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Ferro-Gallego P, Vila-Sanjurjo A, Valderrama Pereira AK, Porres Pérez G, Domínguez-Gerpe L. Circular PCR as an efficient and precise umbrella of methods for the generation of circular dsDNA with staggered nicks: Mechanism and types. Biol Methods Protoc 2024; 9:bpae051. [PMID: 39139995 PMCID: PMC11319657 DOI: 10.1093/biomethods/bpae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Here, we introduce the highly versatile circular polymerase chain reaction (CiPCR) technique, propose a mechanism of action, and describe a number of examples demonstrating the versatility of this technique. CiPCR takes place between two fragments of dsDNA with two homologous regions, as long as one of the fragments carries said regions at its 3'- and 5'-ends. Upon hybridization, elongation by a polymerase occurs from all 3'-ends continuously until a 5'-end is reached, leading to stable circular dsDNA with staggered nicks. When both dsDNA fragments carry the homology at their 3'- and 5'-ends (Type I CiPCR), all four 3'-ends effectively prime amplification of the intervening region and CiPCR products can function as template during the reaction. In contrast, when only one of the two dsDNA fragments carries the homologous regions at its 3'- and 5'-ends and the other carries such regions internally (Type II CiPCR), only two 3'-ends can be amplified and CiPCR products possess no template activity. We demonstrate the applicability of both CiPCR types via well-illustrated experimental examples. CiPCR is well adapted to the quick resolution of most of the molecular cloning challenges faced by the biology/biomedicine laboratory, including the generation of insertions, deletions, and mutations.
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Affiliation(s)
- Pedro Ferro-Gallego
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
- Present Address: IBIMA, Instituto de Investigación Biomédica y Plataforma en Nanomedicina, BIONAND, Málaga, 29590, Spain
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Biology Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Andrea Katherine Valderrama Pereira
- Chemistry Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Gonzalo Porres Pérez
- Grupo GIBE, Biology Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Lourdes Domínguez-Gerpe
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
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2
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Dong P, Wang H, Li Y, Yu J, Liu X, Wang Y, Dai L, Wang S. Active peptides from Eupolyphaga sinensis walker attenuates experimental hyperlipidemia by regulating the gut microbiota and biomarkers in rats with dyslipidemia. Biomed Pharmacother 2024; 170:116064. [PMID: 38154268 DOI: 10.1016/j.biopha.2023.116064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023] Open
Abstract
Eupolyphaga sinensis Walker (ESW) is a traditional Chinese medicine formulation used to treat hyperlipidemia. However, the hypolipidemic effect of the active peptides from E. sinensis Walker (APE) is incompletely understood. We studied the hypolipidemic effect of APE and explored the impact of APE on the gut microbiota (GM) in rats suffering from hyperlipidemia. APE was prepared by enzymatic digestion, and its structure was characterized using various methods. The anti-hyperlipidemic activity of APE was assessed using a high-fat diet (HFD)-induced model in zebrafish and rats. In rats, HFD administration caused abnormalities of lipid metabolism and disturbances of the GM and amino acid (AA) profile in plasma. The abundance of bacteria of the phyla Firmicutes and Bacteroides was increased significantly (p < 0.05), and the relative abundance of Lactobacillus species and Clostridium species was decreased significantly (p < 0.05). HFD therapy affected the levels of 12 AAs in vivo: 10 AAs showed increased levels and two AAs had decreased levels (p < 0.05). Similar results were demonstrated in an experiment on fecal microbiota transplantation. APE treatment dose-dependently decreased lipid factors and liver damage (p < 0.05). Sequencing of the 16 S rRNA gene indicated that APE improved the intestinal-flora structure of rats with HL markedly, and increased the relative abundance of Lactobacillus species and Clostridium species. Metabolomics analysis indicated that APE could alter the levels of 10 AAs affected by HFD consumption. Spearman correlation analysis revealed that gamma-aminobutyric acid (GABA) could be a crucial metabolite, and Lactobacillus species and Clostridium species might be important bacteria for the action of APE against hyperlipidemia. We speculate that APE exhibited an anti-hyperlipidemic effect by regulating GABA synthesis in the presence of Lactobacillus species and Clostridium species.
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Affiliation(s)
- Pingping Dong
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao 999078, China
| | - Hong Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250300, China
| | - Yanan Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250300, China
| | - Jiayi Yu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Xin Liu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yinglei Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
| | - Long Dai
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
| | - Shaoping Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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3
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Abstract
TonB-dependent transporters (TBDTs) are present in all gram-negative bacteria and mediate energy-dependent uptake of molecules that are too scarce or large to be taken up efficiently by outer membrane (OM) diffusion channels. This process requires energy that is derived from the proton motive force and delivered to TBDTs by the TonB-ExbBD motor complex in the inner membrane. Together with the need to preserve the OM permeability barrier, this has led to an extremely complex and fascinating transport mechanism for which the fundamentals, despite decades of research, are still unclear. In this review, we describe our current understanding of the transport mechanism of TBDTs, their potential role in the delivery of novel antibiotics, and the important contributions made by TBDT-associated (lipo)proteins.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
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4
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Wimalasiri VW, Jurczak KA, Wieliniec MK, Nilaweera TD, Nakamoto RK, Cafiso DS. A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters. Protein Sci 2023; 32:e4704. [PMID: 37312651 PMCID: PMC10288552 DOI: 10.1002/pro.4704] [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: 02/17/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Pulse EPR measurements provide information on distances and distance distributions in proteins but require the incorporation of pairs of spin labels that are usually attached to engineered cysteine residues. In previous work, we demonstrated that efficient in vivo labeling of the Escherichia coli outer membrane vitamin B12 transporter, BtuB, could only be achieved using strains defective in the periplasmic disulfide bond formation (Dsb) system. Here, we extend these in vivo measurements to FecA, the E. coli ferric citrate transporter. As seen for BtuB, pairs of cysteines cannot be labeled when the protein is present in a standard expression strain. However, incorporating plasmids that permit an arabinose induced expression of FecA into a strain defective in the thiol disulfide oxidoreductase, DsbA, enables efficient spin-labeling and pulse EPR of FecA in cells. A comparison of the measurements made on FecA in cells with measurements made in reconstituted phospholipid bilayers suggests that the cellular environment alters the behavior of the extracellular loops of FecA. In addition to these in situ EPR measurements, the use of a DsbA minus strain for the expression of BtuB improves the EPR signals and pulse EPR data obtained in vitro from BtuB that is labeled, purified, and reconstituted into phospholipid bilayers. The in vitro data also indicate the presence of intermolecular BtuB-BtuB interactions, which had not previously been observed in a reconstituted bilayer system. This result suggests that in vitro EPR measurements on other outer membrane proteins would benefit from protein expression in a DsbA minus strain.
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Affiliation(s)
- Viranga W. Wimalasiri
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Kinga A. Jurczak
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Monika K. Wieliniec
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Thushani D. Nilaweera
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Present address:
Genetics and Biochemistry BranchNational Institute of Diabetes and Digestive and Kidney DiseasesBethesdaMarylandUSA
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - David S. Cafiso
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
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5
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Braun V, Ratliff AC, Celia H, Buchanan SK. Energization of Outer Membrane Transport by the ExbB ExbD Molecular Motor. J Bacteriol 2023; 205:e0003523. [PMID: 37219427 PMCID: PMC10294619 DOI: 10.1128/jb.00035-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The outer membranes (OM) of Gram-negative bacteria contain a class of proteins (TBDTs) that require energy for the import of nutrients and to serve as receptors for phages and protein toxins. Energy is derived from the proton motif force (pmf) of the cytoplasmic membrane (CM) through the action of three proteins, namely, TonB, ExbB, and ExbD, which are located in the CM and extend into the periplasm. The leaky phenotype of exbB exbD mutants is caused by partial complementation by homologous tolQ tolR. TonB, ExbB, and ExbD are genuine components of an energy transmission system from the CM into the OM. Mutant analyses, cross-linking experiments, and most recently X-ray and cryo-EM determinations were undertaken to arrive at a model that describes the energy transfer from the CM into the OM. These results are discussed in this paper. ExbB forms a pentamer with a pore inside, in which an ExbD dimer resides. This complex harvests the energy of the pmf and transmits it to TonB. TonB interacts with the TBDT at the TonB box, which triggers a conformational change in the TBDT that releases bound nutrients and opens the pore, through which nutrients pass into the periplasm. The structurally altered TBDT also changes the interactions of its periplasmic signaling domain with anti-sigma factors, with the consequence being that the sigma factors initiate transcription.
