1
|
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B. An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality. Nat Struct Mol Biol 2024; 31:1072-1082. [PMID: 38548954 DOI: 10.1038/s41594-024-01256-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 02/23/2024] [Indexed: 07/20/2024]
Abstract
Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.
Collapse
Affiliation(s)
- Xiaolin Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing, China
| | - Zhenli Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yao Zhao
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xiaoting Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shan Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane Queensland, Australia
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Laboratory of Structural Biology, Tsinghua University, Beijing, China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
| |
Collapse
|
2
|
Alcorlo M, Abdullah MR, Steil L, Sotomayor F, López-de Oro L, de Castro S, Velázquez S, Kohler TP, Jiménez E, Medina A, Usón I, Keller LE, Bradshaw JL, McDaniel LS, Camarasa MJ, Völker U, Hammerschmidt S, Hermoso JA. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. PLoS Pathog 2024; 20:e1011883. [PMID: 38838057 PMCID: PMC11192437 DOI: 10.1371/journal.ppat.1011883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 06/21/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
ATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiont Streptococcus pneumoniae (pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the unexpected remarkable promiscuity of some of these proteins when expressed in Escherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed, through in silico modelling, some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism and the in vivo implications for this human pathogen.
Collapse
Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Mohammed R. Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Francisco Sotomayor
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Laura López-de Oro
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | | | | | - Thomas P. Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona; Spain
| | - Lance E. Keller
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Jessica L. Bradshaw
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Larry S. McDaniel
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | | | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| |
Collapse
|
3
|
Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides. Biochemistry 2024; 63:1322-1334. [PMID: 38696389 DOI: 10.1021/acs.biochem.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that MeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.
Collapse
Affiliation(s)
- Oliver B Smith
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Marina G Rahman
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
4
|
Hu T, Yang X, Zhu Y, Liu F, Yang X, Xiong Z, Liang J, Lin Z, Ran Y, Guddat LW, Rao Z, Zhang B. Molecular basis for substrate transport of Mycobacterium tuberculosis ABC importer DppABCD. SCIENCE ADVANCES 2024; 10:eadk8521. [PMID: 38507491 PMCID: PMC10954201 DOI: 10.1126/sciadv.adk8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
The type I adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter DppABCD is believed to be responsible for the import of exogenous heme as an iron source into the cytoplasm of the human pathogen Mycobacterium tuberculosis (Mtb). Additionally, this system is also known to be involved in the acquisition of tri- or tetra-peptides. Here, we report the cryo-electron microscopy structures of the dual-function Mtb DppABCD transporter in three forms, namely, the apo, substrate-bound, and ATP-bound states. The apo structure reveals an unexpected and previously uncharacterized assembly mode for ABC importers, where the lipoprotein DppA, a cluster C substrate-binding protein (SBP), stands upright on the translocator DppBCD primarily through its hinge region and N-lobe. These structural data, along with biochemical studies, reveal the assembly of DppABCD complex and the detailed mechanism of DppABCD-mediated transport. Together, these findings provide a molecular roadmap for understanding the transport mechanism of a cluster C SBP and its translocator.
Collapse
Affiliation(s)
- Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaolin Yang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yuanchen Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Zhenli Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuting Ran
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| |
Collapse
|
5
|
Rivera K, Tanaka KJ, Buechel ER, Origel O, Harrison A, Mason KM, Pinkett HW. Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae. Biochemistry 2024; 63:294-311. [PMID: 38189237 PMCID: PMC10851439 DOI: 10.1021/acs.biochem.3c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen associated with respiratory diseases, including otitis media and exacerbations of chronic obstructive pulmonary disease. NTHi exhibits resistance to killing by host antimicrobial peptides (AMPs) mediated by SapA, the substrate binding protein of the sensitivity to antimicrobial peptides (Sap) transporter. However, the specific mechanisms by which SapA selectively binds various AMPs such as defensins and cathelicidin are unknown. In this study, we report mutational analyses of both defensin AMPs and the SapA binding pocket to define the specificity of AMP recognition. Bactericidal assays revealed that NTHi lacking SapA are more susceptible to human beta defensins and LL-37, while remaining highly resistant to a human alpha defensin. In contrast to homologues, our research underscores the distinct specificity of NTHi SapA, which selectively recognizes and binds to peptides containing the charged-hydrophobic motif PKE and RRY. These findings provide valuable insight into the divergence of SapA among bacterial species and NTHi SapA's ability to selectively interact with specific AMPs to mediate resistance.
