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Xing Q, Zhang S, Tao X, Mesbah NM, Mao X, Wang H, Wiegel J, Zhao B. The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K . Appl Environ Microbiol 2024; 90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.
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Affiliation(s)
- Qinghua Xing
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
- Luo Yang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Luoyang, China
| | - Xinyi Tao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Xinwei Mao
- Department of Civil Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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2
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Wang FP, Wang JF, He T, Tian P, Song XQ, Li QS. Urea reduces the sustainability of soil Cd immobilization by upregulating the expression of AmSTOP1 and AmMATE genes in edible amaranth roots. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123505. [PMID: 38325515 DOI: 10.1016/j.envpol.2024.123505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/18/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
After cadmium (Cd) immobilization remediation in contaminated farmland soil, which forms of nitrogen fertilizer should be implemented to keep its sustainability? Urea and nitrate were used to compare for their effects on the remobilization of stabilized Cd in the rhizosphere soil of edible amaranth at nitrogen concentrations of 60, 95, and 130 mg kg-1. The results showed that compared to nitrate nitrogen, the Cd content in shoots increased by 76.2%, 65.6%, and 148% after applying three different concentrations of urea, and the total remobilization amount of Cd also increased by 16.0%, 24.9%, and 14.0% respectively. Urea application promotes root secretion of citric acid, malic acid, pyruvate, and γ-aminobutyric acid, crucial in remobilizing stable Cd. The application of urea promoted the expression of genes involved in sucrose transport, glycolysis, the TCA cycle, amino acid secretion, citric acid efflux, and proton efflux. Arabidopsis heterologous expression and yeast one-hybrid assays identify critical roles of AmMATE42 and AmMATE43 in citric acid and fumaric acid efflux, with AmSTOP1 activating their transcription. Inhibition of SIZ1 expression in urea treatment reduce AmSTOP1 SUMOylation, leading to increased expression of AmMATE42 and AmMATE43 and enhanced organic acids efflux. Using edible amaranth as a model vegetable, we discovered that urea is not beneficial to preserving the sustainability of stabilized Cd during the reuse of remediated farmlands contaminated with Cd.
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Affiliation(s)
- Fo-Peng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Tao He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Ping Tian
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Xiao-Qian Song
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
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3
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Wu Y, Bell A, Thomas GH, Bolam DN, Sargent F, Juge N, Palmer T, Severi E. Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001448. [PMID: 38488830 PMCID: PMC10955332 DOI: 10.1099/mic.0.001448] [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: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Sialic acid (Sia) transporters are critical to the capacity of host-associated bacteria to utilise Sia for growth and/or cell surface modification. While N-acetyl-neuraminic acid (Neu5Ac)-specific transporters have been studied extensively, little is known on transporters dedicated to anhydro-Sia forms such as 2,7-anhydro-Neu5Ac (2,7-AN) or 2,3-dehydro-2-deoxy-Neu5Ac (Neu5Ac2en). Here, we used a Sia-transport-null strain of Escherichia coli to investigate the function of members of anhydro-Sia transporter families previously identified by computational studies. First, we showed that the transporter NanG, from the Glycoside-Pentoside-Hexuronide:cation symporter family, is a specific 2,7-AN transporter, and identified by mutagenesis a crucial functional residue within the putative substrate-binding site. We then demonstrated that NanX transporters, of the Major Facilitator Superfamily, also only transport 2,7-AN and not Neu5Ac2en nor Neu5Ac. Finally, we provided evidence that SiaX transporters, of the Sodium-Solute Symporter superfamily, are promiscuous Neu5Ac/Neu5Ac2en transporters able to acquire either substrate equally well. The characterisation of anhydro-Sia transporters expands our current understanding of prokaryotic Sia metabolism within host-associated microbial communities.
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Affiliation(s)
- Yunhan Wu
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Bell
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Gavin H. Thomas
- Department of Biology and York Biomedical Research Institute (YBRI), Wentworth Way, University of York, York YO10 5DD, UK
| | - David N. Bolam
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Frank Sargent
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Tracy Palmer
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Emmanuele Severi
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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4
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Currie MJ, Davies JS, Scalise M, Gulati A, Wright JD, Newton-Vesty MC, Abeysekera GS, Subramanian R, Wahlgren WY, Friemann R, Allison JR, Mace PD, Griffin MDW, Demeler B, Wakatsuki S, Drew D, Indiveri C, Dobson RCJ, North RA. Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter. eLife 2024; 12:RP92307. [PMID: 38349818 PMCID: PMC10942642 DOI: 10.7554/elife.92307] [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] [Indexed: 02/15/2024] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-electron microscopy (cryo-EM) structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the Haemophilus influenzae N-acetylneuraminate TRAP transporter (HiSiaQM) at 2.99 Å resolution (extending to 2.2 Å at the core), revealing new features. The improved resolution (the previous HiSiaQM structure is 4.7 Å resolution) permits accurate assignment of two Na+ sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the HiSiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity (KD) for the complex between the soluble HiSiaP protein and HiSiaQM is in the micromolar range and that a related SiaP can bind HiSiaQM. This work provides key data that enhances our understanding of the 'elevator-with-an-operator' mechanism of TRAP transporters.