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Affiliation(s)
- Volkmar Braun
- Max-Planck-Institute for Biology, Department of Protein Evolution, Tübingen, Germany
| | - Anna C. Ratliff
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
| | - Herve Celia
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
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6
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Zou Z, Potter RF, McCoy WH, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight 2023; 8:e161461. [PMID: 36512427 PMCID: PMC9977300 DOI: 10.1172/jci.insight.161461] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Urinary catheterization facilitates urinary tract colonization by E. coli and increases infection risk. Here, we aimed to identify strain-specific characteristics associated with the transition from colonization to infection in catheterized patients. In a single-site study population, we compared E. coli isolates from patients with catheter-associated asymptomatic bacteriuria (CAASB) to those with catheter-associated urinary tract infection (CAUTI). CAUTI isolates were dominated by a phylotype B2 subclade containing the multidrug-resistant ST131 lineage relative to CAASB isolates, which were phylogenetically more diverse. A distinctive combination of virulence-associated genes was present in the CAUTI-associated B2 subclade. Catheter-associated biofilm formation was widespread among isolates and did not distinguish CAUTI from CAASB strains. Preincubation with CAASB strains could inhibit catheter colonization by multiple ST131 CAUTI isolates. Comparative genomic analysis identified a group of variable genes associated with high catheter biofilm formation present in both CAUTI and CAASB strains. Among these, ferric citrate transport (Fec) system genes were experimentally associated with enhanced catheter biofilm formation using reporter and fecA deletion strains. These results are consistent with a variable role for catheter biofilm formation in promoting CAUTI by ST131-like strains or resisting CAUTI by lower-risk strains that engage in niche exclusion.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
| | - William H. McCoy
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John A. Wildenthal
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - George L. Katumba
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Peter J. Mucha
- Department of Mathematics, Dartmouth College, Hanover, New Hampshire, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
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7
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Conrad RA, Evenhuis JP, Lipscomb RS, Pérez-Pascual D, Stevick RJ, Birkett C, Ghigo JM, McBride MJ. Flavobacterium columnare ferric iron uptake systems are required for virulence. Front Cell Infect Microbiol 2022; 12:1029833. [PMID: 36325469 PMCID: PMC9618737 DOI: 10.3389/fcimb.2022.1029833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Flavobacterium columnare, which causes columnaris disease, is one of the costliest pathogens in the freshwater fish-farming industry. The virulence mechanisms of F. columnare are not well understood and current methods to control columnaris outbreaks are inadequate. Iron is an essential nutrient needed for metabolic processes and is often required for bacterial virulence. F. columnare produces siderophores that bind ferric iron for transport into the cell. The genes needed for siderophore production have been identified, but other components involved in F. columnare iron uptake have not been studied in detail. We identified the genes encoding the predicted secreted heme-binding protein HmuY, the outer membrane iron receptors FhuA, FhuE, and FecA, and components of an ATP binding cassette (ABC) transporter predicted to transport ferric iron across the cytoplasmic membrane. Deletion mutants were constructed and examined for growth defects under iron-limited conditions and for virulence against zebrafish and rainbow trout. Mutants with deletions in genes encoding outer membrane receptors, and ABC transporter components exhibited growth defects under iron-limited conditions. Mutants lacking multiple outer membrane receptors, the ABC transporter, or HmuY retained virulence against zebrafish and rainbow trout mirroring that exhibited by the wild type. Some mutants predicted to be deficient in multiple steps of iron uptake exhibited decreased virulence. Survivors of exposure to such mutants were partially protected against later infection by wild-type F. columnare.
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Affiliation(s)
- Rachel A. Conrad
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Jason P. Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Ryan S. Lipscomb
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - David Pérez-Pascual
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Rebecca J. Stevick
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Clayton Birkett
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Mark J. McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
- *Correspondence: Mark J. McBride,
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8
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The (Bio)Chemistry of Non-Transferrin-Bound Iron. Molecules 2022; 27:molecules27061784. [PMID: 35335148 PMCID: PMC8951307 DOI: 10.3390/molecules27061784] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
In healthy individuals, virtually all blood plasma iron is bound by transferrin. However, in several diseases and clinical conditions, hazardous non-transferrin-bound iron (NTBI) species occur. NTBI represents a potentially toxic iron form, being a direct cause of oxidative stress in the circulating compartment and tissue iron loading. The accumulation of these species can cause cellular damage in several organs, namely, the liver, spleen, and heart. Despite its pathophysiological relevance, the chemical nature of NTBI remains elusive. This has precluded its use as a clinical biochemical marker and the development of targeted therapies. Herein, we make a critical assessment of the current knowledge of NTBI speciation. The currently accepted hypotheses suggest that NTBI is mostly iron bound to citric acid and iron bound to serum albumin, but the chemistry of this system remains fuzzy. We explore the complex chemistry of iron complexation by citric acid and its implications towards NTBI reactivity. Further, the ability of albumin to bind iron is revised and the role of protein post-translational modifications on iron binding is discussed. The characterization of the NTBI species structure may be the starting point for the development of a standardized analytical assay, the better understanding of these species’ reactivity or the identification of NTBI uptake mechanisms by different cell types, and finally, to the development of new therapies.
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9
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The Yersinia High-Pathogenicity Island Encodes a Siderophore-Dependent Copper Response System in Uropathogenic Escherichia coli. mBio 2022; 13:e0239121. [PMID: 35089085 PMCID: PMC8725597 DOI: 10.1128/mbio.02391-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Siderophores are iron chelators used by microbes to bind and acquire iron, which, once in the cell, inhibits siderophore production through feedback repression mediated by the ferric uptake repressor (Fur). Yersiniabactin (Ybt), a siderophore associated with enhanced pathogenic potential among Enterobacteriaceae, also binds copper ions during human and experimental murine infections. In contrast to iron, we found that extracellular copper ions rapidly and selectively stimulate Ybt production in extraintestinal pathogenic Escherichia coli. The stimulatory pathway requires formation of an extracellular copper-Ybt (Cu(II)-Ybt) complex, internalization of Cu(II)-Ybt entry through the canonical TonB-dependent outer membrane transporter, and Fur-independent transcriptional regulation by the specialized transcription factor YbtA. Dual regulation by iron and copper is consistent with a multifunctional metallophore role for Ybt. Feed-forward regulation is typical of stress responses, implicating Ybt in prevention of, or response to, copper stress during infection pathogenesis. IMPORTANCE Interactions between bacteria and transition metal ions play an important role in encounters between humans and bacteria. Siderophore systems have long been prominent mediators of these interactions. These systems secrete small-molecule chelators that bind oxidized iron(III) and express proteins that specifically recognize and import these complexes as a nutritional iron source. While E. coli and other Enterobacteriaceae secrete enterobactin, clinical isolates often secrete an additional siderophore, yersiniabactin (Ybt), which has been found to also bind copper and other non-iron metal ions. The observation here that an extraintestinal E. coli isolate secretes Ybt in a copper-inducible manner suggests an important gain of function over the enterobactin system. Copper recognition involves using Ybt to bind Cu(II) ions, consistent with a distinctively extracellular mode of copper detection. The resulting Cu(II)-Ybt complex signals upregulation of Ybt biosynthesis genes as a rapid response against potentially toxic extracellular copper ions. The Ybt system is distinguishable from other copper response systems that sense cytosolic and periplasmic copper ions. The Ybt dependence of the copper response presents an implicit feed-forward regulatory scheme that is typical of bacterial stress responses. The distinctive extracellular copper recognition-response functionality of the Ybt system may enhance the pathogenic potential of infection-associated Enterobacteriaceae.
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Braun V, Hartmann MD, Hantke K. Transcription regulation of iron carrier transport genes by ECF sigma factors through signaling from the cell surface into the cytoplasm. FEMS Microbiol Rev 2022; 46:6524835. [PMID: 35138377 PMCID: PMC9249621 DOI: 10.1093/femsre/fuac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteria are usually iron-deficient because the Fe3+ in their environment is insoluble or is incorporated into proteins. To overcome their natural iron limitation, bacteria have developed sophisticated iron transport and regulation systems. In gram-negative bacteria, these include iron carriers, such as citrate, siderophores, and heme, which when loaded with Fe3+ adsorb with high specificity and affinity to outer membrane proteins. Binding of the iron carriers to the cell surface elicits a signal that initiates transcription of iron carrier transport and synthesis genes, referred to as “cell surface signaling”. Transcriptional regulation is not coupled to transport. Outer membrane proteins with signaling functions contain an additional N-terminal domain that in the periplasm makes contact with an anti-sigma factor regulatory protein that extends from the outer membrane into the cytoplasm. Binding of the iron carriers to the outer membrane receptors elicits proteolysis of the anti-sigma factor by two different proteases, Prc in the periplasm, and RseP in the cytoplasmic membrane, inactivates the anti-sigma function or results in the generation of an N-terminal peptide of ∼50 residues with pro-sigma activity yielding an active extracytoplasmic function (ECF) sigma factor. Signal recognition and signal transmission into the cytoplasm is discussed herein.