Collapse
Affiliation(s)
- Kristen
G. Rivera
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Kari J. Tanaka
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Evan R. Buechel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Octavio Origel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Alistair Harrison
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Kevin M. Mason
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Heather W. Pinkett
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
6
|
Ackroyd BK, Dodson EJ, Mehboob J, Dowle AA, Thomas GH, Wilkinson AJ. Structure and ligand binding in the putative anti-microbial peptide transporter protein, YejA. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001430. [PMID: 38334478 PMCID: PMC10924461 DOI: 10.1099/mic.0.001430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024]
Abstract
YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of Escherichia coli to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10-19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8-26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this 'auto-binding' is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.
Collapse
Affiliation(s)
- Bryony K. Ackroyd
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Eleanor J. Dodson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Javeria Mehboob
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Adam A. Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H. Thomas
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
7
|
Vaval Taylor DM, Xayarath B, Freitag NE. Two Permeases Associated with the Multifunctional CtaP Cysteine Transport System in Listeria monocytogenes Play Distinct Roles in Pathogenesis. Microbiol Spectr 2023; 11:e0331722. [PMID: 37199604 PMCID: PMC10269559 DOI: 10.1128/spectrum.03317-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 04/05/2023] [Indexed: 05/19/2023] Open
Abstract
The soil-dwelling bacterium Listeria monocytogenes survives a multitude of conditions when residing in the outside environment and as a pathogen within host cells. Key to survival within the infected mammalian host is the expression of bacterial gene products necessary for nutrient acquisition. Similar to many bacteria, L. monocytogenes uses peptide import to acquire amino acids. Peptide transport systems play an important role in nutrient uptake as well as in additional functions that include bacterial quorum sensing and signal transduction, recycling of peptidoglycan fragments, adherence to eukaryotic cells, and alterations in antibiotic susceptibility. It has been previously described that CtaP, encoded by lmo0135, is a multifunctional protein associated with activities that include cysteine transport, resistance to acid, membrane integrity, and bacterial adherence to host cells. ctaP is located next to two genes predicted to encode membrane-bound permeases lmo0136 and lmo0137, termed CtpP1 and CtpP2, respectively. Here, we show that CtpP1 and CtpP2 are required for bacterial growth in the presence of low concentrations of cysteine and for virulence in mouse infection models. Taken together, the data identify distinct nonoverlapping roles for two related permeases that are important for the growth and survival of L. monocytogenes within host cells. IMPORTANCE Bacterial peptide transport systems are important for nutrient uptake and may additionally function in a variety of other roles, including bacterial communication, signal transduction, and bacterial adherence to eukaryotic cells. Peptide transport systems often consist of a substrate-binding protein associated with a membrane-spanning permease. The environmental bacterial pathogen Listeria monocytogenes uses the substrate-binding protein CtaP not only for cysteine transport but also for resistance to acid, maintenance of membrane integrity, and bacterial adherence to host cells. In this study, we demonstrate complementary yet distinct functional roles for two membrane permeases, CtpP1 and CtpP2, that are encoded by genes linked to ctaP and that contribute to bacterial growth, invasion, and pathogenicity.
Collapse
Affiliation(s)
- Diandra M. Vaval Taylor
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bobbi Xayarath
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nancy E. Freitag
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
8
|
Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria. mBio 2023; 14:e0021723. [PMID: 36802165 PMCID: PMC10128002 DOI: 10.1128/mbio.00217-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Phazolicin (PHZ) is a peptide antibiotic exhibiting narrow-spectrum activity against rhizobia closely related to its producer, Rhizobium sp. strain Pop5. Here, we show that the frequency of spontaneous PHZ-resistant mutants in Sinorhizobium meliloti is below the detection limit. We find that PHZ can enter S. meliloti cells through two distinct promiscuous peptide transporters, BacA and YejABEF, which belong to the SLiPT (SbmA-like peptide transporter) and ABC (ATP-binding cassette) transporter families, respectively. The dual-uptake mode explains the lack of observed resistance acquisition because the simultaneous inactivation of both transporters is necessary for resistance to PHZ. Since both BacA and YejABEF are essential for the development of functional symbiosis of S. meliloti with leguminous plants, the unlikely acquisition of PHZ resistance via the inactivation of these transporters is further disfavored. A whole-genome transposon sequencing screen did not reveal additional genes that can provide strong PHZ resistance when inactivated. However, it was found that the capsular polysaccharide KPS, the novel putative envelope polysaccharide PPP (PHZ-protecting polysaccharide), as well as the peptidoglycan layer jointly contribute to the sensitivity of S. meliloti to PHZ, most likely serving as barriers that reduce the amount of PHZ transported inside the cell. IMPORTANCE Many bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides act either by membrane disruption or by inhibiting essential intracellular processes. The Achilles' heel of the latter type of antimicrobials is their dependence on transporters to enter susceptible cells. Transporter inactivation results in resistance. Here, we show that a rhizobial ribosome-targeting peptide, phazolicin (PHZ), uses two different transporters, BacA and YejABEF, to enter the cells of a symbiotic bacterium, Sinorhizobium meliloti. This dual-entry mode dramatically reduces the probability of the appearance of PHZ-resistant mutants. Since these transporters are also crucial for S. meliloti symbiotic associations with host plants, their inactivation in natural settings is strongly disfavored, making PHZ an attractive lead for the development of biocontrol agents for agriculture.