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Affiliation(s)
- Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - James S Davies
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of CalabriaArcavacata di RendeItaly
| | - Ashutosh Gulati
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Joshua D Wright
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Gayan S Abeysekera
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Ramaswamy Subramanian
- Biological Sciences and Biomedical Engineering, Bindley Bioscience Center, Purdue University West LafayetteWest LafayetteUnited States
| | - Weixiao Y Wahlgren
- Department of Chemistry and Molecular Biology, Biochemistry and Structural Biology, University of GothenburgGothenburgSweden
| | - Rosmarie Friemann
- Centre for Antibiotic Resistance Research (CARe) at University of GothenburgGothenburgSweden
| | - Jane R Allison
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of AucklandAucklandNew Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of OtagoDunedinNew Zealand
| | - Michael DW Griffin
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of MontanaMissoulaUnited States
- Department of Chemistry and Biochemistry, University of LethbridgeLethbridgeCanada
| | - Soichi Wakatsuki
- Biological Sciences Division, SLAC National Accelerator LaboratoryMenlo ParkUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of CalabriaArcavacata di RendeItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Renwick CJ Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
- School of Medical Sciences, Faculty of Medicine and Health, University of SydneySydneyAustralia
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5
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Zmyslia M, Fröhlich K, Dao T, Schmidt A, Jessen-Trefzer C. Deep Proteomic Investigation of Metabolic Adaptation in Mycobacteria under Different Growth Conditions. Proteomes 2023; 11:39. [PMID: 38133153 PMCID: PMC10747050 DOI: 10.3390/proteomes11040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the complex mechanisms of mycobacterial pathophysiology and adaptive responses presents challenges that can hinder drug development. However, employing physiologically relevant conditions, such as those found in human macrophages or simulating physiological growth conditions, holds promise for more effective drug screening. A valuable tool in this pursuit is proteomics, which allows for a comprehensive analysis of adaptive responses. In our study, we focused on Mycobacterium smegmatis, a model organism closely related to the pathogenic Mycobacterium tuberculosis, to investigate the impact of various carbon sources on mycobacterial growth. To facilitate this research, we developed a cost-effective, straightforward, and high-quality pipeline for proteome analysis and compared six different carbon source conditions. Additionally, we have created an online tool to present and analyze our data, making it easily accessible to the community. This user-friendly platform allows researchers and interested parties to explore and interpret the results effectively. Our findings shed light on mycobacterial adaptive physiology and present potential targets for drug development, contributing to the fight against tuberculosis.
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Affiliation(s)
- Mariia Zmyslia
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
| | - Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Trinh Dao
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Claudia Jessen-Trefzer
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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6
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Xing Q, Mesbah NM, Wang H, Zhang Y, Li J, Zhao B. Tandem mass tag-based quantitative proteomics reveals osmotic adaptation mechanisms in Alkalicoccus halolimnae BZ-SZ-XJ29 T , a halophilic bacterium with a broad salinity range for optimal growth. Environ Microbiol 2023; 25:1967-1987. [PMID: 37271582 DOI: 10.1111/1462-2920.16428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
The moderate halophilic bacterium Alkalicoccus halolimnae BZ-SZ-XJ29T exhibits optimum growth over a wide range of NaCl concentrations (8.3-12.3%, w/v; 1.42-2.1 mol L-1 ). However, its adaptive mechanisms to cope with high salt-induced osmotic stress remain unclear. Using TMT-based quantitative proteomics, the cellular proteome was assessed under low (4% NaCl, 0.68 mol L-1 NaCl, control (CK) group), moderate (8% NaCl, 1.37 mol L-1 NaCl), high (12% NaCl, 2.05 mol L-1 NaCl), and extremely high (16% NaCl, 2.74 mol L-1 NaCl) salinity conditions. Digital droplet PCR confirmed the transcription of candidate genes related to salinity. A. halolimnae utilized distinct adaptation strategies to cope with different salinity conditions. Mechanisms such as accumulating different amounts and types of compatible solutes (i.e., ectoine, glycine betaine, glutamate, and glutamine) and the uptake of glycine betaine and glutamate were employed to cope with osmotic stress. Ectoine synthesis and accumulation were critical to the salt adaptation of A. halolimnae. The expression of EctA, EctB, and EctC, as well as the intracellular accumulation of ectoine, significantly and consistently increased with increasing salinity. Glycine betaine and glutamate concentrations remained constant under the four NaCl concentrations. The total content of glutamine and glutamate maintained a dynamic balance and, when exposed to different salinities, may play a role in low salinity-induced osmoadaptation. Moreover, cellular metabolism was severely affected at high salt concentrations, but the synthesis of amino acids, carbohydrate metabolism, and membrane transport related to haloadptation was preserved to maintain cytoplasmic concentration at high salinity. These findings provide insights into the osmoadaptation mechanisms of moderate halophiles and can serve as a theoretical underpinning for industrial production and application of compatible solutes.
