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Li Z, Liu X, Ning N, Li T, Wang H. Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli. Genes (Basel) 2024; 15:236. [PMID: 38397225 PMCID: PMC10888264 DOI: 10.3390/genes15020236] [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: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as E. coli K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in E. coli genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats.
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Affiliation(s)
- Zhan Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Xiong Liu
- Chinese PLA Center for Disease Control and Prevention, Dongda Street 20#, Fengtai District, Beijing 100071, China;
| | - Nianzhi Ning
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Tao Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
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2
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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] [MESH Headings] [Track Full Text] [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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3
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Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
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4
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Yin Y, Mimura H. Mitigation of Hyper KCl Stress at 42ºC with Externally Existing Sodium Glutamate to a Halotolerant Brevibacterium sp. JCM 6894. Biocontrol Sci 2020; 25:139-147. [PMID: 32938843 DOI: 10.4265/bio.25.139] [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] [Indexed: 11/01/2022]
Abstract
Halotolerant Brevibacterium sp. JCM 6894 grew at 37ºC in the presence of 2.3 M KCl, while the growth was repressed with the same concentration of NaCl. When resting cells, 107.4 ± 0.1 (CFU·mL-1), prepared from cells grown in the absence of salts at 30ºC, were exposed to 3.3 M NaCl for 36 h at 42ºC, reduction of the number of resting cells was maintained within a 1-log cycle in the presence of proline, betaine, or ectoine (50 mM). In the presence of 3.3 M KCl, the most functional osmoprotectant was sodium glutamate (50 mM), and the value was 107.2 ± 0.1 (CFU·mL-1) when exposed for 72 h at 42ºC. In the absence of osmoprotectants, the value was reduced to four orders of magnitude in each experimental condition. The number of resting cells, 106.8 ± 0.1 (CFU·mL-1), prepared from grown cells pre-adapted to 2.3 M KCl at 37ºC, was hardly reduced when exposed to 3.3 M KCl in the presence of sodium glutamate more than 50 mM for 72 h at 42ºC. Those results indicate that the isolate can sense the difference in hyper KCl stress as opposed to hyper NaCl stress, and different kinds of osmoadaptation systems can function to cope with each hyper salt stress.
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Affiliation(s)
- Yue Yin
- Graduate School of Maritime Sciences, Kobe University
| | - Haruo Mimura
- Graduate School of Maritime Sciences, Kobe University
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5
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Zhekova HR, Sakuma T, Johnson R, Concilio SC, Lech PJ, Zdravkovic I, Damergi M, Suksanpaisan L, Peng KW, Russell SJ, Noskov S. Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). J Chem Inf Model 2020; 60:1652-1665. [PMID: 32134653 DOI: 10.1021/acs.jcim.9b01114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human sodium iodide symporter (hNIS) is a theranostic reporter gene which concentrates several clinically approved SPECT and PET radiotracers and plays an essential role for the synthesis of thyroid hormones as an iodide transporter in the thyroid gland. Development of hNIS mutants which could enhance translocation of the desired imaging ions is currently underway. Unfortunately, it is hindered by lack of understanding of the 3D organization of hNIS and its relation to anion transport. There are no known crystal structures of hNIS in any of its conformational states. Homology modeling can be very effective in such situations; however, the low sequence identity between hNIS and relevant secondary transporters with available experimental structures makes the choice of a template and the generation of 3D models nontrivial. Here, we report a combined application of homology modeling and molecular dynamics refining of the hNIS structure in its semioccluded state. The modeling was based on templates from the LeuT-fold protein family and was done with emphasis on the refinement of the substrate-ion binding pocket. The consensus model developed in this work is compared to available biophysical and biochemical experimental data for a number of different LeuT-fold proteins. Some functionally important residues contributing to the formation of putative binding sites and permeation pathways for the cotransported Na+ ions and I- substrate were identified. The model predictions were experimentally tested by generation of mutant versions of hNIS and measurement of relative (to WT hNIS) 125I- uptake of 35 hNIS variants.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Toshie Sakuma
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Ryan Johnson
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Susanna C Concilio
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Patrycja J Lech
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Igor Zdravkovic
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mirna Damergi
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Kah-Whye Peng
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Stephen J Russell