Collapse
|
9
|
Rojas-Tapias DF, Brown EM, Temple ER, Onyekaba MA, Mohamed AMT, Duncan K, Schirmer M, Walker RL, Mayassi T, Pierce KA, Ávila-Pacheco J, Clish CB, Vlamakis H, Xavier RJ. Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine. Nat Microbiol 2022; 7:1673-1685. [PMID: 36138166 PMCID: PMC9728153 DOI: 10.1038/s41564-022-01224-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 08/03/2022] [Indexed: 12/13/2022]
Abstract
Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.
Collapse
Affiliation(s)
- Daniel F Rojas-Tapias
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Agricultural Microbiology, Colombian Corporation for Agricultural Research-Agrosavia, Bogotá, Colombia
| | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kellyanne Duncan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Emmy Noether Group, ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Toufic Mayassi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kerry A Pierce
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
10
|
Chai HH, Ham JS, Kim TH, Lim D. Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by structure-based molecular modeling. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
11
|
Yokoyama H, Kamei N, Konishi K, Hara K, Ishikawa Y, Matsui I, Forterre P, Hashimoto H. Structural basis for peptide recognition by archaeal oligopeptide permease A. Proteins 2022; 90:1434-1442. [DOI: 10.1002/prot.26324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Hideshi Yokoyama
- Faculty of Pharmaceutical Sciences Tokyo University of Science Noda Chiba Japan
| | - Nanami Kamei
- School of Pharmaceutical Sciences University of Shizuoka Suruga‐ku Shizuoka Japan
| | - Keijiro Konishi
- School of Pharmaceutical Sciences University of Shizuoka Suruga‐ku Shizuoka Japan
| | - Kodai Hara
- School of Pharmaceutical Sciences University of Shizuoka Suruga‐ku Shizuoka Japan
| | - Yoshinobu Ishikawa
- School of Pharmaceutical Sciences University of Shizuoka Suruga‐ku Shizuoka Japan
| | - Ikuo Matsui
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki Japan
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), Microbiology Department CEA, CNRS, Université Paris‐Sud, Université Paris‐Saclay Paris France
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences University of Shizuoka Suruga‐ku Shizuoka Japan
| |
Collapse
|
12
|
Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
Collapse
Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| |
Collapse
|
13
|
Yokoyama H, Kamei N, Konishi K, Hara K, Ishikawa Y, Matsui I, Forterre P, Hashimoto H. Preparation, Crystallization, and X-ray Data Collection of Archaeal Oligopeptide Permease A. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521070221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Lukacik P, Owen CD, Harris G, Bolla JR, Picaud S, Alibay I, Nettleship JE, Bird LE, Owens RJ, Biggin PC, Filippakopoulos P, Robinson CV, Walsh MA. The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif. PLoS One 2021; 16:e0256070. [PMID: 34653190 PMCID: PMC8519434 DOI: 10.1371/journal.pone.0256070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.
Collapse
Affiliation(s)
- Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - C. David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Irfan Alibay
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joanne E. Nettleship
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Louise E. Bird
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Raymond J. Owens
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- * E-mail:
| |
Collapse
|
15
|
Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
Collapse
Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| |
Collapse
|
16
|
Jiang Y, Shi Y, Li R, Hang F, Zhao J, Zhang H, Chen W. The peptides in oat and malt extracts that are preferentially absorbed by
Lactobacillus plantarum
and stimulates its proliferation in milk. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yuanzhi Jiang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- Food Biotechnology Institute of Jiangnan University Yangzhou Jiangsu 225004 China
| | - Yangyang Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- Food Biotechnology Institute of Jiangnan University Yangzhou Jiangsu 225004 China
| | - Rui Li
- Food Biotechnology Institute of Jiangnan University Yangzhou Jiangsu 225004 China
| | - Feng Hang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- Food Biotechnology Institute of Jiangnan University Yangzhou Jiangsu 225004 China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- National Engineering Research Center for Functional Food Jiangnan University Wuxi Jiangsu 214122 China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- Food Biotechnology Institute of Jiangnan University Yangzhou Jiangsu 225004 China
- National Engineering Research Center for Functional Food Jiangnan University Wuxi Jiangsu 214122 China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 China
- National Engineering Research Center for Functional Food Jiangnan University Wuxi Jiangsu 214122 China
- Beijing Innovation Centre of Food Nutrition and Human Health Beijing Technology & Business University Beijing 100048 China
| |
Collapse
|
17
|
Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. SCIENCE ADVANCES 2021; 7:eabh3355. [PMID: 34433568 PMCID: PMC8386928 DOI: 10.1126/sciadv.abh3355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family.
