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Xie X, Deng X, Chen L, Yuan J, Chen H, Wei C, Liu X, Wuertz S, Qiu G. Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100353. [PMID: 39221073 PMCID: PMC11361876 DOI: 10.1016/j.ese.2023.100353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
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2
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Billini M, Hoffmann T, Kühn J, Bremer E, Thanbichler M. The cytoplasmic phosphate level has a central regulatory role in the phosphate starvation response of Caulobacter crescentus. Commun Biol 2024; 7:772. [PMID: 38926609 PMCID: PMC11208175 DOI: 10.1038/s42003-024-06469-y] [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: 10/07/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoR-PhoB two-component signal transduction pathway, which uses the flux through the PstSCAB phosphate transporter as a readout of the extracellular phosphate level to control phosphate-responsive genes. While the sensing of environmental phosphate is well-investigated, the regulatory effects of cytoplasmic phosphate are unclear. Here, we disentangle the physiological and transcriptional responses of Caulobacter crescentus to changes in the environmental and cytoplasmic phosphate levels by uncoupling phosphate uptake from the activity of the PstSCAB system, using an additional, heterologously produced phosphate transporter. This approach reveals a two-pronged response of C. crescentus to phosphate limitation, in which PhoR-PhoB signaling mostly facilitates the utilization of alternative phosphate sources, whereas the cytoplasmic phosphate level controls the morphological and physiological adaptation of cells to growth under global phosphate limitation. These findings open the door to a comprehensive understanding of phosphate signaling in bacteria.
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Affiliation(s)
- Maria Billini
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Juliane Kühn
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology, 35043, Marburg, Germany.
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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Matsui H, Harada H, Maeda K, Sugiyama T, Fukuchi Y, Kimura N, Nawaly H, Tsuji Y, Matsuda Y. Coordinated phosphate uptake by extracellular alkaline phosphatase and solute carrier transporters in marine diatoms. THE NEW PHYTOLOGIST 2024; 241:1210-1221. [PMID: 38013640 DOI: 10.1111/nph.19410] [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: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
Marine diatoms express genes encoding potential phosphate transporter and alkaline phosphatase (APase) under phosphate-limited (-P) condition. This indicates that diatoms use high-affinity phosphate uptake system with organic phosphate hydration. The function of molecules playing roles for Pi uptake was determined in this study. Pi uptake and APase activity of two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, were monitored during acclimation to -P condition. The transcript levels of Pi transporter were analyzed, and Pi transporters were localized with GFP tagging in diatom cells. KO mutants of plasma membrane solute carrier proteins (SLC34s) or APase were established, and their phenotype was evaluated. Some Na+ /Pi transporter candidates, SLC34s in P. tricornutum and T. pseudonana, increased transcript under -P condition. Whole-cell Pi transport was specifically stimulated by sodium ion but independent of potassium, lithium, or proton. Genome-editing KO of PtSLC34-5 and APase (Pt49678) in P. tricornutum was highly inhibitory for Pi uptake, and KO of TpSLC34-2 was also highly inhibitory for Pi uptake in T. pseudonana. SLC34s and APase were co-expressed under -P conditions in marine diatoms. SLC34s play a major role in the initial acclimation stage of diatom cells to -P condition and APase plays an increasing role in the prolonged Pi-starved condition.
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Affiliation(s)
- Hiroaki Matsui
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Hisashi Harada
- Department of Chemistry and Biotechnology, Tottori University, Tottori, 680-8550, Japan
| | - Kanako Maeda
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Toshiki Sugiyama
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yohei Fukuchi
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Nanae Kimura
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Hermanus Nawaly
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yoshinori Tsuji
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yusuke Matsuda
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
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Stephens AC, Banerjee SK, Richardson AR. Specialized phosphate transport is essential for Staphylococcus aureus nitric oxide resistance. mBio 2023; 14:e0245123. [PMID: 37937971 PMCID: PMC10746193 DOI: 10.1128/mbio.02451-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE Staphylococcus aureus is a bacterial pathogen capable of causing a wide variety of disease in humans. S. aureus is unique in its ability to resist the host immune response, including the antibacterial compound known as nitric oxide (NO·). We used an RNA-sequencing approach to better understand the impact of NO· on S. aureus in different environments. We discovered that inorganic phosphate transport is induced by the presence of NO·. Phosphate is important for the generation of energy from glucose, a carbon source favored by S. aureus. We show that the absence of these phosphate transporters causes lowered energy levels in S. aureus. We find that these phosphate transporters are essential for S. aureus to grow in the presence of NO· and to cause infection. Our work here contributes significantly to our understanding of S. aureus NO· resistance and provides a new context in which S. aureus phosphate transporters are essential.
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Affiliation(s)
- Amelia C. Stephens
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Srijon K. Banerjee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Bruna RE, Kendra CG, Pontes MH. Phosphorus starvation response and PhoB-independent utilization of organic phosphate sources by Salmonella enterica. Microbiol Spectr 2023; 11:e0226023. [PMID: 37787565 PMCID: PMC10715179 DOI: 10.1128/spectrum.02260-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Phosphorus (P) is the fifth most abundant element in living cells. This element is acquired mainly as inorganic phosphate (Pi, PO4 3-). In enteric bacteria, P starvation activates a two-component signal transduction system which is composed of the membrane sensor protein PhoR and its cognate transcription regulator PhoB. PhoB, in turn, promotes the transcription of genes that help maintain Pi homeostasis. Here, we characterize the P starvation response of the bacterium Salmonella enterica. We determine the PhoB-dependent and independent transcriptional changes promoted by P starvation and identify proteins enabling the utilization of a range of organic substrates as sole P sources. We show that transcription and activity of a subset of these proteins are independent of PhoB and Pi availability. These results establish that Salmonella enterica can maintain Pi homeostasis and repress PhoB/PhoR activation even when cells are grown in medium lacking Pi.
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Affiliation(s)
- Roberto E. Bruna
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher G. Kendra
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mauricio H. Pontes
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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7
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Razmilic V, Nouioui I, Karlyshev A, Jawad R, Trujillo ME, Igual JM, Andrews BA, Asenjo JA, Carro L, Goodfellow M. Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059605 DOI: 10.1099/ijsem.0.006189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.
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Affiliation(s)
- Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Andrey Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Rana Jawad
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Jose M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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Chen J, Qu C, Lu M, Zhang M, Wu Y, Gao C, Huang Q, Cai P. Extracellular polymeric substances and mineral interfacial reactions control the simultaneous immobilization and reduction of arsenic (As(V)). JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131651. [PMID: 37245361 DOI: 10.1016/j.jhazmat.2023.131651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 05/14/2023] [Indexed: 05/30/2023]
Abstract
Extracellular polymeric substances (EPS) play a crucial role in controlling the mobility and bioavailability of heavy metal(loid)s in water, soils, and sediments. The formation of EPS-mineral complex changes the reactivity of the end-member materials. However, little is known about the adsorption and redox mechanisms of arsenate (As(V)) in EPS and EPS-mineral complexes. Here we examined the reaction sites, valence state, thermodynamic parameters and distribution of As in the complexes using potentiometric titration, isothermal titration calorimetry (ITC), FTIR, XPS, and SEM-EDS. The results showed that ∼54% of As(V) was reduced to As(III) by EPS, potentially driven by an enthalpy change (ΔH) of - 24.95 kJ/mol. The EPS coating on minerals clearly affected the reactivity to As(V). The strong masking of functional sites between EPS and goethite inhibited both the adsorption and reduction of As. In contrast, the weak binding of EPS onto montmorillonite retained more reactive sites for the reaction with As. Meanwhile, montmorillonite facilitated the immobilization of As to EPS through the formation of As-organic bounds. Our findings deepen the understanding of EPS-mineral interfacial reactions in controlling the redox and mobility of As, and the knowledge is important for predicting the behavior of As in natural environments.