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Affiliation(s)
- Volkmar Braun
- Max Planck Institute for Biology, Department of Protein Evolution, Max Planck Ring 5, 72076 Tübingen, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Biology, Department of Protein Evolution, Max Planck Ring 5, 72076 Tübingen, Germany
| | - Klaus Hantke
- IMIT Institute, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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11
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Jayashree S, Sivakumar R, Karthikeyan R, Gunasekaran P, Rajendhran J. Genome-wide identification of probiotic Escherichia coli Nissle 1917 (EcN) fitness genes during adhesion to the intestinal epithelial cells Caco-2. Gene 2021; 803:145890. [PMID: 34375634 DOI: 10.1016/j.gene.2021.145890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Escherichia coli Nissle 1917 (EcN) is an efficient probiotic strain extensively used worldwide because of its several health benefits. Adhesion to the intestinal cells is one of the prerequisites for a probiotic strain. To identify the genes essential for the adhesion of EcN on the intestinal cells, we utilized a quantitative genetic footprinting approach called transposon insertion sequencing (INSeq). A transposon insertion mutant library of EcN comprising of ~17,000 mutants was used to screen the adherence to the intestinal epithelial cells, Caco-2. The transposon insertion sites were identified from the input and output population by employing next-generation sequencing using the Ion torrent platform. Based on the relative abundance of reads in the input and output pools, we identified 113 candidate genes that are essential for the fitness of EcN during the adhesion and colonization on the Caco-2 cells. Functional categorization revealed that these fitness genes are associated with carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, post-translational modification, stress response, motility and adhesion, and signal transduction. To further validate the genes identified in our INSeq analysis, we constructed individual knock-out mutants in five genes (cyclic di-GMP phosphodiesterase (gmp), hda, uidC, leuO, and hypothetical protein-coding gene). We investigated their ability to adhere to Caco-2 cells. Evaluation of these mutants showed reduced adhesion on Caco-2 cells, confirming their role in adhesion. Understanding the functions of these genes may provide novel insights into molecular regulation during colonization of probiotic bacteria to the intestinal cells, and useful to develop designer probiotic strains.
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Affiliation(s)
| | - Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Raman Karthikeyan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India.
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12
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Zhen ZH, Qin S, Ren QM, Wang Y, Ma YY, Wang YC. Reciprocal Effect of Copper and Iron Regulation on the Proteome of Synechocystis sp. PCC 6803. Front Bioeng Biotechnol 2021; 9:673402. [PMID: 34041232 PMCID: PMC8141849 DOI: 10.3389/fbioe.2021.673402] [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: 02/27/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria can acclimate to changing copper and iron concentrations in the environment via metal homeostasis, but a general mechanism for interpreting their dynamic relationships is sparse. In this study, we assessed growth and chlorophyll fluorescence of Synechocystis sp. PCC 6803 and investigated proteomic responses to copper and iron deductions. Results showed that copper and iron exerted reciprocal effect on the growth and photosynthesis of Synechocystis sp. PCC 6803 at combinations of different concentrations. And some proteins involved in the uptake of copper and iron and the photosynthetic electron transport system exhibit Cu-Fe proteomic association. The protein abundance under copper and iron deduction affected the photosynthetic electronic activity of Synechocystis sp. PCC 6803 and eventually affected the growth and photosynthesis. Based on these results, we hypothesize that the Cu-Fe proteomic association of Synechocystis sp. PCC 6803 can be elucidated via the uptake system of outer membrane-periplasmic space-inner plasma membrane-thylakoid membrane, and this association is mainly required to maintain electron transfer. This study provides a broader view regarding the proteomic association between Cu and Fe in cyanobacteria, which will shed light on the role of these two metal elements in cyanobacterial energy metabolism and biomass accumulation.
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Affiliation(s)
- Zhang-He Zhen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qing-Min Ren
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yu-Ying Ma
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yin-Chu Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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13
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Thomas MD, Ewunkem AJ, Boyd S, Williams DK, Moore A, Rhinehardt KL, Van Beveren E, Yang B, Tapia A, Han J, Harrison SH, Graves JL. Too much of a good thing: Adaption to iron (II) intoxication in Escherichia coli. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:53-67. [PMID: 33717488 PMCID: PMC7937436 DOI: 10.1093/emph/eoaa051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022]
Abstract
Background There has been an increased usage of metallic antimicrobial materials to control pathogenic and multi-drug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. Methodology Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. Results After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-h optical densities compared to controls. Furthermore, these populations showed increased resistance toward other metals [iron (III) and gallium (III)] and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. Conclusions and implications Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern. Lay summary: The evolution of iron resistance in E. coli leads to multi-drug and general metal resistance through the acquisition of mutations in three genes (fecA, ptsP and ilvG) while also initiating cellular defenses as part of their normal growth process.
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Affiliation(s)
- Misty D Thomas
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- BEACON, Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Sada Boyd
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Danielle K Williams
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Adiya Moore
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Kristen L Rhinehardt
- Computational Data Science and Engineering, North Carolina Agricultural and Technical State University, 1601 E. Market Street, Greensboro, NC 27411, USA
| | - Emma Van Beveren
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Bobi Yang
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Anna Tapia
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Jian Han
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Scott H Harrison
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
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14
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Native Cell Environment Constrains Loop Structure in the Escherichia coli Cobalamin Transporter BtuB. Biophys J 2020; 119:1550-1557. [PMID: 32946767 DOI: 10.1016/j.bpj.2020.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 11/23/2022] Open
Abstract
The extracellular loops of bacterial outer membrane (OM) transporters are thought to sample a range of conformations in the apo state but to undergo a gating motion and assume a more defined conformation upon the binding of substrate. Here, we use pulse electron paramagnetic resonance to examine the conformations of the extracellular loops of BtuB, the Escherichia coli TonB-dependent vitamin B12 transporter, in whole cells. Unlike previous measurements carried out in vitro, the loops assume well-defined configurations in situ that closely match the in surfo crystal structures. Moreover, there is no evidence that the loops undergo significant gating motions upon the binding of substrate. The results demonstrate that the structure of BtuB is dependent upon an intact native OM environment, in which a critical component is likely to be the extracellular lipopolysaccharide. In general, this work indicates that measurements on OM proteins in reconstituted membrane systems may not reflect the native state of the protein in vivo.
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15
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Abstract
Coxiella burnetii, the causative agent of Query (Q) fever in humans, is a highly infectious obligate intracellular bacterium. Following uptake into a host cell, C. burnetii replicates within a phagolysosome-derived compartment referred to as the Coxiella-containing vacuole (CCV). During infection, C. burnetii exhibits tropism for tissues related to iron storage and recycling (e.g., the liver and splenic red pulp), suggesting that pathogen physiology is linked to host iron metabolism. Iron has been described to have a limited role in C. burnetii virulence regulation, despite evidence that C. burnetii -infected host cells increase expression of transferrin receptors, thereby suggesting that active iron acquisition by the bacterium occurs upon infection. Through the use of host cell-free culture, C. burnetii was separated from the host cell in order to directly assess the role of different forms of iron in C. burnetii replication and viability, and therefore virulence. Results indicate that C. burnetii tolerates molecular iron over a broad concentration range (i.e., ∼0.001 to 1 mM) and undergoes gross loss of viability upon iron starvation. C. burnetii protein synthesis and energy metabolism, however, occur nearly uninhibited under iron concentrations not permissive to replication. Despite the apparent absence of genes related to acquisition of host-associated iron-containing proteins, C. burnetii replication is supported by hemoglobin, transferrin, and ferritin, likely due to release of iron from such proteins under acidic conditions. Moreover, chelation of host iron pools inhibited pathogen replication during infection of cultured cells.IMPORTANCE Host organisms restrict the availability of iron to invading pathogens in order to reduce pathogen replication. To counteract the host's response to infection, bacteria can rely on redundant mechanisms to obtain biologically diverse forms of iron during infection. C. burnetii appears specifically dependent on molecular iron for replication and viability and exhibits a response to iron akin to bacteria that colonize iron-rich environments. Physiological adaptation of C. burnetii to the unique acidic and degradative environment of the CCV is consistent with access of this pathogen to molecular iron.
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16
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Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli. PLoS Comput Biol 2020; 16:e1008024. [PMID: 32609716 PMCID: PMC7360065 DOI: 10.1371/journal.pcbi.1008024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/14/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Vitamin B12 (or cobalamin) is an enzymatic cofactor essential both for mammals and bacteria. However, cobalamin can be synthesized only by few microorganisms so most bacteria need to take it up from the environment through the TonB-dependent transport system. The first stage of cobalamin import to E. coli cells occurs through the outer-membrane receptor called BtuB. Vitamin B12 binds with high affinity to the extracellular side of the BtuB protein. BtuB forms a β-barrel with inner luminal domain and extracellular loops. To mechanically allow for cobalamin passage, the luminal domain needs to partially unfold with the help of the inner-membrane TonB protein. However, the mechanism of cobalamin permeation is unknown. Using all-atom molecular dynamics, we simulated the transport of cobalamin through the BtuB receptor embedded in an asymmetric and heterogeneous E. coli outer-membrane. To enhance conformational sampling of the BtuB loops, we developed the Gaussian force-simulated annealing method (GF-SA) and coupled it with umbrella sampling. We found that cobalamin needs to rotate in order to permeate through BtuB. We showed that the mobility of BtuB extracellular loops is crucial for cobalamin binding and transport and resembles an induced-fit mechanism. Loop mobility depends not only on the position of cobalamin but also on the extension of luminal domain. We provided atomistic details of cobalamin transport through the BtuB receptor showing the essential role of the mobility of BtuB extracellular loops. A similar TonB-dependent transport system is used also by many other compounds, such as haem and siderophores, and importantly, can be hijacked by natural antibiotics. Our work could have implications for future delivery of antibiotics to bacteria using this transport system.