Collapse
Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| |
Collapse
|
18
|
Segawa T, Johnson CM, Berntsson RPA, Dunny GM. Two ABC transport systems carry out peptide uptake in Enterococcus faecalis: Their roles in growth and in uptake of sex pheromones. Mol Microbiol 2021; 116:459-469. [PMID: 33817866 DOI: 10.1111/mmi.14725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
Enterococcal pheromone-inducible plasmids encode a predicted OppA-family secreted lipoprotein. In the case of plasmid pCF10, the protein is PrgZ, which enhances the mating response to cCF10 pheromone. OppA proteins generally function with associated OppBCDF ABC transporters to import peptides. In this study, we analyzed the potential interactions of PrgZ with two host-encoded Opp transporters using two pheromone-inducible fluorescent reporter constructs. Based on our results, we propose renaming these loci opp1 (OG1RF_10634-10639) and opp2 (OG1RF_12366-12370). We also examined the ability of the Opp1 and Opp2 systems to mediate import in the absence of PrgZ. Cells expressing PrgZ were able to import pheromone if either opp1 or opp2 was functional, but not if both opp loci were disrupted. In the absence of PrgZ, pheromone import was dependent on a functional opp2 system, including opp2A. Comparative structural analysis of the peptide-binding pockets of PrgZ, Opp1A, Opp2A, and the related Lactococcus lactis OppA protein, suggested that the robust pheromone-binding ability of PrgZ relates to a nearly optimal fit of the hydrophobic peptide, whereas binding ability of Opp2A likely results from a more open, promiscuous peptide-binding pocket similar to L. lactis OppA.
Collapse
Affiliation(s)
- Takaya Segawa
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Christopher M Johnson
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umea University, Umea, Sweden.,Wallenberg Center for Molecular Medicine, Umea University, Umea, Sweden
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| |
Collapse
|
19
|
Groshong AM, McLain MA, Radolf JD. Host-specific functional compartmentalization within the oligopeptide transporter during the Borrelia burgdorferi enzootic cycle. PLoS Pathog 2021; 17:e1009180. [PMID: 33428666 PMCID: PMC7822543 DOI: 10.1371/journal.ppat.1009180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/22/2021] [Accepted: 11/23/2020] [Indexed: 12/27/2022] Open
Abstract
Borrelia burgdorferi must acquire all of its amino acids (AAs) from its arthropod vector and vertebrate host. Previously, we determined that peptide uptake via the oligopeptide (Opp) ABC transporter is essential for spirochete viability in vitro and during infection. Our prior study also suggested that B. burgdorferi employs temporal regulation in concert with structural variation of oligopeptide-binding proteins (OppAs) to meet its AA requirements in each biological niche. Herein, we evaluated the contributions to the B. burgdorferi enzootic cycle of three of the spirochete's five OppAs (OppA1, OppA2, and OppA5). An oppA1 transposon (tn) mutant lysed in the hyperosmolar environment of the feeding tick, suggesting that OppA1 imports amino acids required for osmoprotection. The oppA2tn mutant displayed a profound defect in hematogenous dissemination in mice, yet persisted within skin while inducing only a minimal antibody response. These results, along with slightly decreased growth of the oppA2tn mutant within DMCs, suggest that OppA2 serves a minor nutritive role, while its dissemination defect points to an as yet uncharacterized signaling function. Previously, we identified a role for OppA5 in spirochete persistence within the mammalian host. We now show that the oppA5tn mutant displayed no defect during the tick phase of the cycle and could be tick-transmitted to naïve mice. Instead of working in tandem, however, OppA2 and OppA5 appear to function in a hierarchical manner; the ability of OppA5 to promote persistence relies upon the ability of OppA2 to facilitate dissemination. Structural homology models demonstrated variations within the binding pockets of OppA1, 2, and 5 indicative of different peptide repertoires. Rather than being redundant, B. burgdorferi's multiplicity of Opp binding proteins enables host-specific functional compartmentalization during the spirochete lifecycle.