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Affiliation(s)
- Qinghua Xing
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Noha M Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingjie Zhang
- China Patent Technology Development Co, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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7
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Henríquez T, Hsu JS, Hernandez JS, Kuppermann S, Eder M, Jung H. Contribution of Uncharacterized Target Genes of MxtR/ErdR to Carbon Source Utilization by Pseudomonas putida KT2440. Microbiol Spectr 2023; 11:e0292322. [PMID: 36511656 PMCID: PMC9927547 DOI: 10.1128/spectrum.02923-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
MxtR/ErdR is a two-component system that has been previously described as a regulator of the utilization of acetate in Vibrio cholerae and in some Pseudomonas species. Regulation is achieved by controlling the expression of the acs gene (acetyl-coenzyme A [CoA] synthetase). However, the physiological significance of other identified target genes is not fully understood. Here, we investigated the role of pp_0154 (scpC) and pp_0354/pp_0353 in the soil bacterium Pseudomonas putida KT2440. To this end, the genes were individually deleted and complemented in trans. Then, the growth of the resulting strains on different carbon sources was analyzed. To obtain information on protein function, a bioinformatic analysis was performed, and ScpC was purified and characterized in vitro. Our results indicated that scpC is important for P. putida KT2440 to cope with high concentrations of acetate. The encoded enzyme catalyzes the transfer of coenzyme A between acetate and succinate. On the contrary, pp_0353 and pp_0354 proved to be unimportant for the growth of the strain on acetate under our conditions. Extending the phenotypic analysis to other carbon sources led to the discovery that mxtR, erdR, and pp_0353 are important for the utilization of pyruvate as a carbon source. Taken together, the findings of this study expand the knowledge about the role of the MxtR/ErdR two-component system in carbon source utilization and about the specific functions of its target genes. IMPORTANCE MxtR/ErdR and homologous two-component systems play important roles in the regulatory networks that control cell metabolism and influence bacterial-host interactions. Using the MxtR/ErdR two-component system of the plant growth-promoting soil bacterium Pseudomonas putida KT2440 as a model, this work elucidates the function of previously uncharacterized target genes of MxtR/ErdR and extends the knowledge of the physiological significance of the two-component system. Our results suggest that the target gene scpC encodes an acetate:succinate CoA transferase that is involved in the detoxification of acetate when it is present in large amounts. Furthermore, it is shown that MxtR/ErdR controls the metabolism of not only acetate but also pyruvate. This control involves the target gene pp_0353 (putative exonuclease). These findings may facilitate the optimization of P. putida KT2440 as a chassis for biotechnological applications and may contribute to a better understanding of the regulatory network of pathogens like Pseudomonas aeruginosa.
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Affiliation(s)
- Tania Henríquez
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Jyh-Shiuan Hsu
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | | | - Sonja Kuppermann
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Michelle Eder
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Heinrich Jung
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
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8
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Proline transporters ProT and PutP are required for Staphylococcus aureus infection. PLoS Pathog 2023; 19:e1011098. [PMID: 36652494 PMCID: PMC9886301 DOI: 10.1371/journal.ppat.1011098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/30/2023] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Proline acquired via specific transporters can serve as a proteinogenic substrate, carbon and nitrogen source, or osmolyte. Previous reports have documented that Staphylococcus aureus, a major community and nosocomial pathogen, encodes at least four proline transporters, PutP, OpuC, OpuD, and ProP. A combination of genetic approaches and 3H-proline transport assays reveal that a previously unrecognized transporter, ProT, in addition to PutP, are the major proline transporters in S. aureus. Complementation experiments using constitutively expressed non-cognate promoters found that proline transport via OpuD, OpuC, and ProP is minimal. Both proline biosynthesis from arginine and proline transport via ProT are critical for growth when S. aureus is grown under conditions of high salinity. Further, proline transport mediated by ProT or PutP are required for growth in media with and without glucose, indicating both transporters function to acquire proline for proteinogenic purposes in addition to acquisition of proline as a carbon/nitrogen source. Lastly, inactivation of proT and putP resulted in a significant reduction (5 log10) of bacterial burden in murine skin-and-soft tissue infection and bacteremia models, suggesting that proline transport is required to establish a S. aureus infection.