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Affiliation(s)
- Jinzhao Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenchen Qu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
| | - Man Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yichao Wu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunhui Gao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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Bruna RE, Kendra CG, Pontes MH. An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system in Salmonella enterica. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533958. [PMID: 36993483 PMCID: PMC10055408 DOI: 10.1101/2023.03.23.533958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation is thought to promote PhoR kinase activity by altering the conformation of a membrane signaling complex comprised by PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. However, the identity of the low Pi signal and how it controls PhoR activity remain unknown. Here we characterize the PhoB-dependent and independent transcriptional changes elicited by Salmonella in response to P starvation, and identify PhoB-independent genes that are required for the utilization of several organic-P sources. We use this knowledge to identify the cellular compartment where the PhoR signaling complex senses the Pi-limiting signal. We demonstrate that the PhoB and PhoR signal transduction proteins can be maintained in an inactive state even when Salmonella is grown in media lacking Pi. Our results establish that PhoR activity is controlled by an intracellular signal resulting from P insufficiency.
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Affiliation(s)
- Roberto E. Bruna
- Department of Pathology and Laboratory Medicine, Pennsylvania State College of Medicine, Hershey, PA 17033, United States of America
| | - Christopher G. Kendra
- Department of Pathology and Laboratory Medicine, Pennsylvania State College of Medicine, Hershey, PA 17033, United States of America
| | - Mauricio H. Pontes
- Department of Pathology and Laboratory Medicine, Pennsylvania State College of Medicine, Hershey, PA 17033, United States of America
- Department of Microbiology and Immunology, Pennsylvania State College of Medicine, Hershey, PA 17033, United States of America
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10
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Transient Glycolytic Complexation of Arsenate Enhances Resistance in the Enteropathogen Vibrio cholerae. mBio 2022; 13:e0165422. [PMID: 36102515 PMCID: PMC9601151 DOI: 10.1128/mbio.01654-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous presence of toxic arsenate (AsV) in the environment has raised mechanisms of resistance in all living organisms. Generally, bacterial detoxification of AsV relies on its reduction to arsenite (AsIII) by ArsC, followed by the export of AsIII by ArsB. However, how pathogenic species resist this metalloid remains largely unknown. Here, we found that Vibrio cholerae, the etiologic agent of the diarrheal disease cholera, outcompetes other enteropathogens when grown on millimolar concentrations of AsV. To do so, V. cholerae uses, instead of ArsCB, the AsV-inducible vc1068-1071 operon (renamed var for vibrio arsenate resistance), which encodes the arsenate repressor ArsR, an alternative glyceraldehyde-3-phosphate dehydrogenase, a putative phosphatase, and the AsV transporter ArsJ. In addition to Var, V. cholerae induces oxidative stress-related systems to counter reactive oxygen species (ROS) production caused by intracellular AsV. Characterization of the var mutants suggested that these proteins function independently from one another and play critical roles in preventing deleterious effects on the cell membrane potential and growth derived from the accumulation AsV. Mechanistically, we demonstrate that V. cholerae complexes AsV with the glycolytic intermediate 3-phosphoglycerate into 1-arseno-3-phosphoglycerate (1As3PG). We further show that 1As3PG is not transported outside the cell; instead, it is subsequently dissociated to enable extrusion of free AsV through ArsJ. Collectively, we propose the formation of 1As3PG as a transient metabolic storage of AsV to curb the noxious effect of free AsV. This study advances our understanding of AsV resistance in bacteria and underscores new points of vulnerability that might be an attractive target for antimicrobial interventions. IMPORTANCE Even though resistance to arsenate has been extensively investigated in environmental bacteria, how enteric pathogens tolerate this toxic compound remains unknown. Here, we found that the cholera pathogen V. cholerae exhibits increased resistance to arsenate compared to closely related enteric pathogens. Such resistance is promoted not by ArsC-dependent reduction of arsenate to arsenite but by an operon encoding an arsenate transporter (ArsJ), an alternative glyceraldehyde 3-phosphate dehydrogenase (VarG), and a putative, uncharacterized phosphatase (VarH). Mechanistically, we demonstrate that V. cholerae detoxifies arsenate by complexing it with the glycolytic intermediate 3-phosphoglycerate into 1-arseno-3-phosphoglycerate (1As3PG). 1As3PG is not transported outside the cell; instead, it is subsequently dissociated by VarH to enable extrusion of free arsenate through ArsJ. Collectively, this study proposes a novel mechanism for arsenate detoxification, entirely independent of arsenate reduction and arsenite extrusion, that enhances V. cholerae resistance to this metalloid compared to other enteric pathogens.
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Time-Dependent Biosensor Fluorescence as a Measure of Bacterial Arsenic Uptake Kinetics and Its Inhibition by Dissolved Organic Matter. Appl Environ Microbiol 2022; 88:e0089122. [PMID: 35913152 PMCID: PMC9397108 DOI: 10.1128/aem.00891-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Microbe-mediated transformations of arsenic (As) often require As to be taken up into cells prior to enzymatic reaction. Despite the importance of these microbial reactions for As speciation and toxicity, understanding of how As bioavailability and uptake are regulated by aspects of extracellular water chemistry, notably dissolved organic matter (DOM), remains limited. Whole-cell biosensors utilizing fluorescent proteins are increasingly used for high-throughput quantification of the bioavailable fraction of As in water. Here, we present a mathematical framework for interpreting the time series of biosensor fluorescence as a measure of As uptake kinetics, which we used to evaluate the effects of different forms of DOM on uptake of trivalent arsenite. We found that thiol-containing organic compounds significantly inhibited uptake of arsenite into cells, possibly through the formation of aqueous complexes between arsenite and thiol ligands. While there was no evidence for competitive interactions between arsenite and low-molecular-weight neutral molecules (urea, glycine, and glyceraldehyde) for uptake through the aquaglyceroporin channel GlpF, which mediates transport of arsenite across cell membranes, there was evidence that labile DOM fractions may inhibit arsenite uptake through a catabolite repression-like mechanism. The observation of significant inhibition of arsenite uptake at DOM/As ratios commonly encountered in wetland pore waters suggests that DOM may be an important control on the microbial uptake of arsenite in the environment, with aspects of DOM quality playing an important role in the extent of inhibition. IMPORTANCE The speciation and toxicity of arsenic in environments like rice paddy soils and groundwater aquifers are controlled by microbe-mediated reactions. These reactions often require As to be taken up into cells prior to enzymatic reaction, but there is limited understanding of how microbial arsenic uptake is affected by variations in water chemistry. In this study, we explored the effect of dissolved organic matter (DOM) quantity and quality on microbial As uptake, with a focus on the role of thiol functional groups that are well known to form aqueous complexes with arsenic. We developed a quantitative framework for interpreting fluorescence time series from whole-cell biosensors and used this technique to evaluate effects of DOM on the rates of microbial arsenic uptake. We show that thiol-containing compounds significantly decrease rates of As uptake into microbial cells at environmentally relevant DOM/As ratios, revealing the importance of DOM quality in regulating arsenic uptake, and subsequent biotransformation, in the environment.
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Coordination of Phosphate and Magnesium Metabolism in Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1362:135-150. [PMID: 35288878 DOI: 10.1007/978-3-030-91623-7_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The majority of cellular phosphate (PO4-3; Pi) exists as nucleoside triphosphates, mainly adenosine triphosphate (ATP), and ribosomal RNA (rRNA). ATP and rRNA are also the largest cytoplasmic reservoirs of magnesium (Mg2+), the most abundant divalent cation in living cells. The co-occurrence of these ionic species in the cytoplasm is not coincidental. Decades of work in the Pi and Mg2+ starvation responses of two model enteric bacteria, Escherichia coli and Salmonella enterica, have led to the realization that the metabolisms of Pi and Mg2+ are interconnected. Bacteria must acquire these nutrients in a coordinated manner to achieve balanced growth and avoid loss of viability. In this chapter, we will review how bacteria sense and respond to fluctuations in environmental and intracellular Pi and Mg2+ levels. We will also discuss how these two compounds are functionally linked, and how cells elicit physiological responses to maintain their homeostasis.
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13
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Luneau JS, Cerutti A, Roux B, Carrère S, Jardinaud M, Gaillac A, Gris C, Lauber E, Berthomé R, Arlat M, Boulanger A, Noël LD. Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptations at early infection stages. MOLECULAR PLANT PATHOLOGY 2022; 23:159-174. [PMID: 34837293 PMCID: PMC8743013 DOI: 10.1111/mpp.13117] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/01/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes, which are organs localized at leaf margins. To decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analysed 3 days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and despite a biotrophic lifestyle, 18% of Xcc genes were differentially expressed, including a striking repression of chemotaxis and motility functions. The Xcc full repertoire of virulence factors had not yet been activated but the expression of the HrpG regulon composed of 95 genes, including genes coding for the type III secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulphur and phosphate metabolism was upregulated while limited stress responses were observed 3 days postinfection. We confirmed experimentally that high-affinity phosphate transport is needed for bacterial fitness inside hydathodes. This analysis provides information about the nutritional and stress status of bacteria during the early biotrophic infection stages and helps to decipher the adaptive strategy of Xcc to the hydathode environment.