Collapse
Affiliation(s)
- Ashley M. Groshong
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
- Department of Pediatrics, UConn Health, Farmington, Connecticut, United States of America
- * E-mail:
| | - Melissa A. McLain
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
- Department of Pediatrics, UConn Health, Farmington, Connecticut, United States of America
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Science, UConn Health, Farmington, Connecticut, United States of America
- Department of Immunology, UConn Health, Farmington, Connecticut, United States of America
| |
Collapse
|
20
|
Escobar Garduño E, Scior T, Soto Urzúa L, Martínez Morales LJ. Identification of residues for chaperone-like activity of OppA protein in Yersinia pseudotuberculosis. AMB Express 2020; 10:153. [PMID: 32821976 PMCID: PMC7442780 DOI: 10.1186/s13568-020-01090-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022] Open
Abstract
Periplasmic oligopeptide binding protein (OppA) is part of a multimeric cytoplasmic membrane protein complex, whose function is known as peptide transporters found in Gram-negative bacteria. A chaperone-like activity has been found for the OppA from Yersinia pseudotuberculosis, using biochemical experiments. Through computational analysis, we selected two amino acid residues (R41 and D42) that probably are involved in the chaperone-like activity. Our results to corroborate how OppA assists refolding and renaturation of lactate dehydrogenase and alpha-glucosidase denatured enzymes.
Collapse
|
21
|
Abideen ZU, Ahmad A, Usman M, Majaz S, Ali W, Noreen S, Mahmood T, Nouroz F. Dynamics and conformational propensities of staphylococcal CntA. J Biomol Struct Dyn 2020; 39:4923-4935. [PMID: 32573341 DOI: 10.1080/07391102.2020.1782263] [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: 10/24/2022]
Abstract
Enzymes use transition metals as co-factors for catalytic roles in biological processes. Notably, manganese, iron, cobalt, nickel, copper and zinc are abundantly used. Staphylococcus aureus, a commensal bacterium asymptomatically, lies on the human body causing variety of infections. S. aureus is equipped by advanced virulence-regulatory circuits of metal acquisition like Cnt that acquires metals at infection sites by utilizing a nicotianamine-like metallophore staphylopine. Despite significant growth in structural studies, how CntA of Cnt system transmits conformational signal upon staphylopine recognition remains elusive. Here, we analyzed the structural changes adopted by CntA during close-to-open transition by computational approaches. CntA uses a bi-domain architectural form of domain II which performed 37° rigid body rotation and 1.1 Å translation assisted by inter-domain hinge cluster residues. Important clustered communities were found regulating the conformational changes in CntA where communities 4 and 5 are found crucial. Besides open and close states, the fluctuating regions sampled two additional intermediate states which were considered close or open previously. CntA prefers fluctuating the non-conserved regions rather than conserved where domain II turned out to be rigid and maintains a stable fold. Overall, the CntA system is a potential target for structural biologist to hamper such conformational behaviors at family level.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zain Ul Abideen
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Muhammad Usman
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Sidra Majaz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Waqar Ali
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Shumaila Noreen
- Department of Zoology, University of Peshawar, Peshawar, KPK, Pakistan
| | - Tariq Mahmood
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan.,Department of Agriculture, Hazara University, Mansehra, KPK, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan.,Department of Botany, Hazara University, Mansehra, KPK, Pakistan
| |
Collapse
|
22
|
Sung WY, Yu JW, Hwang JT, Nam HJ, Park JY, Kim Y, Cho JH. Insight into the bovine milk peptide LPcin-YK3 selection in the proteolytic system of Lactobacillus species. J Pept Sci 2020; 26:e3268. [PMID: 32567752 PMCID: PMC7379261 DOI: 10.1002/psc.3268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/07/2022]
Abstract
Antimicrobial peptides are class of small, positively charged peptides known for their broad-spectrum antimicrobial activity. Antimicrobial activities for most antimicrobial peptides have largely remained elusive, particularly in the lactic acid bacteria. However, recently our investigation using LPcin-YK3, an antimicrobial peptide from bovine milk, suggests that in vitro antimicrobial activity was reduced over 100-fold compared with pathogenic bacteria. Additionally, for the structural study of how antimicrobial peptide undergoes its reaction at the proteolytic pathway of lactic acid bacteria based on degradation assay and propidium iodide staining, we performed molecular docking for interaction between oligopeptide-binding protein A and LPcin-YK3 peptide. Given that degradation related to the LPcin-YK3 peptide in lactic acid bacteria proteolytic system, the inhibitory inactivity of LPcin-YK3 against beneficial lactic acid bacteria strains may be one of the primary pharmacological properties of recombinant peptide discovered in bovine milk. These results provide structural and functional insights into the proteolytic mechanism and possibility as a putative substrate of oligopeptide-binding protein A in respect of LPcin-YK3 peptide.
