae, the transcriptional profile of the pandemic V. cholerae El Tor C6706 strain was examined upon overexpression of cpxR. Our data show that the Cpx regulon of V. cholerae is enriched in genes encoding membrane-localized and transport proteins, including a large number of genes known or predicted to be iron regulated. Activation of the Cpx pathway further led to the expression of TolC, the major outer membrane pore, and of components of two RND efflux systems in V. cholerae. We show that iron chelation, toxic compounds, or deletion of specific RND efflux components leads to Cpx pathway activation. Furthermore, mutations that eliminate the Cpx response or members of its regulon result in growth phenotypes in the presence of these inducers that, together with Cpx pathway activation, are partially suppressed by iron. Cumulatively, our results suggest that a major function of the Cpx response in V. cholerae is to mediate adaptation to envelope perturbations caused by toxic compounds and the depletion of iron.
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Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 2014; 5:4910. [PMID: 25222563 PMCID: PMC4167408 DOI: 10.1038/ncomms5910] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/05/2014] [Indexed: 02/07/2023] Open
Abstract
The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism. However, the full regulatory potential of Fur remains undefined. Here we comprehensively reconstruct the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Integrative data analysis reveals that a total of 81 genes in 42 transcription units are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation and holo-Fur repression. We show that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development is found. These results show how Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate the overall response of E. coli to iron availability.
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Affiliation(s)
- Sang Woo Seo
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Donghyuk Kim
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Haythem Latif
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Edward J O'Brien
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA
| | - Bernhard O Palsson
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Jones CJ, Newsom D, Kelly B, Irie Y, Jennings LK, Xu B, Limoli DH, Harrison JJ, Parsek MR, White P, Wozniak DJ. ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa. PLoS Pathog 2014; 10:e1003984. [PMID: 24603766 PMCID: PMC3946381 DOI: 10.1371/journal.ppat.1003984] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 01/23/2014] [Indexed: 11/28/2022] Open
Abstract
The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression of gene(s) encoding a DGC. In support of this, we observed elevated c-di-GMP in the ΔamrZ mutant compared to the wild type strain. Consistent with other strains that accumulate c-di-GMP, when grown as a biofilm, the ΔamrZ mutant formed larger microcolonies than the wild-type strain. This enhanced biofilm formation was abrogated by expression of a PDE. To identify potential target DGCs, a ChIP-Seq was performed and identified regions of the genome that are bound by AmrZ. RNA-Seq experiments revealed the entire AmrZ regulon, and characterized AmrZ as an activator or repressor at each binding site. We identified an AmrZ-repressed DGC-encoding gene (PA4843) from this cohort, which we named AmrZ dependent cyclase A (adcA). PAO1 overexpressing adcA accumulates 29-fold more c-di-GMP than the wild type strain, confirming the cyclase activity of AdcA. In biofilm reactors, a ΔamrZ ΔadcA double mutant formed smaller microcolonies than the single ΔamrZ mutant, indicating adcA is responsible for the hyper biofilm phenotype of the ΔamrZ mutant. This study combined the techniques of ChIP-Seq and RNA-Seq to define the comprehensive regulon of a bifunctional transcriptional regulator. Moreover, we identified a c-di-GMP mediated mechanism for AmrZ regulation of biofilm formation and chronicity. Pathogenic bacteria such as Pseudomonas aeruginosa utilize a wide variety of systems to sense and respond to the changing conditions during an infection. When a stress is sensed, signals are transmitted to impact expression of many genes that allow the bacterium to adapt to the changing conditions. AmrZ is a protein that regulates production of several virulence-associated gene products, though we predicted that its role in virulence was more expansive than previously described. Transcription factors such as AmrZ often affect the expression of a gene by binding and promoting or inhibiting expression of the target gene. Two global techniques were utilized to determine where AmrZ binds in the genome, and what effect AmrZ has once bound. This approach revealed that AmrZ represses the production of a signaling molecule called cyclic diguanylate, which is known to induce the formation of difficult to treat communities of bacteria called biofilms. This study also identified many novel targets of AmrZ to promote future studies of this regulator. Collectively, these data can be utilized to develop treatments to inhibit biofilm formation during devastating chronic infections.
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Affiliation(s)
- Christopher J. Jones
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Infection and Immunity and Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio, United States of America
| | - David Newsom
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Benjamin Kelly
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Yasuhiko Irie
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Laura K. Jennings
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Binjie Xu
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Dominique H. Limoli
- Department of Infection and Immunity and Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Joe J. Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Matthew R. Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Peter White
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Daniel J. Wozniak
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Picossi S, Flores E, Herrero A. ChIP analysis unravels an exceptionally wide distribution of DNA binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium. BMC Genomics 2014; 15:22. [PMID: 24417914 PMCID: PMC3898017 DOI: 10.1186/1471-2164-15-22] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/26/2013] [Indexed: 11/20/2022] Open
Abstract
Background The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. Canonical NtcA-activated promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. In strains of the Anabaena/Nostoc genera NtcA is pivotal for the differentiation of heterocysts in response to N stress. Results In this study, we have used chromatin immunoprecipitation followed by high-throughput sequencing to identify the whole catalog of NtcA-binding sites in cells of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 three hours after the withdrawal of combined N. NtcA has been found to bind to 2,424 DNA regions in the genome of Anabaena, which have been ascribed to 2,153 genes. Interestingly, only a small proportion of those genes are involved in N assimilation and metabolism, and 65% of the binding regions were located intragenically. Conclusions The distribution of NtcA-binding sites identified here reveals the largest bacterial regulon described to date. Our results show that NtcA has a much wider role in the physiology of the cell than it has been previously thought, acting both as a global transcriptional regulator and possibly also as a factor influencing the superstructure of the chromosome (and plasmids).