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Affiliation(s)
- Julien S. Luneau
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Aude Cerutti
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Brice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
- Present address:
Brice Roux, HalioDx, Luminy Biotech EntreprisesMarseille Cedex 9France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | | | - Antoine Gaillac
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Matthieu Arlat
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Alice Boulanger
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Laurent D. Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M. Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. BMC Genomics 2022; 23:70. [PMID: 35062865 PMCID: PMC8783487 DOI: 10.1186/s12864-021-08257-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants. RESULTS The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription. CONCLUSIONS Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.
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Affiliation(s)
- Imen Nouioui
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Sung-Min Ha
- Department of Integrative Biology and Physiology, University of California Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Inwoo Baek
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jongsik Chun
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- ChunLab, Inc, Seoul, Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, NE1 7RU, Newcastle upon Tyne, UK
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Kawai R, Toya Y, Miyoshi K, Murakami M, Niide T, Horinouchi T, Maeda T, Shibai A, Furusawa C, Shimizu H. Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution. Biotechnol Bioeng 2021; 119:936-945. [PMID: 34914093 DOI: 10.1002/bit.28007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/23/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
Co-culture is a promising way to alleviate metabolic burden by dividing the metabolic pathways into several modules and sharing the conversion processes with multiple strains. Since an intermediate is passed from the donor to the recipient via the extracellular environment, it is inevitably diluted. Therefore, enhancing the intermediate consumption rate is important for increasing target productivity. In the present study, we demonstrated the enhancement of mevalonate consumption in Escherichia coli by adaptive laboratory evolution and applied the evolved strain to isoprenol production in an E. coli (upstream: glucose to mevalonate)-E. coli (downstream: mevalonate to isoprenol) co-culture. An engineered mevalonate auxotroph strain was repeatedly sub-cultured in a synthetic medium supplemented with mevalonate, where the mevalonate concentration was decreased stepwise from 100 to 20 µM. In five parallel evolution experiments, all growth rates gradually increased, resulting in five evolved strains. Whole-genome re-sequencing and reverse engineering identified three mutations involved in enhancing mevalonate consumption. After introducing nudF gene for producing isoprenol, the isoprenol-producing parental and evolved strains were respectively co-cultured with a mevalonate-producing strain. At an inoculation ratio of 1:3 (upstream:downstream), isoprenol production using the evolved strain was 3.3 times higher than that using the parental strain.
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Affiliation(s)
- Ryutaro Kawai
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Kenta Miyoshi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Manami Murakami
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Teppei Niide
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | | | - Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Atsushi Shibai
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,Department of Physics, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
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17
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Galván AE, Paul NP, Chen J, Yoshinaga-Sakurai K, Utturkar SM, Rosen BP, Yoshinaga M. Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin. Microbiol Spectr 2021; 9:e0050221. [PMID: 34378964 PMCID: PMC8552651 DOI: 10.1128/spectrum.00502-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/15/2021] [Indexed: 01/11/2023] Open
Abstract
The soil bacterium Burkholderia gladioli GSRB05 produces the natural compound arsinothricin [2-amino-4-(hydroxymethylarsinoyl) butanoate] (AST), which has been demonstrated to be a broad-spectrum antibiotic. To identify the genes responsible for AST biosynthesis, a draft genome sequence of B. gladioli GSRB05 was constructed. Three genes, arsQML, in an arsenic resistance operon were found to be a biosynthetic gene cluster responsible for synthesis of AST and its precursor, hydroxyarsinothricin [2-amino-4-(dihydroxyarsinoyl) butanoate] (AST-OH). The arsL gene product is a noncanonical radical S-adenosylmethionine (SAM) enzyme that is predicted to transfer the 3-amino-3-carboxypropyl (ACP) group from SAM to the arsenic atom in inorganic arsenite, forming AST-OH, which is methylated by the arsM gene product, a SAM methyltransferase, to produce AST. Finally, the arsQ gene product is an efflux permease that extrudes AST from the cells, a common final step in antibiotic-producing bacteria. Elucidation of the biosynthetic gene cluster for this novel arsenic-containing antibiotic adds an important new tool for continuation of the antibiotic era. IMPORTANCE Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. Here, we report identification of the biosynthetic gene cluster for arsinothricin and demonstrate that only three genes, two of which are novel, are required for the biosynthesis and transport of arsinothricin, in contrast to the phosphonate counterpart, phosphinothricin, which requires over 20 genes. Our discoveries will provide insight for the development of more effective organoarsenical antibiotics and illustrate the previously unknown complexity of the arsenic biogeochemical cycle, as well as bring new perspective to environmental arsenic biochemistry.
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Affiliation(s)
- Adriana E. Galván
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Ngozi P. Paul
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Kunie Yoshinaga-Sakurai
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Sagar M. Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
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Mondal S, Pramanik K, Ghosh SK, Pal P, Mondal T, Soren T, Maiti TK. Unraveling the role of plant growth-promoting rhizobacteria in the alleviation of arsenic phytotoxicity: A review. Microbiol Res 2021; 250:126809. [PMID: 34166969 DOI: 10.1016/j.micres.2021.126809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
The toxic metalloid arsenic (As), is a major pollutant of soil and water, imposing severe health concerns on human lives. It enters the food chain mainly through As-contaminated crops. The uptake, translocation and accumulation of As in plant tissue are often controlled by certain soil-inhabiting microbial communities. Among them, indigenous, free-living As-resistant plant growth-promoting rhizobacteria (PGPR) plays a pivotal role in As-immobilization. Besides, the plant's inability to withstand As after a threshold level is actively managed by these PGPR increasing As-tolerance in host plants by a synergistic plant-microbe interaction. The dual functionality of As-resistant PGPR i.e., phytostimulation and minimization of As-induced phytotoxic damages are one of the main focal points of this review article. It is known that such PGPR having the functional arsenic-resistant genes (in ars operon) including As-transporters, As-transforming genes contributed to the As accumulation and detoxification/transformation respectively. Apart from assisting in nutrient acquisition and modulating phytohormone levels, As-resistant PGPR also influences the antioxidative defense system in plants by maneuvering multiple enzymatic and non-enzymatic antioxidants. Furthermore, they are effective in reducing membrane damage and electrolyte leakage in plant cells. As-induced photosynthetic damage is also found to be salvaged by As-resistant PGPR. Briefly, the eco-physiological, biochemical and molecular mechanisms of As-resistant PGPR are thus elaborated here with regard to the As-exposed crops.
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Affiliation(s)
- Sayanta Mondal
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
| | - Krishnendu Pramanik
- Mycology and Plant Pathology Laboratory, Department of Botany, Siksha Bhavana, Visva-Bharati, Santiniketan, Birbhum, PIN-731235, West Bengal, India.
| | - Sudip Kumar Ghosh
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
| | - Priyanka Pal
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
| | - Tanushree Mondal
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
| | - Tithi Soren
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
| | - Tushar Kanti Maiti
- Microbiology Laboratory, Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, P.O.-Rajbati, PIN-713104, West Bengal, India.
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Abstract
Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabolomes. We apply these constraints to a metabolic network of Escherichia coli that represents 90% of its metabolome. We show that the quantitative metabolomes allowed by the abiotic constraints are consistent with metabolomic and isotope-labeling data. We find that: (i) abiotic constraints drive the evolution of high-affinity phosphate transporters; (ii) Charge-, hydrogen- and magnesium-related constraints underlie transcriptional regulatory responses to osmotic stress; and (iii) hydrogen-ion and charge imbalance underlie transcriptional regulatory responses to acid stress. Thus, quantifying the constraints that the inorganic world imposes on living systems provides insights into their key characteristics, helps understand the outcomes of evolutionary adaptation, and should be considered as a fundamental part of theoretical biology and for understanding the constraints on evolution.