Collapse
Affiliation(s)
- Woo Yong Sung
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| | - Ji Won Yu
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| | - Jong Tae Hwang
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| | - Hee Jin Nam
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| | - Ji Ye Park
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| | - Yongae Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Republic of Korea
| | - Jang-Hee Cho
- Biomaterial Research Center, CellinBio, Suwon, Republic of Korea
| |
Collapse
|
23
|
Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
Collapse
Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| |
Collapse
|
24
|
Krypotou E, Scortti M, Grundström C, Oelker M, Luisi BF, Sauer-Eriksson AE, Vázquez-Boland J. Control of Bacterial Virulence through the Peptide Signature of the Habitat. Cell Rep 2020; 26:1815-1827.e5. [PMID: 30759392 PMCID: PMC6389498 DOI: 10.1016/j.celrep.2019.01.073] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/09/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022] Open
Abstract
To optimize fitness, pathogens selectively activate their virulence program upon host entry. Here, we report that the facultative intracellular bacterium Listeria monocytogenes exploits exogenous oligopeptides, a ubiquitous organic N source, to sense the environment and control the activity of its virulence transcriptional activator, PrfA. Using a genetic screen in adsorbent-treated (PrfA-inducing) medium, we found that PrfA is functionally regulated by the balance between activating and inhibitory nutritional peptides scavenged via the Opp transport system. Activating peptides provide essential cysteine precursor for the PrfA-inducing cofactor glutathione (GSH). Non-cysteine-containing peptides cause promiscuous PrfA inhibition. Biophysical and co-crystallization studies reveal that peptides inhibit PrfA through steric blockade of the GSH binding site, a regulation mechanism directly linking bacterial virulence and metabolism. L. monocytogenes mutant analysis in macrophages and our functional data support a model in which changes in the balance of antagonistic Opp-imported oligopeptides promote PrfA induction intracellularly and PrfA repression outside the host. Listeria PrfA virulence regulation is controlled by antagonistic nutritional peptides Opp-imported peptides regulate PrfA upstream of the activating cofactor GSH PrfA is activated by peptides that provide essential cysteine for GSH biosynthesis Blockade of PrfA’s GSH binding site by peptides inhibits virulence gene activation
Collapse
Affiliation(s)
- Emilia Krypotou
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mariela Scortti
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Christin Grundström
- Department of Chemistry and Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Melanie Oelker
- Department of Chemistry and Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - José Vázquez-Boland
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK.
| |
Collapse
|
25
|
Kordafshari S, Marenda MS, Agnew R, Shil P, Shahid MA, Marth C, Konsak BM, Noormohammadi AH. Complementation of the Mycoplasma synoviae MS-H vaccine strain with wild-type oppF1 influences its growth characteristics. Avian Pathol 2020; 49:275-285. [PMID: 32054292 DOI: 10.1080/03079457.2020.1729957] [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: 10/25/2022]
Abstract
The Mycoplasma synoviae (MS) vaccine strain MS-H harbours a frameshift mutation in oppF1 (oligopeptide permease transporter) which results in expression of a truncated OppF1. The effect of this mutation on growth and attenuation of the MS-H is unknown. In this study, the impact of the mutation on the vaccine phenotype was investigated in vitro by introducing a wild-type copy of oppF1 gene in the MS-H genome. Wild-type oppF1 was cloned under the vlhA promoter into an oriC vector carrying a tetracycline resistance gene. MS-H was successfully transformed with the final construct pMS-oppF1-tetM or with a similar vector lacking oppF1 coding sequence (pMS-tetM). The MS-H transformed with pMS-oppF1-tetM exhibited smaller colony size than MS-H transformed with pMS-tetM. Monospecific rabbit sera against C-terminus of OppF1 detected bands of expected size for full-length OppF1 in the 86079/7NS parental strain of MS-H and the MS-H transformed with pMS-oppF1-tetM, but not in MS-H and MS-H transformed with pMS-tetM. Comparison of the growth curve of MS-H transformants harvested from media with/without tetracycline was conducted using vlhA Q-PCR which revealed that MS-H transformed with pMS-tetM had a higher growth rate than MS-H transformed with pMS-oppF1-tetM in the media with/without tetracycline. Lastly, the whole genome sequencing of MS-H transformed with pMS-oppF1-tetM (passage 27) showed that the chromosomal copy of the mutated oppF1 had been replaced with a wild-type version of the gene. This study reveals that the truncation of oppF1 impacts on growth characteristics of the MS-H and provides insight into the molecular pathogenesis of MS and perhaps broader mycoplasma species.RESEARCH HIGHLIGHTS The full-length OppF1 was expressed in Mycoplasma synoviae MS-H vaccine.Truncation of oppF1 impacts on growth characteristics of the MS-H.Chromosomal copy of the mutated oppF1 in MS-H was replaced with wild-type oppF1.