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9
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Proline Transport and Growth Changes in Proline Transport Mutants of Staphylococcus aureus. Microorganisms 2022; 10:microorganisms10101888. [DOI: 10.3390/microorganisms10101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is a major cause of skin/soft tissue infections and more serious infections in humans. The species usually requires the importation of proline to be able to survive. Previous work has shown that single mutations in genes that encode for proline transporters affect the ability of S. aureus to survive in vitro and in vivo. To better understand proline transport in S. aureus, double and triple gene mutant strains were created that targeted the opuD, proP, and putP genes. Single gene mutants had some effect on proline transport, whereas double mutants exhibited significantly lower proline transport. An opuD prop putP triple gene mutant displayed the lowest proline transport under low- and high-affinity conditions. To assess growth differences caused by the mutations, the same mutants were grown in brain heart infusion (BHI) broth and defined staphylococcal medium (DSM) with various concentrations of proline. The triple mutant did not grow in DSM with a low concentration of proline and grew poorly in both DSM with a high proline concentration and BHI broth. These results show that S. aureus has multiple mechanisms to import proline into the cell and knocking out three of the main proline transporters significantly hinders S. aureus growth.
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10
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Czech L, Gertzen C, Smits SHJ, Bremer E. Guilty by association: importers, exporters and
MscS
‐type mechanosensitive channels encoded in biosynthetic gene clusters for the stress‐protectant ectoine. Environ Microbiol 2022; 24:5306-5331. [DOI: 10.1111/1462-2920.16203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Czech
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
- Department of Chemistry and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Christoph Gertzen
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Pharmaceutical and Medicinal Chemistry Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
| | - Sander H. J. Smits
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Biochemistry Heinrich Heine University Düsseldorf Düsseldorf Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
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11
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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Ramos AL, Aquino M, García G, Gaspar M, de la Cruz C, Saavedra-Flores A, Brom S, Cervantes-Rivera R, Galindo-Sánchez CE, Hernandez R, Puhar A, Lupas AN, Sepulveda E. RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234. Front Microbiol 2022; 13:871077. [PMID: 35572670 PMCID: PMC9100948 DOI: 10.3389/fmicb.2022.871077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
The SLC5/STAC histidine kinases comprise a recently identified family of sensor proteins in two-component signal transduction systems (TCSTS), in which the signaling domain is fused to an SLC5 solute symporter domain through a STAC domain. Only two members of this family have been characterized experimentally, the CrbS/R system that regulates acetate utilization in Vibrio and Pseudomonas, and the CbrA/B system that regulates the utilization of histidine in Pseudomonas and glucose in Azotobacter. In an attempt to expand the characterized members of this family beyond the Gammaproteobacteria, we identified two putative TCSTS in the Alphaproteobacterium Sinorhizobium fredii NGR234 whose sensor histidine kinases belong to the SLC5/STAC family. Using reverse genetics, we were able to identify the first TCSTS as a CrbS/R homolog that is also needed for growth on acetate, while the second TCSTS, RpuS/R, is a novel system required for optimal growth on pyruvate. Using RNAseq and transcriptional fusions, we determined that in S. fredii the RpuS/R system upregulates the expression of an operon coding for the pyruvate symporter MctP when pyruvate is the sole carbon source. In addition, we identified a conserved DNA sequence motif in the putative promoter region of the mctP operon that is essential for the RpuR-mediated transcriptional activation of genes under pyruvate-utilizing conditions. Finally, we show that S. fredii mutants lacking these TCSTS are affected in nodulation, producing fewer nodules than the parent strain and at a slower rate.