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20
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Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent. Nat Commun 2020; 11:2642. [PMID: 32457313 PMCID: PMC7250820 DOI: 10.1038/s41467-020-16428-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria. The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.
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21
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Abstract
Phosphorus is required for many biological molecules and essential functions, including DNA replication, transcription of RNA, protein translation, posttranslational modifications, and numerous facets of metabolism. In order to maintain the proper level of phosphate for these processes, many bacteria adapt to changes in environmental phosphate levels. The mechanisms for sensing phosphate levels and adapting to changes have been extensively studied for multiple organisms. The phosphate response of Escherichia coli alters the expression of numerous genes, many of which are involved in the acquisition and scavenging of phosphate more efficiently. This review shares findings on the mechanisms by which E. coli cells sense and respond to changes in environmental inorganic phosphate concentrations by reviewing the genes and proteins that regulate this response. The PhoR/PhoB two-component signal transduction system is central to this process and works in association with the high-affinity phosphate transporter encoded by the pstSCAB genes and the PhoU protein. Multiple models to explain how this process is regulated are discussed.
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22
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Qiao Z, Huang J, Cao Y, Shi K, Wang G. Genetics and proteomics analyses reveal the roles of PhoB1 and PhoB2 regulators in bacterial responses to arsenite and phosphate. Res Microbiol 2019; 170:263-271. [PMID: 31279088 DOI: 10.1016/j.resmic.2019.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 11/25/2022]
Abstract
In bacteria, phosphate (Pi) stress response is governed by the two-component regulatory system, sensor kinase PhoR and its cognate response regulatory protein PhoB. The arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 contains two phoB genes, phoB1 and phoB2. phoB1 is adjacent to As(III)-oxidizing genes, however, the functions of PhoB1 and PhoB2 remain unclear. Here, phoB1 and phoB2 were each deleted in-frame, and proteomics, qRT-PCR and protein-DNA interaction were performed. We found that (1) phoB1 and phoB2 were both upregulated under low Pi conditions and phoB1 was induced by As(III), but phoB2 was not; (2) deletion of phoB1 reduced As(III)-oxidizing efficiency and protein-DNA interaction analysis showed PhoB1 could interact with aioXSR promoter to regulate As(III) oxidation; (3) deletions of phoB1 or phoB2 both reduced exopolysaccharides (EPS) synthesis; and (4) PhoB1 influenced Pi uptake, As(III) oxidation, EPS synthesis, TCA cycle, energy production and stress response with As(III), and PhoB2 was associated with Pi uptake and EPS synthesis in low Pi conditions. These results showed PhoB1 and PhoB2 were both involved in Pi acquisition, PhoB1 was more important with As(III) and PhoB2 played a major role without As(III). Strain GW4 uses these two regulators to survive under low Pi and arsenic-rich environments.
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Affiliation(s)
- Zixu Qiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Jing Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Yajing Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G. Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. Front Microbiol 2019; 10:1514. [PMID: 31333619 PMCID: PMC6620896 DOI: 10.3389/fmicb.2019.01514] [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: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2T, and Thioalkalivibrio thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lucia Cavalca
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Milena Colombo
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - J Merijn Schuurmans
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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24
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Metabolism of sucrose in a non-fermentative Escherichia coli under oxygen limitation. Appl Microbiol Biotechnol 2019; 103:6245-6256. [PMID: 31147757 PMCID: PMC6616217 DOI: 10.1007/s00253-019-09909-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/21/2023]
Abstract
Biotechnological industry strives to develop anaerobic bioprocesses fueled by abundant and cheap carbon sources, like sucrose. However, oxygen-limiting conditions often lead to by-product formation and reduced ATP yields. While by-product formation is typically decreased by gene deletion, the breakdown of oligosaccharides with inorganic phosphate instead of water could increment the ATP yield. To observe the effect of oxygen limitation during sucrose consumption, a non-fermentative Escherichia coli K-12 strain was transformed with genes enabling sucrose assimilation. It was observed that the combined deletion of the genes adhE, adhP, mhpF, ldhA, and pta abolished the anaerobic growth using sucrose. Therefore, the biomass-specific conversion rates were obtained using oxygen-limited continuous cultures. Strains performing the breakdown of the sucrose by hydrolysis (SUC-HYD) or phosphorolysis (SUC-PHOSP) were studied in such conditions. An experimentally validated in silico model, modified to account for plasmid and protein burdens, was employed to calculate carbon and electron consistent conversion rates. In both strains, the biomass yields were lower than expected and, strikingly, SUC-PHOSP showed a yield lower than SUC-HYD. Flux balance analyses indicated a significant increase in the non-growth-associated ATP expenses by comparison with the growth on glucose. The observed fructose-1,6-biphosphatase and phosphoglucomutase activities, as well as the concentrations of glycogen, suggest the operation of ATP futile cycles triggered by a combination of the oxygen limitation and the metabolites released during the sucrose breakdown.
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25
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Stasi R, Neves HI, Spira B. Phosphate uptake by the phosphonate transport system PhnCDE. BMC Microbiol 2019; 19:79. [PMID: 30991951 PMCID: PMC6469041 DOI: 10.1186/s12866-019-1445-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/26/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Phosphate is a fundamental nutrient for all creatures. It is thus not surprising that a single bacterium carries different transport systems for this molecule, each usually operating under different environmental conditions. The phosphonate transport system of E. coli K-12 is cryptic due to an 8 bp insertion in the phnE ORF. RESULTS Here we report that an E. coli K-12 strain carrying the triple knockout ΔpitA Δpst Δugp reverted the phnE mutation when plated on complex medium containing phosphate as the main phosphorus source. It is also shown that PhnCDE takes up orthophosphate with transport kinetics compatible with that of the canonical transport system PitA and that Pi-uptake via PhnCDE is sufficient to enable bacterial growth. Ugp, a glycerol phosphate transporter, is unable to take up phosphate. CONCLUSIONS The phosphonate transport system, which is normally cryptic in E. coli laboratory strains is activated upon selection in rich medium and takes up orthophosphate in the absence of the two canonical phosphate-uptake systems. Based on these findings, the PhnCDE system can be considered a genuine phosphate transport system.
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Affiliation(s)
- Raffaele Stasi
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo-SP, Brazil
| | - Henrique Iglesias Neves
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo-SP, Brazil
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo-SP, Brazil.
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26
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Transport and detoxification of metalloids in plants in relation to plant-metalloid tolerance. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100171] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Shi LD, Chen YS, Du JJ, Hu YQ, Shapleigh JP, Zhao HP. Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. Front Microbiol 2019; 9:3297. [PMID: 30687279 PMCID: PMC6333641 DOI: 10.3389/fmicb.2018.03297] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023] Open
Abstract
Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH4-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.
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Affiliation(s)
- Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Shi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jia-Jie Du
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yi-Qing Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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28
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Yan G, Chen X, Du S, Deng Z, Wang L, Chen S. Genetic mechanisms of arsenic detoxification and metabolism in bacteria. Curr Genet 2018; 65:329-338. [PMID: 30349994 DOI: 10.1007/s00294-018-0894-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/25/2018] [Accepted: 10/13/2018] [Indexed: 02/06/2023]
Abstract
Arsenic, distributed pervasively in the natural environment, is an extremely toxic substance which can severely impair the normal functions of living cells. Research on the genetic mechanisms of arsenic metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. This review summarizes arsenic detoxification as well as arsenic respiratory metabolic pathways in bacteria and discusses novel arsenic resistance pathways in various bacterial strains. This knowledge provides insights into the mechanisms of arsenic biotransformation in bacteria. Multiple detoxification strategies among bacteria imply possible functional relationships among different arsenic detoxification/metabolism pathways. In addition, this review sheds light on the bioremediation of arsenic-contaminated environments and prevention of antibiotic resistance.
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Affiliation(s)
- Ge Yan
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xingxiang Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Shiming Du
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Lianrong Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Shi Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China. .,Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
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29
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Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations. Proc Natl Acad Sci U S A 2018; 115:E8614-E8623. [PMID: 30104376 DOI: 10.1073/pnas.1807984115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 ± 1.6 μM, kcat = 9,810 ± 220 seconds-1), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.