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Affiliation(s)
- Silvia Picossi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, Seville E-41092, Spain.
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Zappa S, Bauer CE. The LysR-type transcription factor HbrL is a global regulator of iron homeostasis and porphyrin synthesis in Rhodobacter capsulatus. Mol Microbiol 2013; 90:1277-92. [PMID: 24134691 PMCID: PMC3890261 DOI: 10.1111/mmi.12431] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2013] [Indexed: 01/27/2023]
Abstract
The purple bacterium Rhodobacter capsulatus is unique among Rhodobacteriacae as it contains a putative iron response regulator (Irr) but does not possess a copy of the ferric uptake regulator (Fur). Interestingly, an in-frame deletion mutant of Irr shows no major role in iron homeostasis. Instead, we showed that the previously identified activator of haem gene expression HbrL is a crucial regulator of iron homeostasis. We demonstrated that an HbrL deletion strain is unable to grow in iron-limited medium in aerobic, semi-aerobic and photosynthetic conditions and that suppressor strains can be isolated with mutations in iron uptake genes. Gene expression studies revealed that HbrL is a transcriptional activator of multiple ferrous and ferric iron uptake systems in addition to a haem uptake system. Finally, HbrL activates the expression of numerous haem biosynthesis genes. Thus, HbrL has a central role in controlling the amount of iron transport in conjunction with the synthesis of its cognate tetrapyrrole haem.
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Affiliation(s)
- Sébastien Zappa
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall, 212 S Hawthorne Dr., Bloomington, IN 47405, U. S. A
| | - Carl E. Bauer
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall, 212 S Hawthorne Dr., Bloomington, IN 47405, U. S. A
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Balasubramanian D, Kumari H, Jaric M, Fernandez M, Turner KH, Dove SL, Narasimhan G, Lory S, Mathee K. Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. Nucleic Acids Res 2013; 42:979-98. [PMID: 24157832 PMCID: PMC3902932 DOI: 10.1093/nar/gkt942] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Pathogenicity of Pseudomonas aeruginosa, a major cause of many acute and chronic human infections, is determined by tightly regulated expression of multiple virulence factors. Quorum sensing (QS) controls expression of many of these pathogenic determinants. Previous microarray studies have shown that the AmpC β-lactamase regulator AmpR, a member of the LysR family of transcription factors, also controls non-β-lactam resistance and multiple virulence mechanisms. Using RNA-Seq and complementary assays, this study further expands the AmpR regulon to include diverse processes such as oxidative stress, heat shock and iron uptake. Importantly, AmpR affects many of these phenotypes, in part, by regulating expression of non-coding RNAs such as rgP32, asRgsA, asPrrF1 and rgRsmZ. AmpR positively regulates expression of the major QS regulators LasR, RhlR and MvfR, and genes of the Pseudomonas quinolone system. Chromatin immunoprecipitation (ChIP)-Seq and ChIP–quantitative real-time polymerase chain reaction studies show that AmpR binds to the ampC promoter both in the absence and presence of β-lactams. In addition, AmpR directly binds the lasR promoter, encoding the QS master regulator. Comparison of the AmpR-binding sequences from the transcriptome and ChIP-Seq analyses identified an AT-rich consensus-binding motif. This study further attests to the role of AmpR in regulating virulence and physiological processes in P. aeruginosa.
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Affiliation(s)
- Deepak Balasubramanian
- Department of Biological Sciences, College of Arts and Science, Florida International University, Miami, FL 33199, USA, Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA, BioRG, School of Computing and Information Science, College of Engineering and Computing, Florida International University, Miami, FL 33199, USA, Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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Runyen-Janecky LJ. Role and regulation of heme iron acquisition in gram-negative pathogens. Front Cell Infect Microbiol 2013; 3:55. [PMID: 24116354 PMCID: PMC3792355 DOI: 10.3389/fcimb.2013.00055] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/10/2013] [Indexed: 12/14/2022] Open
Abstract
Bacteria that reside in animal tissues and/or cells must acquire iron from their host. However, almost all of the host iron is sequestered in iron-containing compounds and proteins, the majority of which is found within heme molecules. Thus, likely iron sources for bacterial pathogens (and non-pathogenic symbionts) are free heme and heme-containing proteins. Furthermore, the cellular location of the bacterial within the host (intra or extracellular) influences the amount and nature of the iron containing compounds available for transport. The low level of free iron in the host, coupled with the presence of numerous different heme sources, has resulted in a wide range of high-affinity iron acquisition strategies within bacteria. However, since excess iron and heme are toxic to bacteria, expression of these acquisition systems is highly regulated. Precise expression in the correct host environment at the appropriate times enables heme iron acquisitions systems to contribute to the growth of bacterial pathogens within the host. This mini-review will highlight some of the recent findings in these areas for gram-negative pathogens.
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