Collapse
Affiliation(s)
- Somayeh Kordafshari
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Marc S Marenda
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Rebecca Agnew
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Pollob Shil
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Muhammad A Shahid
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Christina Marth
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Barbara M Konsak
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Amir H Noormohammadi
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Australia
| |
Collapse
|
26
|
Babel H, Naranjo-Meneses P, Trauth S, Schulmeister S, Malengo G, Sourjik V, Bischofs IB. Ratiometric population sensing by a pump-probe signaling system in Bacillus subtilis. Nat Commun 2020; 11:1176. [PMID: 32132526 PMCID: PMC7055314 DOI: 10.1038/s41467-020-14840-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/04/2020] [Indexed: 12/20/2022] Open
Abstract
Communication by means of diffusible signaling molecules facilitates higher-level organization of cellular populations. Gram-positive bacteria frequently use signaling peptides, which are either detected at the cell surface or ‘probed’ by intracellular receptors after being pumped into the cytoplasm. While the former type is used to monitor cell density, the functions of pump-probe networks are less clear. Here we show that pump-probe networks can, in principle, perform different tasks and mediate quorum-sensing, chronometric and ratiometric control. We characterize the properties of the prototypical PhrA-RapA system in Bacillus subtilis using FRET. We find that changes in extracellular PhrA concentrations are tracked rather poorly; instead, cells accumulate and strongly amplify the signal in a dose-dependent manner. This suggests that the PhrA-RapA system, and others like it, have evolved to sense changes in the composition of heterogeneous populations and infer the fraction of signal-producing cells in a mixed population to coordinate cellular behaviors. Gram-positive bacteria can release signaling peptides that are ‘probed’ by intracellular receptors after being pumped into the cytoplasm. Here, Babel et al. show that these pump-probe networks can infer the fraction of signal-producing cells in a mixed population, and do not necessarily mediate typical quorum-sensing control.
Collapse
Affiliation(s)
- Heiko Babel
- BioQuant Center of the University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Pablo Naranjo-Meneses
- BioQuant Center of the University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Stephanie Trauth
- BioQuant Center of the University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Sonja Schulmeister
- BioQuant Center of the University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Gabriele Malengo
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Str. 16, 35043, Marburg, Germany
| | - Victor Sourjik
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Str. 16, 35043, Marburg, Germany
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany. .,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| |
Collapse
|
27
|
Fernández M, Rico-Jiménez M, Ortega Á, Daddaoua A, García García AI, Martín-Mora D, Torres NM, Tajuelo A, Matilla MA, Krell T. Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins. Int J Mol Sci 2019; 20:ijms20205156. [PMID: 31627455 PMCID: PMC6829864 DOI: 10.3390/ijms20205156] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 01/05/2023] Open
Abstract
Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of 98 proteins. Bioinformatic predictions indicate that many of these proteins have a redundant ligand profile such as 27 SBPs for proteinogenic amino acids, 13 proteins for spermidine/putrescine, or 9 proteins for quaternary amines. To assess the precision of these bioinformatic predictions, we have purified 17 SBPs that were subsequently submitted to high-throughput ligand screening approaches followed by isothermal titration calorimetry studies, resulting in the identification of ligands for 15 of them. Experimentation revealed that PA0222 was specific for γ-aminobutyrate (GABA), DppA2 for tripeptides, DppA3 for dipeptides, CysP for thiosulphate, OpuCC for betaine, and AotJ for arginine. Furthermore, RbsB bound D-ribose and D-allose, ModA bound molybdate, tungstate, and chromate, whereas AatJ recognized aspartate and glutamate. The majority of experimentally identified ligands were found to be chemoattractants. Data show that the ligand class recognized by SPBs can be predicted with confidence using bioinformatic methods, but experimental work is necessary to identify the precise ligand profile.
Collapse
Affiliation(s)
- Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
- present address: Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.
| | - Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Ana Isabel García García
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Noel Mesa Torres
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Ana Tajuelo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| |
Collapse
|
28
|
Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori. J Bacteriol 2019; 201:JB.00400-19. [PMID: 31358613 DOI: 10.1128/jb.00400-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
The gastric pathogen Helicobacter pylori has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by H. pylori requires an ATP binding cassette (ABC) transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA, which captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, H. pylori DppA binds, with micromolar affinity, peptides of diverse amino acid sequences ranging between two and eight residues in length. We present analysis of the 1.45-Å-resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that H. pylori DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the H. pylori protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the greatest contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides.IMPORTANCE The World Health Organization listed Helicobacter pylori as a high-priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides, termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for H. pylori, our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.