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30
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Streptococcus pneumoniae two-component regulatory systems: The interplay of the pneumococcus with its environment. Int J Med Microbiol 2018; 308:722-737. [DOI: 10.1016/j.ijmm.2017.11.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 02/06/2023] Open
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31
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Sindhu KJ, Kureel AK, Saini S, Kumari S, Verma P, Rai AK. Characterization of phosphate transporter(s) and understanding their role in Leishmania donovani parasite. Acta Parasitol 2018; 63:75-88. [PMID: 29351081 DOI: 10.1515/ap-2018-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/12/2017] [Indexed: 11/15/2022]
Abstract
Inorganic phosphate (Pi) is shown to be involved in excretion of methylglyoxal (MG) in the promastigote form of Leishmania donovani parasite. Absence of Pi leads to its accumulation inside the parasite. Accumulation of MG is toxic to the parasite and utilizes glyoxylase as well as excretory pathways for its detoxification. In addition, Pi is also reported to regulate activities of ectoenzymes and energy metabolism (glucose to pyruvate) etc. Thus, it is known to cumulatively affect the growth of Leishmania parasite. Hence the transporters, which allow the movement of Pi across the membrane, can prove to be a crucial drug target. Therefore, we characterized two phosphate transporters in Leishmania (i) H+ dependent myo-inositol transporter (LdPHO84), and (ii) Na+ dependent transporter (LdPHO89), based on similar studies done previously on other lower organisms and trypanosomatids. We tried to understand the secondary structure of these two proteins and confirm modulation in their expression with the change in Pi concentration outside. Moreover, their modes of action were also measured in the presence of specific inhibitors (LiF, CCCP). Further analysis on the physiological role of these transporters in various stages of the parasite life cycle needs to be entrenched.
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Affiliation(s)
- K J Sindhu
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
| | - Amit Kumar Kureel
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
| | - Sheetal Saini
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
| | - Smita Kumari
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
| | - Pankaj Verma
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
| | - Ambak Kumar Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, U.P., India
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32
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Malykh EA, Butov IA, Ravcheeva AB, Krylov AA, Mashko SV, Stoynova NV. Specific features of L-histidine production by Escherichia coli concerned with feedback control of AICAR formation and inorganic phosphate/metal transport. Microb Cell Fact 2018; 17:42. [PMID: 29544475 PMCID: PMC5852967 DOI: 10.1186/s12934-018-0890-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/08/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND In the L-histidine (His) biosynthetic pathway of Escherichia coli, the first key enzyme, ATP-phosphoribosyltransferase (ATP-PRT, HisG), is subject to different types of inhibition. Eliminating the feedback inhibition of HisG by the His end product is an important step that enables the oversynthesis of His in breeding strains. However, the previously reported feedback inhibition-resistant mutant enzyme from E. coli, HisGE271K, is inhibited by purine nucleotides, particularly ADP and AMP, via competitive inhibition with its ATP substrate. 5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR), which is formed not only during His biosynthesis but also during de novo purine biosynthesis, acts as a natural analog of AMP and substitutes for it in some enzymatic reactions. We hypothesized that AICAR could control its own formation, particularly through the His biosynthetic pathway, by negatively influencing HisG enzymatic activity, which would make preventing ATP-PRT transferase inhibition by AICAR crucial for His overproduction. RESULTS For the first time, both the native E. coli HisG and the previously described feedback-resistant mutant HisGE271K enzymes were shown to be sensitive to inhibition by AICAR, a structural analog of AMP. To circumvent the negative effect that AICAR has on His synthesis, we constructed the new His-producing strain EA83 and demonstrated its improved histidine production. This increased production was particularly associated with the improved conversion of AICAR to ATP due to purH and purA gene overexpression; additionally, the PitA-dependent phosphate/metal (Me2+-Pi) transport system was modified by a pitA gene deletion. This His-producing strain unexpectedly exhibited decreased alkaline phosphatase activity at low Pi concentrations. AICAR was consequently hypothesized inhibit the two-component PhoBR system, which controls Pho regulon gene expression. CONCLUSIONS Inhibition of a key enzyme in the His biosynthetic pathway, HisG, by AICAR, which is formed in this pathway, generates a serious bottleneck during His production. The constructed His-producing strain demonstrated the enhanced expression of genes that encode enzymes involved in the metabolism of AICAR to ATP, which is a substrate of HisG, and thus led to improved His accumulation.
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Affiliation(s)
- Evgeniya A Malykh
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation
| | - Ivan A Butov
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation
| | - Anna B Ravcheeva
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation
| | - Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation
| | - Nataliya V Stoynova
- Ajinomoto-Genetika Research Institute, 1-st Dorozny pr., 1-1, Moscow, 117545, Russian Federation.
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33
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Pontes MH, Groisman EA. Protein synthesis controls phosphate homeostasis. Genes Dev 2018; 32:79-92. [PMID: 29437726 PMCID: PMC5828397 DOI: 10.1101/gad.309245.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
In this study, Pontes et al. show that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu in yeast and bacteria. Their findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature. Phosphorus is an essential element assimilated largely as orthophosphate (Pi). Cells respond to Pi starvation by importing Pi from their surroundings. We now report that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu. In the bacterium Salmonella enterica serovar Typhimurium, this response entails phosphorylation of the regulatory protein PhoB and transcription of PhoB-dependent Pi transporter genes and is eliminated upon stimulation of adenosine triphosphate (ATP) hydrolysis. When protein synthesis is impaired due to low cytoplasmic magnesium (Mg2+), Salmonella triggers the Pi starvation response because ribosomes are destabilized, which reduces ATP consumption and thus free cytoplasmic Pi. This response is transient because low cytoplasmic Mg2+ promotes an uptake in Mg2+ and a decrease in ATP levels, which stabilizes ribosomes, resulting in ATP consumption and Pi increase, thus ending the response. Notably, pharmacological inhibition of protein synthesis also elicited a Pi starvation response in the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae. Our findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature.
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Affiliation(s)
- Mauricio H Pontes
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA.,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA.,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
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34
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Vuppada RK, Hansen CR, Strickland KAP, Kelly KM, McCleary WR. Phosphate signaling through alternate conformations of the PstSCAB phosphate transporter. BMC Microbiol 2018; 18:8. [PMID: 29351743 PMCID: PMC5775613 DOI: 10.1186/s12866-017-1126-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/15/2017] [Indexed: 12/15/2022] Open
Abstract
Background Phosphate is an essential compound for life. Escherichia coli employs a signal transduction pathway that controls the expression of genes that are required for the high-affinity acquisition of phosphate and the utilization of alternate sources of phosphorous. These genes are only expressed when environmental phosphate is limiting. The seven genes for this signaling pathway encode the two-component regulatory proteins PhoB and PhoR, as well as the high-affinity phosphate transporter PstSCAB and an auxiliary protein called PhoU. As the sensor kinase PhoR has no periplasmic sensory domain, the mechanism by which these cells sense environmental phosphate is not known. This paper explores the hypothesis that it is the alternating conformations of the PstSCAB transporter which are formed as part of the normal phosphate transport cycle that signal phosphate sufficiency or phosphate limitation. Results We tested two variants of PstB that are predicted to lock the protein in either of two conformations for their signaling output. We observed that the pstBQ160K mutant, predicted to reside in an inward-facing, open conformation signaled phosphate sufficiency whereas the pstBE179Q mutant, predicted to reside in an outward-facing, closed conformation signaled phosphate starvation. Neither mutant showed phosphate transport. Conclusions These results support the hypothesis that the alternating conformations of the PstSCAB transporter are sensed by PhoR and PhoU. This sensory mechanism thus controls the alternate autokinase and phospho-PhoB phosphatase activities of PhoR, which ultimately control the signaling state of the response regulator PhoB.