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17
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Abstract
The transcription initiation signal elicited by the binding of ferric citrate to the outer membrane FecA protein is transmitted by the FecR protein across the cytoplasmic membrane to the FecI extracytoplasmic function (ECF) sigma factor. In this issue of Journal of Bacteriology, I. J. Passmore, J. M. Dow, F. Coll, J. Cuccui, et al. (J Bacteriol 202:e00541-19, 2020, https://doi.org/10.1128/JB.00541-19) report that the FecR sequence contains both the twin-arginine signal motif and the secretory (Sec) avoidance motif typical of proteins secreted by the twin-arginine translocation (TAT) system. The same study shows that FecR is indeed secreted by Tat and represents a new class of bitopic Tat-dependent membrane proteins.
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18
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Samantarrai D, Lakshman Sagar A, Gudla R, Siddavattam D. TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation. Microorganisms 2020; 8:microorganisms8030359. [PMID: 32138166 PMCID: PMC7142613 DOI: 10.3390/microorganisms8030359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane.
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19
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Valderrama K, Balado M, Rey-Varela D, Rodríguez J, Vila-Sanjurjo A, Jiménez C, Lemos ML. Outer membrane protein FrpA, the siderophore piscibactin receptor of Photobacterium damselae subsp. piscicida, as a subunit vaccine against photobacteriosis in sole (Solea senegalensis). FISH & SHELLFISH IMMUNOLOGY 2019; 94:723-729. [PMID: 31580933 DOI: 10.1016/j.fsi.2019.09.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/03/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
Photobacteriosis caused by Photobacterium damselae subsp. piscicida (Pdp) remains one of the main infectious diseases affecting cultured fish in Mediterranean countries. Diverse vaccine formulations based in the use of inactivated bacterial cells have been used with unsatisfactory results, especially in newly cultured species like sole (Solea senegalensis). In this work, we describe the use of the outer membrane receptor (FrpA) of the siderophore piscibactin produced by Pdp as a novel subunit vaccine against photobacteriosis. FrpA has been cloned and expressed in Escherichia coli under an arabinose-inducible promoter. A recombinant protein (rFrpA) containing the pelB localization signal and a His tag was constructed to obtain a pure native form of the protein from E. coli outer membranes. The immunogenicity of rFrpA, and its protective effect against photobacteriosis, was tested by i.p. injection of 30 μg of the protein, mixed with Freund's adjuvant, in sole fingerlings with two immunizations separated by 30 days. Results showed that using either pure rFrpA or whole cells as immobilized antigens in ELISA assays, rFrpA induces the production of specific antibodies in sole. An experimental infection using fish vaccinated with rFrpA or formalin-killed whole cells of Pdp showed that both groups were protected against Pdp infection at similar levels, with no significant differences, reaching RPS values of 73% and 79%, respectively. Thus, FrpA constitutes a promising antigen candidate for the development of novel more effective vaccines against fish photobacteriosis.
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Affiliation(s)
- Katherine Valderrama
- Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Coruña, 15071 A, Spain; Grupo GIBE, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, Coruña, 15071 A, Spain
| | - Miguel Balado
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Diego Rey-Varela
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Jaime Rodríguez
- Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Coruña, 15071 A, Spain
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, Coruña, 15071 A, Spain.
| | - Carlos Jiménez
- Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Coruña, 15071 A, Spain.
| | - Manuel L Lemos
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
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20
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Graves JL, Ewunkem AJ, Ward J, Staley C, Thomas MD, Rhinehardt KL, Han J, Harrison SH. Experimental evolution of gallium resistance in Escherichia coli. EVOLUTION MEDICINE AND PUBLIC HEALTH 2019; 2019:169-180. [PMID: 31890209 PMCID: PMC6928379 DOI: 10.1093/emph/eoz025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/29/2019] [Indexed: 12/26/2022]
Abstract
Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.
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Affiliation(s)
- Joseph L Graves
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Akamu J Ewunkem
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Jason Ward
- High School Science Teacher, Davie Public High School, Davie, NC, USA
| | | | - Misty D Thomas
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - Kristen L Rhinehardt
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Jian Han
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - Scott H Harrison
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
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21
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Josts I, Veith K, Tidow H. Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake. eLife 2019; 8:48528. [PMID: 31385808 PMCID: PMC6699858 DOI: 10.7554/elife.48528] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/05/2019] [Indexed: 01/27/2023] Open
Abstract
Many microbes and fungi acquire the essential ion Fe3+ through the synthesis and secretion of high-affinity chelators termed siderophores. In Gram-negative bacteria, these ferric-siderophore complexes are actively taken up using highly specific TonB-dependent transporters (TBDTs) located in the outer bacterial membrane (OM). However, the detailed mechanism of how the inner-membrane protein TonB connects to the transporters in the OM as well as the interplay between siderophore- and TonB-binding to the transporter is still poorly understood. Here, we present three crystal structures of the TBDT FoxA from Pseudomonas aeruginosa (containing a signalling domain) in complex with the siderophore ferrioxamine B and TonB and combine them with a detailed analysis of binding constants. The structures show that both siderophore and TonB-binding is required to form a translocation-competent state of the FoxA transporter in a two-step TonB-binding mechanism. The complex structure also indicates how TonB-binding influences the orientation of the signalling domain.
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Affiliation(s)
- Inokentijs Josts
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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22
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Moraleda-Muñoz A, Marcos-Torres FJ, Pérez J, Muñoz-Dorado J. Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors. Mol Microbiol 2019; 112:385-398. [PMID: 31187912 PMCID: PMC6851896 DOI: 10.1111/mmi.14328] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
In order to survive, bacteria must adapt to multiple fluctuations in their environment, including coping with changes in metal concentrations. Many metals are essential for viability, since they act as cofactors of indispensable enzymes. But on the other hand, they are potentially toxic because they generate reactive oxygen species or displace other metals from proteins, turning them inactive. This dual effect of metals forces cells to maintain homeostasis using a variety of systems to import and export them. These systems are usually inducible, and their expression is regulated by metal sensors and signal‐transduction mechanisms, one of which is mediated by extracytoplasmic function (ECF) sigma factors. In this review, we have focused on the metal‐responsive ECF sigma factors, several of which are activated by iron depletion (FecI, FpvI and PvdS), while others are activated by excess of metals such as nickel and cobalt (CnrH), copper (CarQ and CorE) or cadmium and zinc (CorE2). We focus particularly on their physiological roles, mechanisms of action and signal transduction pathways.
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Affiliation(s)
- Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
| | - Francisco Javier Marcos-Torres
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
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23
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Mogul R, Barding GA, Lalla S, Lee S, Madrid S, Baki R, Ahmed M, Brasali H, Cepeda I, Gornick T, Gunadi S, Hearn N, Jain C, Kim EJ, Nguyen T, Nguyen VB, Oei A, Perkins N, Rodriguez J, Rodriguez V, Savla G, Schmitz M, Tedjakesuma N, Walker J. Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter. ASTROBIOLOGY 2018; 18:1517-1527. [PMID: 29672134 PMCID: PMC6276816 DOI: 10.1089/ast.2017.1814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 05/17/2023]
Abstract
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gregory A. Barding
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sidharth Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sooji Lee
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Steve Madrid
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ryan Baki
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Mahjabeen Ahmed
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Hania Brasali
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ivonne Cepeda
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Trevor Gornick
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Shawn Gunadi
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Hearn
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Chirag Jain
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Eun Jin Kim
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Thi Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Vinh Bao Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Perkins
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gautam Savla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Megan Schmitz
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicholas Tedjakesuma
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Jillian Walker
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
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24
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Chen X, Sun C, Laborda P, Zhao Y, Palmer I, Fu ZQ, Qiu J, Liu F. Melatonin Treatment Inhibits the Growth of Xanthomonas oryzae pv. oryzae. Front Microbiol 2018; 9:2280. [PMID: 30337911 PMCID: PMC6180160 DOI: 10.3389/fmicb.2018.02280] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes rice bacterial blight (BB), one of the most widespread and destructive diseases in rice-growing regions worldwide. Melatonin enhances pathogen resistance by inducing plant innate immunity, but the direct effect of melatonin on plant pathogenic bacteria is poorly understood. In this study, we investigated the direct effects of melatonin on Xoo. Exogenous melatonin at 200 μg/mL significantly inhibited the proliferation of Xoo and reduced the mRNA expression of five genes involved in cell division. This concentration of melatonin also inhibited the motility and biofilm formation of Xoo. Notably, melatonin was observed to alter the length of Xoo cells. To provide deeper insights into the mechanisms underlying this antibacterial activity, we examined global gene expression changes in Xoo strain PXO99 in response to the application of 200 μg/mL melatonin using RNA sequencing (RNA-Seq). A wide range of differentially expressed genes (DEGs) related to catalytic activity and metal-binding activity were downregulated in Xoo cells in response to the melatonin treatment. In addition, DEGs responsible for carbohydrate and amino acid metabolism were also downregulated. These results suggest that the inhibitory mechanism of melatonin on Xoo proliferation may involve the regulation of cell division in combination with a reduction in the concentration or activity of enzymes involved in metabolism.