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Affiliation(s)
| | - Maria Aquino
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Gema García
- Facultad de Biología, Universidad Autónoma de Sinaloa, Culiacan, Mexico
| | - Miriam Gaspar
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Cristina de la Cruz
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Clara Elizabeth Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Rufina Hernandez
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- CONACYT-Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
- *Correspondence: Edgardo Sepulveda,
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13
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Comprehensive Genome Analysis of Halolamina pelagica CDK2: Insights into Abiotic Stress Tolerance Genes. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halophilic archaeon Halolamina pelagica CDK2, showcasing plant growth-promoting properties and endurance towards harsh environmental conditions (high salinity, heavy metals, high temperature and UV radiation) was sequenced earlier. Pan-genome of Halolamina genus was created and investigated for strain-specific genes of CDK2, which might confer it with features helping it to withstand high abiotic stress. Pathways and subsystems in CDK2 were compared with other Halolamina strain CGHMS and analysed using KEGG and RAST. A genome-scale metabolic model was reconstructed from the genome of H. pelagica CDK2. Results implicated strain-specific genes like thermostable carboxypeptidase and DNA repair protein MutS which might protect the proteins and DNA from high temperature and UV denaturation respectively. A bifunctional trehalose synthase gene responsible for trehalose biosynthesis was also annotated specifying the need for low salt compatible solute strategy, the probable reason behind the ability of this haloarchaea to survive in a wide range of salt concentrations. A modified shikimate and mevalonate pathways were also identified in CDK2, along with many ABC transporters for metal uptakes like zinc and cobalt through pathway analysis. Probable employment of one multifunctional ABC transporter in place of two for similar metals (Nickel/cobalt and molybdenum/tungsten) might be employed as a strategy for energy conservation. The findings of the present study could be utilized for future research relating metabolic model for flux balance analysis and the genetic repertoire imparting resistance to harsh conditions can be transferred to crops for improving their tolerance to abiotic stresses.
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Monteagudo-Cascales E, Santero E, Canosa I. The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions. Genes (Basel) 2022; 13:genes13020375. [PMID: 35205417 PMCID: PMC8871633 DOI: 10.3390/genes13020375] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.
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Affiliation(s)
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
| | - Inés Canosa
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
- Correspondence: ; Tel.: +34-954349052
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Involvement of the MxtR/ErdR (CrbS/CrbR) Two-Component System in Acetate Metabolism in Pseudomonas putida KT2440. Microorganisms 2021; 9:microorganisms9081558. [PMID: 34442637 PMCID: PMC8402216 DOI: 10.3390/microorganisms9081558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022] Open
Abstract
MxtR/ErdR (also called CrbS/CrbR) is a two-component system previously identified as important for the utilization of acetate in Vibrio cholerae and some Pseudomonas species. In addition, evidence has been found in Pseudomonas aeruginosa for a role in regulating the synthesis and expression, respectively, of virulence factors such as siderophores and RND transporters. In this context, we investigated the physiological role of the MxtR/ErdR system in the soil bacterium Pseudomonas putida KT2440. To that end, mxtR and erdR were individually deleted and the ability of the resulting mutants to metabolize different carbon sources was analyzed in comparison to wild type. We also assessed the impact of the deletions on siderophore production, expression of mexEF-oprN (RND transporter), and the biocontrol properties of the strain. Furthermore, the MxtR/ErdR-dependent expression of putative target genes and binding of ErdR to respective promoter regions were analyzed. Our results indicated that the MxtR/ErdR system is active and essential for acetate utilization in P. putida KT2440. Expression of scpC, pp_0354, and acsA-I was stimulated by acetate, while direct interactions of ErdR with the promoter regions of the genes scpC, pp_0354, and actP-I were demonstrated by an electromobility shift assay. Finally, our results suggested that MxtR/ErdR is neither involved in regulating siderophore production nor the expression of mexEF-oprN in P. putida KT2440 under the conditions tested.
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Wirtz L, Eder M, Brand AK, Jung H. HutT functions as the major L-histidine transporter in Pseudomonas putida KT2440. FEBS Lett 2021; 595:2113-2126. [PMID: 34245008 DOI: 10.1002/1873-3468.14159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 11/06/2022]
Abstract
Histidine is an important carbon and nitrogen source of γ-proteobacteria and can affect bacteria-host interactions. The mechanisms of histidine uptake are only partly understood. Here, we analyze functional properties of the putative histidine transporter HutT of the soil bacterium Pseudomonas putida. The hutT gene is part of the histidine utilization operon, and the gene product belongs to the amino acid-polyamine-organocation (APC) family of secondary transporters. Deletion of hutT severely impairs growth of P. putida on histidine, suggesting that the encoded transporter is the major histidine uptake system of P. putida. Transport experiments with cells and purified and reconstituted protein indicate that HutT functions as a high-affinity histidine : proton symporter with high specificity for the amino acid. Substitution analyses identified amino acids crucial for HutT function.
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Affiliation(s)
- Larissa Wirtz
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Michelle Eder
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Anna-Katharina Brand
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Heinrich Jung
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
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