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Affiliation(s)
- Ramesh K Vuppada
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Colby R Hansen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Kirsta A P Strickland
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Keilen M Kelly
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - William R McCleary
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
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35
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Zvobgo G, LwalabaWaLwalaba J, Sagonda T, Mutemachani Mapodzeke J, Muhammad N, Haider Shamsi I, Zhang G. Phosphate alleviates arsenate toxicity by altering expression of phosphate transporters in the tolerant barley genotypes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:832-839. [PMID: 28968924 DOI: 10.1016/j.ecoenv.2017.09.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/27/2017] [Accepted: 09/15/2017] [Indexed: 05/13/2023]
Abstract
The contribution of the phosphate transporters (PHTs) in uptake of arsenate (As5+) and phosphate (P) is a widely recognized mechanism. Here we investigated how P regulates the uptake of As5+ and the subsequent effects on growth and relative expression of PHTs. The study was conducted on 3 barley genotypes differing in As tolerance (ZDB160, As-tolerant; ZDB115, moderately tolerant; ZDB475, As-sensitive) using a hydroponic experiment. There were 3 As5+ (0, 10 and 100µM) and 3P (0, 50 and 500µM) levels. The results showed that the negative effect of As stress on plant growth, photosynthesis and cell ultra-structure is As dose and barley genotype dependent, confirming the distinctly genotypic difference in As tolerance. As uptake and accumulation in plant tissues are closely associated with inhibited extent of growth and photosynthesis, with the tolerant genotype ZDB160 having lower As content than other two genotypes. The toxic effect caused by As stress could be alleviated by P addition, mainly due to reduced As uptake. Moreover, the tolerant genotype showed relatively lower expression PHTs than sensitive ones upon exposure to both As stress and P addition, suggesting regulation of PHTs expression is a major mechanism for relative uptake of As and P, in subsequence affecting As tolerance. Moreover, among 6 PHTs examined in this study, the expressions of PHT1.3, PHT1.4 and PHT1.6 showed the marked difference among the three barley genotypes in responses to As stress and P addition, indicating further research on the contribution of phosphate transporters to As and P uptake should be focused on these PHTs.
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Affiliation(s)
- Gerald Zvobgo
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - Jonas LwalabaWaLwalaba
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - Tichaona Sagonda
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - James Mutemachani Mapodzeke
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - Noor Muhammad
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou 310058, PR China.
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Acquisition of the Phosphate Transporter NptA Enhances Staphylococcus aureus Pathogenesis by Improving Phosphate Uptake in Divergent Environments. Infect Immun 2017; 86:IAI.00631-17. [PMID: 29084897 DOI: 10.1128/iai.00631-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/24/2017] [Indexed: 12/28/2022] Open
Abstract
During infection, pathogens must obtain all inorganic nutrients, such as phosphate, from the host. Despite the essentiality of phosphate for all forms of life, how Staphylococcus aureus obtains this nutrient during infection is unknown. Differing from Escherichia coli, the paradigm for bacterial phosphate acquisition, which has two inorganic phosphate (Pi) importers, genomic analysis suggested that S. aureus possesses three distinct Pi transporters: PstSCAB, PitA, and NptA. While pitA and nptA are expressed in phosphate-replete media, expression of all three transporters is induced by phosphate limitation. The loss of a single transporter did not affect S. aureus However, disruption of any two systems significantly reduced Pi accumulation and growth in divergent environments. These findings indicate that PstSCAB, PitA, and NptA have overlapping but nonredundant functions, thus expanding the environments in which S. aureus can successfully obtain Pi Consistent with this idea, in a systemic mouse model of disease, loss of any one transporter did not decrease staphylococcal virulence. However, loss of NptA in conjunction with either PstSCAB or PitA significantly reduced the ability of S. aureus to cause infection. These observations suggest that Pi acquisition via NptA is particularly important for the pathogenesis of S. aureus While our analysis suggests that NptA homologs are widely distributed among bacteria, closely related less pathogenic staphylococcal species do not possess this importer. Altogether, these observations indicate that Pi uptake by S. aureus differs from established models and that acquisition of a third transporter enhances the ability of the bacterium to cause infection.
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Xue W, Hao T, Mackey HR, Li X, Chan RC, Chen G. The role of sulfate in aerobic granular sludge process for emerging sulfate-laden wastewater treatment. WATER RESEARCH 2017; 124:513-520. [PMID: 28802136 DOI: 10.1016/j.watres.2017.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Sulfate-rich wastewaters pose a major threat to mainstream wastewater treatment due to the unpreventable production of sulfide and associated shift in functional bacteria. Aerobic granular sludge could mitigate these challenges in view of its high tolerance and resilience against changes in various environmental conditions. This study aims to confirm the feasibility of aerobic granular sludge in the treatment of sulfate containing wastewater, investigate the impact of sulfate on nutrient removal and granulation, and reveal metabolic relationships in the above processes. Experiments were conducted using five sequencing batch reactors with different sulfate concentrations operated under alternating anoxic/aerobic condition. Results showed that effect of sulfate on chemical oxygen demand (COD) removal is negligible, while phosphate removal was enhanced from 12% to 87% with an increase in sulfate from 0 to 200 mg/L. However, a long acclimatization of the biomass (more than 70 days) is needed at a sulfate concentration of 500 mg/L and a total deterioration of phosphate removal at 1000 mg/L. Batch tests revealed that sulfide promoted volatile fatty acids (VFAs) uptake, producing more energy for phosphate uptake when sulfate concentrations were beneath 200 mg/L. However, sulfide detoxification became energy dominating, leaving insufficient energy for Polyhydroxyalkanoate (PHA) synthesis and phosphate uptake when sulfate content was further increased. Granulation accelerated with increasing sulfate levels by enhanced production of N-Acyl homoserine lactones (AHLs), a kind of quorum sensing (QS) auto-inducer, using S-Adenosyl Methionine (SAM) as primer. The current study demonstrates interactions among sulfate metabolism, nutrients removal and granulation, and confirms the feasibility of using the aerobic granular sludge process for sulfate-laden wastewaters treatment with low to medium sulfate content.
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Affiliation(s)
- Weiqi Xue
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tianwei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Hamish R Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Xiling Li
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Richard C Chan
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Guanghao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, The Hong Kong University of Science and Technology, Nansha, Guangzhou, China
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38
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PhoU Allows Rapid Adaptation to High Phosphate Concentrations by Modulating PstSCAB Transport Rate in Sinorhizobium meliloti. J Bacteriol 2017; 199:JB.00143-17. [PMID: 28416708 DOI: 10.1128/jb.00143-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/11/2017] [Indexed: 01/14/2023] Open
Abstract
Maintenance of cellular phosphate homeostasis is essential for cellular life. The PhoU protein has emerged as a key regulator of this process in bacteria, and it is suggested to modulate phosphate import by PstSCAB and control activation of the phosphate limitation response by the PhoR-PhoB two-component system. However, a proper understanding of PhoU has remained elusive due to numerous complications of mutating phoU, including loss of viability and the genetic instability of the mutants. Here, we developed two sets of strains of Sinorhizobium meliloti that overcame these limitations and allowed a more detailed and comprehensive analysis of the biological and molecular activities of PhoU. The data showed that phoU cannot be deleted in the presence of phosphate unless PstSCAB is inactivated also. However, phoU deletions were readily recovered in phosphate-free media, and characterization of these mutants revealed that addition of phosphate to the environment resulted in toxic levels of PstSCAB-mediated phosphate accumulation. Phosphate uptake experiments indicated that PhoU significantly decreased the PstSCAB transport rate specifically in phosphate-replete cells but not in phosphate-starved cells and that PhoU could rapidly respond to elevated environmental phosphate concentrations and decrease the PstSCAB transport rate. Site-directed mutagenesis results suggested that the ability of PhoU to respond to phosphate levels was independent of the conformation of the PstSCAB transporter. Additionally, PhoU-PhoU and PhoU-PhoR interactions were detected using a bacterial two-hybrid screen. We propose that PhoU modulates PstSCAB and PhoR-PhoB in response to local, internal fluctuations in phosphate concentrations resulting from PstSCAB-mediated phosphate import.IMPORTANCE Correct maintenance of cellular phosphate homeostasis is critical in all kingdoms of life and in bacteria involves the PhoU protein. This work provides novel insights into the role of the Sinorhizobium meliloti PhoU protein, which plays a key role in rapid adaptation to elevated phosphate concentrations. It is shown that PhoU rapidly responds to elevated phosphate levels by significantly decreasing the phosphate transport of PstSCAB, thereby preventing phosphate toxicity and cell death. Additionally, a new model for phosphate sensing in bacterial species which involves the PhoR-PhoB two-component system is presented. This work provides new insights into the bacterial response to changing environmental conditions and into regulation of the phosphate limitation response that influences numerous bacterial processes, including antibiotic production and virulence.