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Affiliation(s)
- Xian Chen
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Cheng Sun
- School of Medicine, Yangzhou Polytechnic College, Yangzhou, China
| | - Pedro Laborda
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ian Palmer
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Jingping Qiu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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25
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Braun V. The Outer Membrane Took Center Stage. Annu Rev Microbiol 2018; 72:1-24. [PMID: 30200853 DOI: 10.1146/annurev-micro-090817-062156] [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: 11/09/2022]
Abstract
My interest in membranes was piqued during a lecture series given by one of the founders of molecular biology, Max Delbrück, at Caltech, where I spent a postdoctoral year to learn more about protein chemistry. That general interest was further refined to my ultimate research focal point-the outer membrane of Escherichia coli-through the influence of the work of Wolfhard Weidel, who discovered the murein (peptidoglycan) layer and biochemically characterized the first phage receptors of this bacterium. The discovery of lipoprotein bound to murein was completely unexpected and demonstrated that the protein composition of the outer membrane and the structure and function of proteins could be unraveled at a time when nothing was known about outer membrane proteins. The research of my laboratory over the years covered energy-dependent import of proteinaceous toxins and iron chelates across the outer membrane, which does not contain an energy source, and gene regulation by iron, including transmembrane transcriptional regulation.
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Affiliation(s)
- Volkmar Braun
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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26
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Luscher A, Moynié L, Auguste PS, Bumann D, Mazza L, Pletzer D, Naismith JH, Köhler T. TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates. Antimicrob Agents Chemother 2018; 62:e00097-18. [PMID: 29555629 PMCID: PMC5971595 DOI: 10.1128/aac.00097-18] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
The conjugation of siderophores to antimicrobial molecules is an attractive strategy to overcome the low outer membrane permeability of Gram-negative bacteria. In this Trojan horse approach, the transport of drug conjugates is redirected via TonB-dependent receptors (TBDR), which are involved in the uptake of essential nutrients, including iron. Previous reports have demonstrated the involvement of the TBDRs PiuA and PirA from Pseudomonas aeruginosa and their orthologues in Acinetobacter baumannii in the uptake of siderophore-beta-lactam drug conjugates. By in silico screening, we further identified a PiuA orthologue, termed PiuD, present in clinical isolates, including strain LESB58. The piuD gene in LESB58 is located at the same genetic locus as piuA in strain PAO1. PiuD has a similar crystal structure as PiuA and is involved in the transport of the siderophore-drug conjugates BAL30072, MC-1, and cefiderocol in strain LESB58. To screen for additional siderophore-drug uptake systems, we overexpressed 28 of the 34 TBDRs of strain PAO1 and identified PfuA, OptE, OptJ, and the pyochelin receptor FptA as novel TBDRs conferring increased susceptibility to siderophore-drug conjugates. The existence of a TBDR repertoire in P. aeruginosa able to transport siderophore-drug molecules potentially decreases the likelihood of resistance emergence during therapy.
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Affiliation(s)
- Alexandre Luscher
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lucile Moynié
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | | | - Dirk Bumann
- Biozentrum, University of Basel, Basel, Switzerland
| | - Lena Mazza
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - James H Naismith
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | - Thilo Köhler
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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27
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Genome-Wide Identification of Fitness Factors in Mastitis-Associated Escherichia coli. Appl Environ Microbiol 2018; 84:AEM.02190-17. [PMID: 29101196 DOI: 10.1128/aem.02190-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
Virulence factors of mammary pathogenic Escherichia coli (MPEC) have not been identified, and it is not known how bacterial gene content influences the severity of mastitis. Here, we report a genome-wide identification of genes that contribute to fitness of MPEC under conditions relevant to the natural history of the disease. A highly virulent clinical isolate (M12) was identified that killed Galleria mellonella at low infectious doses and that replicated to high numbers in mouse mammary glands and spread to spleens. Genome sequencing was combined with transposon insertion site sequencing to identify MPEC genes that contribute to growth in unpasteurized whole milk, as well as during G. mellonella and mouse mastitis infections. These analyses show that strain M12 possesses a unique genomic island encoding a group III polysaccharide capsule that greatly enhances virulence in G. mellonella Several genes appear critical for MPEC survival in both G. mellonella and in mice, including those for nutrient-scavenging systems and resistance to cellular stress. Insertions in the ferric dicitrate receptor gene fecA caused significant fitness defects under all conditions (in milk, G. mellonella, and mice). This gene was highly expressed during growth in milk. Targeted deletion of fecA from strain M12 caused attenuation in G. mellonella larvae and reduced growth in unpasteurized cow's milk and lactating mouse mammary glands. Our results confirm that iron scavenging by the ferric dicitrate receptor, which is strongly associated with MPEC strains, is required for MPEC growth and may influence disease severity in mastitis infections.IMPORTANCE Mastitis caused by E. coli inflicts substantial burdens on the health and productivity of dairy animals. Strains causing mastitis may express genes that distinguish them from other E. coli strains and promote infection of mammary glands, but these have not been identified. Using a highly virulent strain, we employed genome-wide mutagenesis and sequencing to discover genes that contribute to mastitis. This extensive data set represents a screen for mastitis-associated E. coli fitness factors and provides the following contributions to the field: (i) global comparison of genes required for different aspects of mastitis infection, (ii) discovery of a unique capsule that contributes to virulence, and (iii) conclusive evidence for the crucial role of iron-scavenging systems in mastitis, particularly the ferric dicitrate transport system. Similar approaches applied to other mastitis-associated strains will uncover conserved targets for prevention or treatment and provide a better understanding of their relationship to other E. coli pathogens.
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28
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Putz I, Brock O. Elastic network model of learned maintained contacts to predict protein motion. PLoS One 2017; 12:e0183889. [PMID: 28854238 PMCID: PMC5576689 DOI: 10.1371/journal.pone.0183889] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
We present a novel elastic network model, lmcENM, to determine protein motion even for localized functional motions that involve substantial changes in the protein's contact topology. Existing elastic network models assume that the contact topology remains unchanged throughout the motion and are thus most appropriate to simulate highly collective function-related movements. lmcENM uses machine learning to differentiate breaking from maintained contacts. We show that lmcENM accurately captures functional transitions unexplained by the classical ENM and three reference ENM variants, while preserving the simplicity of classical ENM. We demonstrate the effectiveness of our approach on a large set of proteins covering different motion types. Our results suggest that accurately predicting a "deformation-invariant" contact topology offers a promising route to increase the general applicability of ENMs. We also find that to correctly predict this contact topology a combination of several features seems to be relevant which may vary slightly depending on the protein. Additionally, we present case studies of two biologically interesting systems, Ferric Citrate membrane transporter FecA and Arachidonate 15-Lipoxygenase.
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Affiliation(s)
- Ines Putz
- Robotics and Biology Laboratory, Department of Computer Science and Electrical Engineering, Technische Universität Berlin, Berlin, Berlin, Germany
| | - Oliver Brock
- Robotics and Biology Laboratory, Department of Computer Science and Electrical Engineering, Technische Universität Berlin, Berlin, Berlin, Germany
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29
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Meneghini LM, Tripathi S, Woodworth MA, Majumdar S, Poulos TL, Weiss GA. Dissecting binding of a β-barrel membrane protein by phage display. MOLECULAR BIOSYSTEMS 2017; 13:1438-1447. [PMID: 28627567 PMCID: PMC5564213 DOI: 10.1039/c7mb00163k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membrane proteins (MPs) constitute a third of all proteomes, and contribute to a myriad of cellular functions including intercellular communication, nutrient transport and energy generation. For example, TonB-dependent transporters (TBDTs) in the outer membrane of Gram-negative bacteria play an essential role transporting iron and other nutrients into the bacterial cell. The inherently hydrophobic surfaces of MPs complicates protein expression, purification, and characterization. Thus, dissecting the functional contributions of individual amino acids or structural features through mutagenesis can be a challenging ordeal. Here, we apply a new approach for the expedited protein characterization of the TBDT ShuA from Shigella dysenteriae, and elucidate the protein's initial steps during heme-uptake. ShuA variants were displayed on the surface of an M13 bacteriophage as fusions to the P8 coat protein. Each ShuA variant was analyzed for its ability to display on the bacteriophage surface, and functionally bind to hemoglobin. This technique streamlines isolation of stable MP variants for rapid characterization of binding to various ligands. Site-directed mutagenesis studies targeting each extracellular loop region of ShuA demonstrate no specific extracellular loop is required for hemoglobin binding. Instead two residues, His420 and His86 mediate this interaction. The results identify a loop susceptible to antibody binding, and also a small molecule motif capable of disrupting ShuA from S. dysenteriae. The approach is generalizable to the dissection of other phage-displayed TBDTs and MPs.