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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Ronzheimer S, Warmbold B, Arnhold C, Bremer E. The GbsR Family of Transcriptional Regulators: Functional Characterization of the OpuAR Repressor. Front Microbiol 2018; 9:2536. [PMID: 30405586 PMCID: PMC6207618 DOI: 10.3389/fmicb.2018.02536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Accumulation of compatible solutes is a common stress response of microorganisms challenged by high osmolarity; it can be achieved either through synthesis or import. These processes have been intensively studied in Bacillus subtilis, where systems for the production of the compatible solutes proline and glycine betaine have been identified, and in which five transporters for osmostress protectants (Opu) have been characterized. Glycine betaine synthesis relies on the import of choline via the substrate-restricted OpuB system and the promiscuous OpuC transporter and its subsequent oxidation by the GbsAB enzymes. Transcription of the opuB and gbsAB operons is under control of the MarR-type regulator GbsR, which acts as an intracellular choline-responsive repressor. Modeling studies using the X-ray structure of the Mj223 protein from Methanocaldococcus jannaschii as the template suggest that GbsR is a homo-dimer with an N-terminal DNA-reading head and C-terminal dimerization domain; a flexible linker connects these two domains. In the vicinity of the linker region, an aromatic cage is predicted as the inducer-binding site, whose envisioned architecture resembles that present in choline and glycine betaine substrate-binding proteins of ABC transporters. We used bioinformatics to assess the phylogenomics of GbsR-type proteins and found that they are widely distributed among Bacteria and Archaea. Alignments of GbsR proteins and analysis of the genetic context of the corresponding structural genes allowed their assignment into four sub-groups. In one of these sub-groups of GbsR-type proteins, gbsR-type genes are associated either with OpuA-, OpuB-, or OpuC-type osmostress protectants uptake systems. We focus here on GbsR-type proteins, named OpuAR by us, that control the expression of opuA-type gene clusters. Using such a system from the marine bacterium Bacillus infantis, we show that OpuAR acts as a repressor of opuA transcription, where several compatible solutes (e.g., choline, glycine betaine, proline betaine) serve as its inducers. Site-directed mutagenesis studies allowed a rational improvement of the putative inducer-binding site in OpuAR with respect to the affinity of choline and glycine betaine binding. Collectively, our data characterize GbsR-/OpuAR-type proteins as an extended sub-group within the MarR-superfamily of transcriptional regulators and identify a novel type of substrate-inducible import system for osmostress protectants.
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Affiliation(s)
- Stefanie Ronzheimer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Bianca Warmbold
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Christian Arnhold
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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7
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Christgen SL, Zhu W, Sanyal N, Bibi B, Tanner JJ, Becker DF. Discovery of the Membrane Binding Domain in Trifunctional Proline Utilization A. Biochemistry 2017; 56:6292-6303. [PMID: 29090935 PMCID: PMC6044449 DOI: 10.1021/acs.biochem.7b01008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli proline utilization A (EcPutA) is the archetype of trifunctional PutA flavoproteins, which function both as regulators of the proline utilization operon and bifunctional enzymes that catalyze the four-electron oxidation of proline to glutamate. EcPutA shifts from a self-regulating transcriptional repressor to a bifunctional enzyme in a process known as functional switching. The flavin redox state dictates the function of EcPutA. Upon proline oxidation, the flavin becomes reduced, triggering a conformational change that causes EcPutA to dissociate from the put regulon and bind to the cellular membrane. Major structure/function domains of EcPutA have been characterized, including the DNA-binding domain, proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase catalytic domains, and an aldehyde dehydrogenase superfamily fold domain. Still lacking is an understanding of the membrane-binding domain, which is essential for EcPutA catalytic turnover and functional switching. Here, we provide evidence for a conserved C-terminal motif (CCM) in EcPutA having a critical role in membrane binding. Deletion of the CCM or replacement of hydrophobic residues with negatively charged residues within the CCM impairs EcPutA functional and physical membrane association. Furthermore, cell-based transcription assays and limited proteolysis indicate that the CCM is essential for functional switching. Using fluorescence resonance energy transfer involving dansyl-labeled liposomes, residues in the α-domain are also implicated in membrane binding. Taken together, these experiments suggest that the CCM and α-domain converge to form a membrane-binding interface near the PRODH domain. The discovery of the membrane-binding region will assist efforts to define flavin redox signaling pathways responsible for EcPutA functional switching.
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Affiliation(s)
- Shelbi L. Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Weidong Zhu
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Nikhilesh Sanyal
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Bushra Bibi
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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8
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The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins. CRYSTALS 2017. [DOI: 10.3390/cryst7040117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
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