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Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF. Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach. Front Microbiol 2017; 8:1020. [PMID: 28659875 PMCID: PMC5468372 DOI: 10.3389/fmicb.2017.01020] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.
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Affiliation(s)
- Stephen R Lindemann
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States.,Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West LafayetteIN, United States.,Department of Nutrition Science, Purdue University, West LafayetteIN, United States
| | - Jennifer M Mobberley
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Jessica K Cole
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - L M Markillie
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West LafayetteIN, United States
| | - Ronald C Taylor
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Eric Huang
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - H S Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, RichlandWA, United States
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Margaret F Romine
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
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Schramke H, Laermann V, Tegetmeyer HE, Brachmann A, Jung K, Altendorf K. Revisiting regulation of potassium homeostasis in Escherichia coli: the connection to phosphate limitation. Microbiologyopen 2017; 6. [PMID: 28097817 PMCID: PMC5458449 DOI: 10.1002/mbo3.438] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 11/10/2022] Open
Abstract
Two-component signal transduction constitutes the predominant strategy used by bacteria to adapt to fluctuating environments. The KdpD/KdpE system is one of the most widespread, and is crucial for K+ homeostasis. In Escherichia coli, the histidine kinase KdpD senses K+ availability, whereas the response regulator KdpE activates synthesis of the high-affinity K+ uptake system KdpFABC. Here we show that, in the absence of KdpD, kdpFABC expression can be activated via phosphorylation of KdpE by the histidine kinase PhoR. PhoR and its cognate response regulator PhoB comprise a phosphate-responsive two-component system, which senses phosphate limitation indirectly through the phosphate transporter PstCAB and its accessory protein PhoU. In vivo two-hybrid interaction studies based on the bacterial adenylate cyclase reveal pairwise interactions between KdpD, PhoR, and PhoU. Finally, we demonstrate that cross-regulation between the kdpFABC and pstSCAB operons occurs in both directions under simultaneous K+ and phosphate limitation, both in vitro and in vivo. This study for the first time demonstrates direct coupling between intracellular K+ and phosphate homeostasis and provides a mechanism for fine-tuning of the balance between positively and negatively charged ions in the bacterial cell.
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Affiliation(s)
- Hannah Schramke
- Department of Biology I, Microbiology, Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Vera Laermann
- Fachbereich Biologie/Chemie, Universität Osnabrück, Osnabrück, Germany
| | - Halina E Tegetmeyer
- Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.,Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Brachmann
- Department of Biology I, Genetics, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Martinsried, Germany
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Kumari N, Jagadevan S. Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review. CHEMOSPHERE 2016; 163:400-412. [PMID: 27565307 DOI: 10.1016/j.chemosphere.2016.08.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.
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Affiliation(s)
- Nisha Kumari
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India.
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Bilbeisi RA, Prakasam T, Lusi M, El Khoury R, Platas-Iglesias C, Charbonnière LJ, Olsen JC, Elhabiri M, Trabolsi A. [C-H···anion] interactions mediate the templation and anion binding properties of topologically non-trivial metal-organic structures in aqueous solutions. Chem Sci 2016; 7:2524-2531. [PMID: 28660022 PMCID: PMC5477011 DOI: 10.1039/c5sc04246a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/09/2016] [Indexed: 02/03/2023] Open
Abstract
Two synthetic approaches-temperature variation and anion templation-allowed for the selective formation of a [2]catenane ([2]C4+ ) or a trefoil knot (TK6+ ), or for the enhanced formation of a Solomon link (SL8+ ), all from a simple set of starting materials (Zn(ii) acetate, diformylpyridine (DFP) and a diamino-2,2'-bipyridine (DAB)) in mixed aqueous solutions. The catenane formed exclusively at 90 °C in a 1 : 1 mixed solvent of D2O and MeOD. In the presence of bromide ion as template, TK6+ formed exclusively at 50 °C in the same solvent. In the solid state, TK6+ hosts two bromide ions in its central cavity by forming six Csp2 -H hydrogen bonds. In D2O, TK6+ , which was originally prepared as a trifluoroacetate (TFA) salt, was found to exchange two TFA counterions for two monovalent anions of different sizes and shapes, which lodged within the knot's central cavity. In contrast to bromide, the larger triflate anion (CF3SO3-) promoted the formation of SL8+ , which was characterized by 1H NMR spectroscopy and mass spectrometry. Two dimensional heteronuclear 19F-1H-HOSEY NMR experiments detected CH···F interactions inside the cavity of SL8+ . Thus, the product distribution of this dynamic link forming system is sensitive to temperature and the size and shape of the anion template, and one of the products, TK6+ , is capable of binding a variety of monovalent anions in D2O with high affinity (with log β2 values of 4 to 6 being typical).
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Affiliation(s)
- Rana A Bilbeisi
- New York University Abu Dhabi (NYUAD) , Experimental Research Building (C1), Saadiyat Island , Abu Dhabi , UAE .
| | - Thirumurugan Prakasam
- New York University Abu Dhabi (NYUAD) , Experimental Research Building (C1), Saadiyat Island , Abu Dhabi , UAE .
| | - Matteo Lusi
- New York University Abu Dhabi (NYUAD) , Experimental Research Building (C1), Saadiyat Island , Abu Dhabi , UAE .
| | - Roberto El Khoury
- New York University Abu Dhabi (NYUAD) , Experimental Research Building (C1), Saadiyat Island , Abu Dhabi , UAE .
| | - Carlos Platas-Iglesias
- Centro de Investigaciones Científicas Avanzadas (CICA) and Departamento de Química Fundamental , Universidade de Coruña , Campus da Zapateira, Rúa da Fraga 10 , 15008 A Coruña , Spain
| | - Loïc J Charbonnière
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse , IPHC , UMR 7178 CNRS/UdS , ECPM , 25 rue Becquerel , 67087 Strasbourg , France
| | - John-Carl Olsen
- School of Sciences , Indiana University Kokomo , Kokomo , IN 46904 , USA
| | - Mourad Elhabiri
- Laboratoire de Chimie Bioorganique et Médicinale , UMR 7509 CNRS/UdS , ECPM , 25 rue Becquerel , 67087 Strasbourg , France .
| | - Ali Trabolsi
- New York University Abu Dhabi (NYUAD) , Experimental Research Building (C1), Saadiyat Island , Abu Dhabi , UAE .
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Marker Exchange Mutagenesis of mxaF, Encoding the Large Subunit of the Mxa Methanol Dehydrogenase, in Methylosinus trichosporium OB3b. Appl Environ Microbiol 2015; 82:1549-1555. [PMID: 26712545 DOI: 10.1128/aem.03615-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/17/2015] [Indexed: 02/05/2023] Open
Abstract
Methanotrophs have remarkable redundancy in multiple steps of the central pathway of methane oxidation to carbon dioxide. For example, it has been known for over 30 years that two forms of methane monooxygenase, responsible for oxidizing methane to methanol, exist in methanotrophs, i.e., soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO), and that expression of these two forms is controlled by the availability of copper. Specifically, sMMO expression occurs in the absence of copper, while pMMO expression increases with increasing copper concentrations. More recently, it was discovered that multiple forms of methanol dehydrogenase (MeDH), Mxa MeDH and Xox MeDH, also exist in methanotrophs and that the expression of these alternative forms is regulated by the availability of cerium. That is, expression of Xox MeDH increases in the presence of cerium, while Mxa MeDH expression decreases in the presence of cerium. As it had been earlier concluded that pMMO and Mxa MeDH form a supercomplex in which electrons from Mxa MeDH are back donated to pMMO to drive the initial oxidation of methane, we speculated that Mxa MeDH could be rendered inactive through marker-exchange mutagenesis but growth on methane could still be possible if cerium was added to increase the expression of Xox MeDH under sMMO-expressing conditions. Here we report that mxaF, encoding the large subunit of Mxa MeDH, could indeed be knocked out in Methylosinus trichosporium OB3b, yet growth on methane was still possible, so long as cerium was added. Interestingly, growth of this mutant occurred in both the presence and the absence of copper, suggesting that Xox MeDH can replace Mxa MeDH regardless of the form of MMO expressed.