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Affiliation(s)
- Luz M Meneghini
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| | - Sarvind Tripathi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| | - Marcus A Woodworth
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA. and Department of Chemistry, University of California, Irvine, CA, USA
| | - Gregory A Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA. and Department of Chemistry, University of California, Irvine, CA, USA
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30
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Sikora A, Joseph B, Matson M, Staley JR, Cafiso DS. Allosteric Signaling Is Bidirectional in an Outer-Membrane Transport Protein. Biophys J 2017; 111:1908-1918. [PMID: 27806272 DOI: 10.1016/j.bpj.2016.09.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/14/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022] Open
Abstract
In BtuB, the Escherichia coli TonB-dependent transporter for vitamin B12, substrate binding to the extracellular surface unfolds a conserved energy coupling motif termed the Ton box into the periplasm. This transmembrane signaling event facilitates an interaction between BtuB and the inner-membrane protein TonB. In this study, continuous-wave and pulse electron paramagnetic resonance in a native outer-membrane preparation demonstrate that signaling also occurs from the periplasmic to the extracellular surface in BtuB. The binding of a TonB fragment to the periplasmic interface alters the configuration of the second extracellular loop and partially dissociates a spin-labeled substrate analog. Moreover, mutants in the periplasmic Ton box that are transport-defective alter the binding site for vitamin B12 in BtuB. This work demonstrates that the Ton box and the extracellular substrate binding site are allosterically coupled in BtuB, and that TonB binding may initiate a partial round of transport.
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Affiliation(s)
- Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Benesh Joseph
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Morgan Matson
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Jacob R Staley
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
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31
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Going Outside the TonB Box: Identification of Novel FepA-TonB Interactions In Vivo. J Bacteriol 2017; 199:JB.00649-16. [PMID: 28264993 DOI: 10.1128/jb.00649-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/15/2017] [Indexed: 01/30/2023] Open
Abstract
In Gram-negative bacteria, the cytoplasmic membrane protein TonB transmits energy derived from proton motive force to energize transport of important nutrients through TonB-dependent transporters in the outer membrane. Each transporter consists of a beta barrel domain and a lumen-occluding cork domain containing an essential sequence called the TonB box. To date, the only identified site of transporter-TonB interaction is between the TonB box and residues ∼158 to 162 of TonB. While the mechanism of ligand transport is a mystery, a current model based on site-directed spin labeling and molecular dynamics simulations is that, following ligand binding, the otherwise-sequestered TonB box extends into the periplasm for recognition by TonB, which mediates transport by pulling or twisting the cork. In this study, we tested that hypothesis with the outer membrane transporter FepA using in vivo photo-cross-linking to explore interactions of its TonB box and determine whether additional FepA-TonB interaction sites exist. We found numerous specific sites of FepA interaction with TonB on the periplasmic face of the FepA cork in addition to the TonB box. Two residues, T32 and A33, might constitute a ligand-sensitive conformational switch. The facts that some interactions were enhanced in the absence of ligand and that other interactions did not require the TonB box argued against the current model and suggested that the transport process is more complex than originally conceived, with subtleties that might provide a mechanism for discrimination among ligand-loaded transporters. These results constitute the first study on the dynamics of TonB-gated transporter interaction with TonB in vivoIMPORTANCE The TonB system of Gram-negative bacteria has a noncanonical active transport mechanism involving signal transduction and proteins integral to both membranes. To achieve transport, the cytoplasmic membrane protein TonB physically contacts outer membrane transporters such as FepA. Only one contact between TonB and outer membrane transporters has been identified to date: the TonB box at the transporter amino terminus. The TonB box has low information content, raising the question of how TonB can discriminate among multiple different TonB-dependent transporters present in the bacterium if it is the only means of contact. Here we identified several additional sites through which FepA contacts TonB in vivo, including two neighboring residues that may explain how FepA signals to TonB that ligand has bound.
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32
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Xia W. Competition for Iron Between Host and Pathogen: A Structural Case Study on Helicobacter pylori. Methods Mol Biol 2017; 1535:65-75. [PMID: 27914073 DOI: 10.1007/978-1-4939-6673-8_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Helicobacter pylori (H. pylori) is a highly successful bacterial pathogen, which colonizes the stomach of more than half of the world's population. To colonize and survive in such an acidic and inhospitable niche, H. pylori cells have evolved complex mechanisms to acquire nutrients from human hosts, including iron, an essential nutrient for both the pathogens and host cells. However, human cells also utilize diverse strategies in withholding of irons to prevent the bacterial outgrowth. The competition for iron is the central battlefield between pathogen and host. This mini-review summarizes the updated scenarios of the battle for iron between H. pylori and human host from a structural biology perspective.
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Affiliation(s)
- Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 135 West Xingang Road, Guangzhou 510275, China.
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33
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Ferreira MR, Dantas JM, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the electron acceptor Fe(iii) citrate studied by NMR. Dalton Trans 2017; 46:2350-2359. [DOI: 10.1039/c6dt04129a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular interactions betweenGeobacter sulfurreducenstriheme cytochromes and Fe(iii) citrate.
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Affiliation(s)
- Marisa R. Ferreira
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Joana M. Dantas
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Carlos A. Salgueiro
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
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34
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TonB-dependent ligand trapping in the BtuB transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3105-3112. [DOI: 10.1016/j.bbamem.2016.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/22/2022]
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35
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Banerjee S, Paul S, Nguyen LT, Chu BCH, Vogel HJ. FecB, a periplasmic ferric-citrate transporter from E. coli, can bind different forms of ferric-citrate as well as a wide variety of metal-free and metal-loaded tricarboxylic acids. Metallomics 2016; 8:125-33. [PMID: 26600288 DOI: 10.1039/c5mt00218d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Escherichia coli Fec system, consisting of an outer membrane receptor (FecA), a periplasmic substrate binding protein (FecB) and an inner membrane permease-ATPase type transporter (FecC/D), plays an important role in the uptake and transport of Fe(3+)-citrate. Although several FecB sequences from various organisms have been reported, there are no biophysical or structural data available for this protein to date. In this work, using isothermal titration calorimetry (ITC), we report for the first time the ability of FecB to bind different species of Fe(3+)-citrate as well as other citrate complexes with trivalent (Ga(3+), Al(3+), Sc(3+) and In(3+)) and a representative divalent metal ion (Mg(2+)) with low μM affinity. Interestingly, ITC experiments with various iron-free di- and tricarboxylic acids show that FecB can bind tricarboxylates with μM affinity but not biologically relevant dicarboxylates. The ability of FecB to bind with metal-free citrate is also observed in (1)H,(15)N HSQC-NMR titration experiments reported here at two different pH values. Further, differential scanning calorimetry (DSC) experiments indicate that the ligand-bound form of FecB has greater thermal stability than ligand-free FecB under all pH and ligand conditions tested, which is consistent with the idea of domain closure subsequent to ligand binding for this type of periplasmic binding proteins.
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Affiliation(s)
- Sambuddha Banerjee
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
| | - Subrata Paul
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
| | - Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
| | - Byron C H Chu
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
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36
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Wu X, Ren G, Gunning WT, Weaver DA, Kalinoski AL, Khuder SA, Huntley JF. FmvB: A Francisella tularensis Magnesium-Responsive Outer Membrane Protein that Plays a Role in Virulence. PLoS One 2016; 11:e0160977. [PMID: 27513341 PMCID: PMC4981453 DOI: 10.1371/journal.pone.0160977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/26/2016] [Indexed: 02/06/2023] Open
Abstract
Francisella tularensis is the causative agent of the lethal disease tularemia. Despite decades of research, little is understood about why F. tularensis is so virulent. Bacterial outer membrane proteins (OMPs) are involved in various virulence processes, including protein secretion, host cell attachment, and intracellular survival. Many pathogenic bacteria require metals for intracellular survival and OMPs often play important roles in metal uptake. Previous studies identified three F. tularensis OMPs that play roles in iron acquisition. In this study, we examined two previously uncharacterized proteins, FTT0267 (named fmvA, for Francisellametal and virulence) and FTT0602c (fmvB), which are homologs of the previously studied F. tularensis iron acquisition genes and are predicted OMPs. To study the potential roles of FmvA and FmvB in metal acquisition and virulence, we first examined fmvA and fmvB expression following pulmonary infection of mice, finding that fmvB was upregulated up to 5-fold during F. tularensis infection of mice. Despite sequence homology to previously-characterized iron-acquisition genes, FmvA and FmvB do not appear to be involved iron uptake, as neither fmvA nor fmvB were upregulated in iron-limiting media and neither ΔfmvA nor ΔfmvB exhibited growth defects in iron limitation. However, when other metals were examined in this study, magnesium-limitation significantly induced fmvB expression, ΔfmvB was found to express significantly higher levels of lipopolysaccharide (LPS) in magnesium-limiting medium, and increased numbers of surface protrusions were observed on ΔfmvB in magnesium-limiting medium, compared to wild-type F. tularensis grown in magnesium-limiting medium. RNA sequencing analysis of ΔfmvB revealed the potential mechanism for increased LPS expression, as LPS synthesis genes kdtA and wbtA were significantly upregulated in ΔfmvB, compared with wild-type F. tularensis. To provide further evidence for the potential role of FmvB in magnesium uptake, we demonstrated that FmvB was outer membrane-localized. Finally, ΔfmvB was found to be attenuated in mice and cytokine analyses revealed that ΔfmvB-infected mice produced lower levels of pro-inflammatory cytokines, including GM-CSF, IL-3, and IL-10, compared with mice infected with wild-type F. tularensis. Taken together, although the function of FmvA remains unknown, FmvB appears to play a role in magnesium uptake and F. tularensis virulence. These results may provide new insights into the importance of magnesium for intracellular pathogens.