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Abstract
This chapter focuses on transition metals. All transition metal cations are toxic-those that are essential for Escherichia coli and belong to the first transition period of the periodic system of the element and also the "toxic-only" metals with higher atomic numbers. Common themes are visible in the metabolism of these ions. First, there is transport. High-rate but low-affinity uptake systems provide a variety of cations and anions to the cells. Control of the respective systems seems to be mainly through regulation of transport activity (flux control), with control of gene expression playing only a minor role. If these systems do not provide sufficient amounts of a needed ion to the cell, genes for ATP-hydrolyzing high-affinity but low-rate uptake systems are induced, e.g., ABC transport systems or P-type ATPases. On the other hand, if the amount of an ion is in surplus, genes for efflux systems are induced. By combining different kinds of uptake and efflux systems with regulation at the levels of gene expression and transport activity, the concentration of a single ion in the cytoplasm and the composition of the cellular ion "bouquet" can be rapidly adjusted and carefully controlled. The toxicity threshold of an ion is defined by its ability to produce radicals (copper, iron, chromate), to bind to sulfide and thiol groups (copper, zinc, all cations of the second and third transition period), or to interfere with the metabolism of other ions. Iron poses an exceptional metabolic problem due its metabolic importance and the low solubility of Fe(III) compounds, combined with the ability to cause dangerous Fenton reactions. This dilemma for the cells led to the evolution of sophisticated multi-channel iron uptake and storage pathways to prevent the occurrence of unbound iron in the cytoplasm. Toxic metals like Cd2+ bind to thiols and sulfide, preventing assembly of iron complexes and releasing the metal from iron-sulfur clusters. In the unique case of mercury, the cation can be reduced to the volatile metallic form. Interference of nickel and cobalt with iron is prevented by the low abundance of these metals in the cytoplasm and their sequestration by metal chaperones, in the case of nickel, or by B12 and its derivatives, in the case of cobalt. The most dangerous metal, copper, catalyzes Fenton-like reactions, binds to thiol groups, and interferes with iron metabolism. E. coli solves this problem probably by preventing copper uptake, combined with rapid efflux if the metal happens to enter the cytoplasm.
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McDonough E, Kamp H, Camilli A. Vibrio cholerae phosphatases required for the utilization of nucleotides and extracellular DNA as phosphate sources. Mol Microbiol 2015; 99:453-69. [PMID: 26175126 PMCID: PMC4714964 DOI: 10.1111/mmi.13128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 01/18/2023]
Abstract
Phosphate is essential for life, being used in many core processes such as signal transduction and synthesis of nucleic acids. The waterborne agent of cholera, Vibrio cholerae, encounters phosphate limitation in both the aquatic environment and human intestinal tract. This bacterium can utilize extracellular DNA (eDNA) as a phosphate source, a phenotype dependent on secreted endo‐ and exonucleases. However, no transporter of nucleotides has been identified in V. cholerae, suggesting that in order for the organism to utilize the DNA as a phosphate source, it must first separate the phosphate and nucleoside groups before transporting phosphate into the cell. In this study, we investigated the factors required for assimilation of phosphate from eDNA. We identified PhoX, and the previously unknown proteins UshA and CpdB as the major phosphatases that allow phosphate acquisition from eDNA and nucleotides. We demonstrated separable but partially overlapping roles for the three phosphatases and showed that the activity of PhoX and CpdB is induced by phosphate limitation. Thus, this study provides mechanistic insight into how V. cholerae can acquire phosphate from extracellular DNA, which is likely to be an important phosphate source in the environment and during infection.
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Affiliation(s)
- EmilyKate McDonough
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Heather Kamp
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Andrew Camilli
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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47
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Recent advances in phosphate biosensors. Biotechnol Lett 2015; 37:1335-45. [DOI: 10.1007/s10529-015-1823-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
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Moreira LM, Facincani AP, Ferreira CB, Ferreira RM, Ferro MIT, Gozzo FC, de Oliveira JCF, Ferro JA, Soares MR. Chemotactic signal transduction and phosphate metabolism as adaptive strategies during citrus canker induction by Xanthomonas citri. Funct Integr Genomics 2014; 15:197-210. [PMID: 25403594 DOI: 10.1007/s10142-014-0414-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 11/03/2014] [Accepted: 11/07/2014] [Indexed: 12/11/2022]
Abstract
The genome of Xanthomonas citri subsp. Citri strain 306 pathotype A (Xac) was completely sequenced more than 10 years; to date, few studies involving functional genomics Xac and its host compatible have been developed, specially related to adaptive events that allow the survival of Xac within the plant. Proteomic analysis of Xac showed that the processes of chemotactic signal transduction and phosphate metabolism are key adaptive strategies during the interaction of a pathogenic bacterium with its plant host. The results also indicate the importance of a group of proteins that may not be directly related to the classical virulence factors, but that are likely fundamental to the success of the initial stages of the infection, such as methyl-accepting chemotaxis protein (Mcp) and phosphate specific transport (Pst). Furthermore, the analysis of the mutant of the gene pstB which codifies to an ABC phosphate transporter subunit revealed a complete absence of citrus canker symptoms when inoculated in compatible hosts. We also conducted an in silico analysis which established the possible network of genes regulated by two-component systems PhoPQ and PhoBR (related to phosphate metabolism), and possible transcriptional factor binding site (TFBS) motifs of regulatory proteins PhoB and PhoP, detaching high degree of conservation of PhoB TFBS in 84 genes of Xac genome. This is the first time that chemotaxis signal transduction and phosphate metabolism were therefore indicated to be fundamental to the process of colonization of plant tissue during the induction of disease associated with Xanthomonas genus bacteria.
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Affiliation(s)
- Leandro Marcio Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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Gonzalez D, Richez M, Bergonzi C, Chabriere E, Elias M. Crystal structure of the phosphate-binding protein (PBP-1) of an ABC-type phosphate transporter from Clostridium perfringens. Sci Rep 2014; 4:6636. [PMID: 25338617 PMCID: PMC5381212 DOI: 10.1038/srep06636] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/25/2014] [Indexed: 11/23/2022] Open
Abstract
Phosphate limitation is an important environmental stress that affects the metabolism of various organisms and, in particular, can trigger the virulence of numerous bacterial pathogens. Clostridium perfringens, a human pathogen, is one of the most common causes of enteritis necroticans, gas gangrene and food poisoning. Here, we focused on the high affinity phosphate-binding protein (PBP-1) of an ABC-type transporter, responsible for cellular phosphate uptake. We report the crystal structure (1.65 Å resolution) of the protein in complex with phosphate. Interestingly, PBP-1 does not form the short, low-barrier hydrogen bond with phosphate that is typical of previously characterized phosphate-binding proteins, but rather a canonical hydrogen bond. In its unique binding configuration, PBP-1 forms an unusually high number of hydrogen bonds (14) with the phosphate anion. Discrimination experiments reveal that PBP-1 is the least selective PBP characterised so far and is able to discriminate phosphate from its close competing anion, arsenate, by ~150-fold.
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Affiliation(s)
- Daniel Gonzalez
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Magali Richez
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Celine Bergonzi
- 1] URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France [2] University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics &Biotechnology Institute, St. Paul, MN 55108, USA
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics &Biotechnology Institute, St. Paul, MN 55108, USA
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Role of an archaeal PitA transporter in the copper and arsenic resistance of Metallosphaera sedula, an extreme thermoacidophile. J Bacteriol 2014; 196:3562-70. [PMID: 25092032 DOI: 10.1128/jb.01707-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Thermoacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, an M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supranormal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to the upregulation of 55 genes. Genome resequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism, or transport. These mutations included 7 nonsynonymous substitutions, 4 insertions, and 1 deletion. One of the insertion mutations mapped to pseudogene Msed_1517 and extended its reading frame an additional 209 amino acids. The extended mutant allele was identified as a homolog of Pho4, a family of phosphate symporters that includes the bacterial PitA proteins. Orthologs of this allele were apparent in related extremely thermoacidophilic species, suggesting M. sedula naturally lacked this gene. Phosphate transport studies combined with physiologic analysis demonstrated M. sedula PitA was a low-affinity, high-velocity secondary transporter implicated in copper resistance and arsenate sensitivity. Genetic analysis demonstrated that spontaneous arsenate-resistant mutants derived from CuR1 all underwent mutation in pitA and nonselectively became copper sensitive. Taken together, these results point to archaeal PitA as a key requirement for the increased metal resistance of strain CuR1 and its accelerated capacity for copper bioleaching.
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