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Affiliation(s)
- Xiaojun Wu
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Guoping Ren
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - William T. Gunning
- Department of Pathology and Electron Microscopy Facility, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - David A. Weaver
- Department of Surgery and Advanced Microscopy and Imaging Center, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Andrea L. Kalinoski
- Department of Surgery and Advanced Microscopy and Imaging Center, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Sadik A. Khuder
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Jason F. Huntley
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
- * E-mail:
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37
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An overview of siderophores for iron acquisition in microorganisms living in the extreme. Biometals 2016; 29:551-71. [PMID: 27457587 DOI: 10.1007/s10534-016-9949-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022]
Abstract
Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.
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Abstract
Two membranes enclose Gram-negative bacteria-an inner membrane consisting of phospholipid and an outer membrane having an asymmetric structure in which the inner leaflet contains phospholipid and the outer leaflet consists primarily of lipopolysaccharide. The impermeable nature of the outer membrane imposes a need for numerous outer membrane pores and transporters to ferry substances in and out of the cell. These outer membrane proteins have structures distinct from their inner membrane counterparts and most often function without any discernable energy source. In this chapter, we review the structures and functions of four classes of outer membrane protein: general and specific porins, specific transporters, TonB-dependent transporters, and export channels. While not an exhaustive list, these classes exemplify small-molecule transport across the outer membrane and illustrate the diversity of structures and functions found in Gram-negative bacteria.
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Naz A, Awan FM, Obaid A, Muhammad SA, Paracha RZ, Ahmad J, Ali A. Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 32:280-291. [PMID: 25818402 DOI: 10.1016/j.meegid.2015.03.027] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori (H. pylori) is an important pathogen associated with diverse gastric disorders ranging from peptic ulcer to malignancy. It has also been recognized by the World Health Organization (WHO) as class I carcinogen. Conventional treatment regimens for H. pylori seem to be ineffective, possibly due to antibiotic resistance mechanisms acquired by the pathogen. In this study we have successfully employed a reverse vaccinology approach to predict the potential vaccine candidates against H. pylori. The predicted potential vaccine candidates include vacA, babA, sabA, fecA and omp16. Host-pathogen interactions analysis elaborated their direct or indirect role in the specific signaling pathways including epithelial cell polarity, metabolism, secretion system and transport. Furthermore, surface-exposed antigenic epitopes were predicted and analyzed for conservation among 39 complete genomes of H. pylori (Genbank) for all the candidate proteins. These epitopes may serve as a base for the development of broad spectrum peptide or multi-component vaccines against H. pylori. We also believe that the proposed pipeline can be extended to other pathogens and for the identification of novel candidates for the development of effective vaccines.
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Affiliation(s)
- Anam Naz
- Computational Biology and Genomics (CBG) Research Group, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
| | - Faryal Mehwish Awan
- Computational Biology and Genomics (CBG) Research Group, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
| | - Ayesha Obaid
- Computational Biology and Genomics (CBG) Research Group, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.
| | - Rehan Zafar Paracha
- Computational Biology and Genomics (CBG) Research Group, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
| | - Jamil Ahmad
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
| | - Amjad Ali
- Computational Biology and Genomics (CBG) Research Group, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad, Pakistan.
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Kleinschmidt JH. Folding of β-barrel membrane proteins in lipid bilayers - Unassisted and assisted folding and insertion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1927-43. [PMID: 25983306 DOI: 10.1016/j.bbamem.2015.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 01/08/2023]
Abstract
In cells, β-barrel membrane proteins are transported in unfolded form to an outer membrane into which they fold and insert. Model systems have been established to investigate the mechanisms of insertion and folding of these versatile proteins into detergent micelles, lipid bilayers and even synthetic amphipathic polymers. In these experiments, insertion into lipid membranes is initiated from unfolded forms that do not display residual β-sheet secondary structure. These studies therefore have allowed the investigation of membrane protein folding and insertion in great detail. Folding of β-barrel membrane proteins into lipid bilayers has been monitored from unfolded forms by dilution of chaotropic denaturants that keep the protein unfolded as well as from unfolded forms present in complexes with molecular chaperones from cells. This review is aimed to provide an overview of the principles and mechanisms observed for the folding of β-barrel transmembrane proteins into lipid bilayers, the importance of lipid-protein interactions and the function of molecular chaperones and folding assistants. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Jörg H Kleinschmidt
- Abteilung Biophysik, Institut für Biologie, FB 10, Universität Kassel and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
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Meyer A, Dierks K, Hussein R, Brillet K, Brognaro H, Betzel C. Systematic analysis of protein-detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials. Acta Crystallogr F Struct Biol Commun 2015; 71:75-81. [PMID: 25615974 PMCID: PMC4304753 DOI: 10.1107/s2053230x14027149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/11/2014] [Indexed: 11/12/2022] Open
Abstract
Detergents are widely used for the isolation and solubilization of membrane proteins to support crystallization and structure determination. Detergents are amphiphilic molecules that form micelles once the characteristic critical micelle concentration (CMC) is achieved and can solubilize membrane proteins by the formation of micelles around them. The results are presented of a study of micelle formation observed by in situ dynamic light-scattering (DLS) analyses performed on selected detergent solutions using a newly designed advanced hardware device. DLS was initially applied in situ to detergent samples with a total volume of approximately 2 µl. When measured with DLS, pure detergents show a monodisperse radial distribution in water at concentrations exceeding the CMC. A series of all-trans n-alkyl-β-D-maltopyranosides, from n-hexyl to n-tetradecyl, were used in the investigations. The results obtained verify that the application of DLS in situ is capable of distinguishing differences in the hydrodynamic radii of micelles formed by detergents differing in length by only a single CH2 group in their aliphatic tails. Subsequently, DLS was applied to investigate the distribution of hydrodynamic radii of membrane proteins and selected water-insoluble proteins in presence of detergent micelles. The results confirm that stable protein-detergent complexes were prepared for (i) bacteriorhodopsin and (ii) FetA in complex with a ligand as examples of transmembrane proteins. A fusion of maltose-binding protein and the Duck hepatitis B virus X protein was added to this investigation as an example of a non-membrane-associated protein with low water solubility. The increased solubility of this protein in the presence of detergent could be monitored, as well as the progress of proteolytic cleavage to separate the fusion partners. This study demonstrates the potential of in situ DLS to optimize solutions of protein-detergent complexes for crystallization applications.
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Affiliation(s)
- Arne Meyer
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karsten Dierks
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- XtalConcepts, Marlowring 19, 22525 Hamburg, Germany
| | - Rana Hussein
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karl Brillet
- UMR 7242–IMPReSs Platform, ESBS, Pôle API, 300 Boulevard Sébastien Brant, CS10413, 67412 Illkirch CEDEX, France
| | - Hevila Brognaro
- Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, Caixa Postal 136, São José do Rio Preto-SP, 15054, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
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Cafiso DS. Identifying and quantitating conformational exchange in membrane proteins using site-directed spin labeling. Acc Chem Res 2014; 47:3102-9. [PMID: 25152957 PMCID: PMC4204925 DOI: 10.1021/ar500228s] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Protein structures are not static but sample different conformations
over a range of amplitudes and time scales. These fluctuations may
involve relatively small changes in bond angles or quite large rearrangements
in secondary structure and tertiary fold. The equilibrium between
discrete structural substates on the microsecond to millisecond time
scale is sometimes termed conformational exchange. Protein dynamics
and conformational exchange are believed to provide the basis for
many important activities, such as protein–protein and protein–ligand
interactions, enzymatic activity and protein allostery; however, for
many proteins, the dynamics and conformational exchange that lead
to function are poorly defined. Spectroscopic methods, such
as NMR, are among the most important
methods to explore protein dynamics and conformational exchange; however,
they are difficult to implement in some systems and with some types
of exchange events. Site-directed spin labeling (SDSL) is an EPR based
approach that is particularly well-suited to high molecular-weight
systems such as membrane proteins. Because of the relatively fast
time scale for EPR spectroscopy, it is an excellent method to examine
exchange. Conformations that are in exchange are captured as distinct
populations in the EPR spectrum, and this feature when combined with
the use of methods that can shift the free energy of conformational
substates allows one to identify regions of proteins that are in dynamic
exchange. In addition, modern pulse EPR methods have the ability to
examine conformational heterogeneity, resolve discrete protein states,
and identify the substates in exchange. Protein crystallography
has provided high-resolution models for
a number of membrane proteins; but because of conformational exchange,
these models do not always reflect the structures that are present
when the protein is in a native bilayer environment. In the case of
the Escherichia coli vitamin B12 transporter,
BtuB, the energy coupling segment of this protein undergoes a substrate-dependent
unfolding, which acts to couple this outer-membrane protein to the
inner-membrane protein TonB. EPR spectroscopy demonstrates that the
energy coupling segment is in equilibrium between ordered and disordered
states, and that substrate binding shifts this equilibrium to favor
an unfolded state. However, in crystal structures of BtuB, this segment
is resolved and folded within the protein, and neither the presence
of this equilibrium nor the substrate-induced change is revealed.
This is a result of the solute environment and the crystal lattice,
both of which act to stabilize one conformational substate of the
transporter. Using SDSL, it can be shown that conformational
exchange is present
in other regions of BtuB and in other members of this transporter
family. Conformational exchange has also been examined in systems
such as the plasma membrane SNARE protein, syntaxin 1A, where dynamics
are controlled by regulatory proteins such as munc18. Regulating the
microsecond to millisecond time scale dynamics in the neuronal SNAREs
is likely to be a key feature that regulates assembly of the SNAREs
and neurotransmitter release.
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Affiliation(s)
- David S. Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904-4319, United States
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Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MSP, Caffrey M. A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2054-68. [PMID: 25084326 PMCID: PMC4118822 DOI: 10.1107/s1399004714001850] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Abstract
The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.
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Affiliation(s)
- Jingquan Tan
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Dianfan Li
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Valerie E. Pye
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Lutz Vogeley
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Alette R. Brinth
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Toufic El Arnaout
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - John C. Whitney
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Martin Caffrey
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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45
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Milner SJ, Snelling AM, Kerr KG, Abd-El-Aziz A, Thomas GH, Hubbard RE, Routledge A, Duhme-Klair AK. Probing linker design in citric acid-ciprofloxacin conjugates. Bioorg Med Chem 2014; 22:4499-505. [PMID: 24794750 DOI: 10.1016/j.bmc.2014.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/01/2014] [Accepted: 04/06/2014] [Indexed: 11/29/2022]
Abstract
A series of structurally related citric acid-ciprofloxacin conjugates was synthesised to investigate the influence of the linker between citric acid and ciprofloxacin on antibacterial activities. Minimum inhibitory concentrations (MICs) were determined against a panel of reference strains and clinical isolates of bacteria associated with infection in humans and correlated with the DNA gyrase inhibitory activity. The observed trend was rationalised by computational modelling.
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Affiliation(s)
- Stephen J Milner
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Anna M Snelling
- Bradford Infection Group, University of Bradford, Bradford BD7 1DP, UK
| | - Kevin G Kerr
- Department of Microbiology, Fewston Wing, Harrogate District Hospital, Harrogate HG2 7SX, UK; Department of Biology (Area 10), University of York, Heslington, York YO10 5DD, UK; Hull York Medical School, Heslington, York YO10 5DD, UK
| | - Ahmad Abd-El-Aziz
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK; Department of Biology (Area 10), University of York, Heslington, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, Heslington, York YO10 5DD, UK
| | - Roderick E Hubbard
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK; Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK
| | - Anne Routledge
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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46
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Treviño-Quintanilla LG, Freyre-González JA, Martínez-Flores I. Anti-Sigma Factors in E. coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability. Curr Genomics 2014; 14:378-87. [PMID: 24396271 PMCID: PMC3861889 DOI: 10.2174/1389202911314060007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/30/2013] [Accepted: 08/01/2013] [Indexed: 11/22/2022] Open
Abstract
In bacteria, transcriptional regulation is a key step in cellular gene expression. All bacteria contain a core RNA polymerase that is catalytically competent but requires an additional σ factor for specific promoter recognition and correct transcriptional initiation. The RNAP core is not able to selectively bind to a given σ factor. In contrast, different σ factors have different affinities for the RNAP core. As a consequence, the concentration of alternate σ factors requires strict regulation in order to properly control the delicate interplay among them, which favors the competence for the RNAP core. This control is archived by different σ/anti-σ controlling mechanisms that shape complex regulatory networks and cascades, and enable the response to sudden environmental cues, whose global understanding is a current challenge for systems biology. Although there have been a number of excellent studies on each of these σ/anti-σ post-transcriptional regulatory systems, no comprehensive comparison of these mechanisms in a single model organism has been conducted. Here, we survey all these systems in E. coli dissecting and analyzing their inner workings and highlightin their differences. Then, following an integral approach, we identify their commonalities and outline some of the principles exploited by the cell to effectively and globally reprogram the transcriptional machinery. These principles provide guidelines for developing biological synthetic circuits enabling an efficient and robust response to sudden stimuli.
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Affiliation(s)
- Luis Gerardo Treviño-Quintanilla
- Departamento de Tecnología Ambiental, Universidad Politécnica del Estado de Morelos. Blvd. Cuauhnáhuac 566, Col. Lomas del Texcal, 62550. Jiutepec, Morelos, México
| | - Julio Augusto Freyre-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Av. Universidad s/n, Col. Chamilpa, 62210. Cuernavaca, Morelos, México
| | - Irma Martínez-Flores
- Departamento de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, 62250. Cuernavaca, Morelos, México
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47
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Gawarzewski I, Tschapek B, Hoeppner A, Jose J, Smits SHJ, Schmitt L. Purification, crystallization and preliminary X-ray crystallographic analysis of the transport unit of the monomeric autotransporter AIDA-I from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1159-1162. [PMID: 24100572 PMCID: PMC3792680 DOI: 10.1107/s1744309113024366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/01/2013] [Indexed: 06/02/2023]
Abstract
The adhesin involved in diffuse adherence (AIDA-I) from Escherichia coli belongs to the group of autotransporters, specifically the type Va secretion system (T5aSS). All autotransporter systems contain a C-terminal β-domain, which forms a barrel-like structure in the outer membrane with a hydrophilic pore allowing passenger translocation across the outer membrane. The passenger domain harbours the biological activity in the extracellular space and functions, for example, as an adhesin, an enzyme and a toxin. The exact transport mechanism of passenger translocation across the outer membrane is not clear at present. Thus, structure determination of the transport unit of AIDA-I could provide new insights into the transport mechanism. Here, the purification, crystallization and preliminary X-ray crystallographic studies of the transport unit of AIDA-I are reported.
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Affiliation(s)
- Iris Gawarzewski
- Institute of Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Britta Tschapek
- Institute of Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Astrid Hoeppner
- Crystal Farm and X-ray Facility, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, Westfälische Wilhems-Universität, Münster, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
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48
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Fukushima T, Allred BE, Sia AK, Nichiporuk R, Andersen UN, Raymond KN. Gram-positive siderophore-shuttle with iron-exchange from Fe-siderophore to apo-siderophore by Bacillus cereus YxeB. Proc Natl Acad Sci U S A 2013; 110:13821-6. [PMID: 23924612 PMCID: PMC3752266 DOI: 10.1073/pnas.1304235110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Small molecule iron-chelators, siderophores, are very important in facilitating the acquisition of Fe(III), an essential element for pathogenic bacteria. Many Gram-negative outer-membrane transporters and Gram-positive lipoprotein siderophore-binding proteins have been characterized, and the binding ability of outer-membrane transporters and siderophore-binding proteins for Fe-siderophores has been determined. However, there is little information regarding the binding ability of these proteins for apo-siderophores, the iron-free chelators. Here we report that Bacillus cereus YxeB facilitates iron-exchange from Fe-siderophore to apo-siderophore bound to the protein, the first Gram-positive siderophore-shuttle system. YxeB binds ferrioxamine B (FO, Fe-siderophore)/desferrioxamine B (DFO, apo-siderophore) in vitro. Disc-diffusion assays and growth assays using the yxeB mutant reveal that YxeB is responsible for importing the FO. Cr-DFO (a FO analog) is bound by YxeB in vitro and B. cereus imports or binds Cr-DFO in vivo. In vivo uptake assays using Cr-DFO and FO and growth assays using DFO and Cr-DFO show that B. cereus selectively imports and uses FO when DFO is present. Moreover, in vitro competition assays using Cr-DFO and FO clearly demonstrate that YxeB binds only FO, not Cr-DFO, when DFO is bound to the protein. Iron-exchange from FO to DFO bound to YxeB must occur when DFO is initially bound by YxeB. Because the metal exchange rate is generally first order in replacement ligand concentration, protein binding of the apo-siderophore acts to dramatically enhance the iron exchange rate, a key component of the Gram-positive siderophore-shuttle mechanism.
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Affiliation(s)
| | | | - Allyson K. Sia
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
| | - Rita Nichiporuk
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
| | - Ulla N. Andersen
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
| | - Kenneth N. Raymond
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
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49
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Raines DJ, Moroz OV, Wilson KS, Duhme-Klair AK. Interactions of a Periplasmic Binding Protein with a Tetradentate Siderophore Mimic. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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Raines DJ, Moroz OV, Wilson KS, Duhme-Klair AK. Interactions of a periplasmic binding protein with a tetradentate siderophore mimic. Angew Chem Int Ed Engl 2013; 52:4595-8. [PMID: 23512642 DOI: 10.1002/anie.201300751] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Indexed: 11/10/2022]
Abstract
Iron-bound structure: The ferric complex of a tetradentate siderophore mimic was synthesized and co-crystallized with the periplasmic binding protein CeuE of Campylobacter jejuni. In addition to electrostatic and hydrogen-bonding interactions between the binding pocket and the substrate, the structure showed direct coordination of two amino acid side chains to the Fe(III) center (orange, see figure).
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Affiliation(s)
- Daniel J Raines
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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