Collapse
|
29
|
Zhang JS, Corredig M, Morales-Rayas R, Hassan A, Griffiths MW, LaPointe G. Downregulation of Salmonella Virulence Gene Expression During Invasion of Epithelial Cells Treated with Lactococcus lactis subsp. cremoris JFR1 Requires OppA. Probiotics Antimicrob Proteins 2019; 12:577-588. [PMID: 31377945 DOI: 10.1007/s12602-019-09574-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Invasion of Salmonella into host intestinal epithelial cells requires the expression of virulence genes. In this study, cell culture models of human intestinal cells (mucus-producing HT29-MTX cells, absorptive Caco-2 cells, and combined cocultures of the two) were used to determine the effects of Lactococcus lactis subsp. cremoris treatments (exopolysaccharide producing and nonproducing strains) on the virulence gene expression of Salmonella Typhimurium and its mutant lacking the oligopeptide permease subunit A (ΔoppA). During the course of epithelial cell (HT29-MTX, Caco-2, and combined) infection by Salmonella Typhimurium DT104, improved barrier function was reflected by increased transepithelial electrical resistance in cells treated with both strains of L. lactis subsp. cremoris. In addition, virulence gene expression was downregulated, accompanied with lower numbers of invasive bacteria into epithelial cells in the presence of L. lactis subsp. cremoris treatments. Similarly, virulence gene expression of Salmonella was also suppressed when coincubated with overnight cultures of both L. lactis subsp. cremoris strains in the absence of epithelial cells. However, in medium or in the presence of cell cultures, Salmonella lacking the OppA permease function remained virulent. HT29-MTX cells and combined cultures stimulated by Salmonella Typhimurium DT104 showed significantly lower secretion levels of pro-inflammatory cytokine IL-8 after treatment with L. lactis subsp. cremoris cell suspensions. Contrarily, these responses were not observed during infection with S. Typhimurium ΔoppA. Both the exopolysaccharide producing and nonproducing strains of L. lactis subsp. cremoris JFR1 exhibited an antivirulence effect against S. Typhimurium DT104 although no significant difference between the two strains was observed. Our results show that an intact peptide transporter is essential for the suppression of Salmonella virulence genes which leads to the protection of the barrier function in the cell culture models studied.
Collapse
Affiliation(s)
- J S Zhang
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - M Corredig
- Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - R Morales-Rayas
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Hassan
- Daisy Brand, Dallas, TX, 75251, USA
| | - M W Griffiths
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Gisèle LaPointe
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
30
|
The oligopeptide ABC-importers are essential communication channels in Gram-positive bacteria. Res Microbiol 2019; 170:338-344. [PMID: 31376485 DOI: 10.1016/j.resmic.2019.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/12/2019] [Indexed: 12/27/2022]
Abstract
The transport of peptides in microorganisms plays an important role in their physiology and behavior, both as a nutrient source and as a proxy to sense their environment. This latter function is evidenced in Gram-positive bacteria where cell-cell communication is mediated by small peptides. Here, we highlight the importance of the oligopeptide permease (Opp) systems in the various major processes controlled by signaling peptides, such as sporulation, virulence and conjugation. We underline that the functioning of these communication systems is tightly linked to the developmental status of the bacteria via the regulation of opp gene expression by transition phase regulators.
Collapse
|
31
|
Proust L, Sourabié A, Pedersen M, Besançon I, Haudebourg E, Monnet V, Juillard V. Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus. Front Microbiol 2019; 10:906. [PMID: 31133999 PMCID: PMC6524704 DOI: 10.3389/fmicb.2019.00906] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
Streptococcus thermophilus, an extensively used lactic starter, is generally produced in yeast extract-based media containing a complex mixture of peptides whose exact composition remains elusive. In this work, we aimed at investigating the peptide content of a commercial yeast extract (YE) and identifying dynamics of peptide utilization during the growth of the industrial S. thermophilus N4L strain, cultivated in 1 l bioreactors under pH-regulation. To reach that goal, we set up a complete analytical workflow based on mass spectrometry (peptidomics). About 4,600 different oligopeptides ranging from 6 to more than 30 amino acids in length were identified during the time-course of the experiment. Due to the low spectral abundance of individual peptides, we performed a clustering approach to decipher the rules of peptide utilization during fermentation. The physicochemical characteristics of consumed peptides perfectly matched the known affinities of the oligopeptide transport system of S. thermophilus. Moreover, by analyzing such a large number of peptides, we were able to establish that peptide net charge is the major factor for oligopeptide transport in S. thermophilus N4L.
Collapse
Affiliation(s)
- Lucas Proust
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Procelys, Lesaffre Group, Maisons-Alfort, France
| | | | | | | | - Eloi Haudebourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Véronique Monnet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Vincent Juillard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
32
|
Norcross S, Sunderraj A, Tantama M. pH- and Temperature-Dependent Peptide Binding to the Lactococcus lactis Oligopeptide-Binding Protein A Measured with a Fluorescence Anisotropy Assay. ACS OMEGA 2019; 4:2812-2822. [PMID: 30842982 PMCID: PMC6396125 DOI: 10.1021/acsomega.8b02427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/22/2019] [Indexed: 05/03/2023]
Abstract
Bacterial ATP-binding cassette transporters are a superfamily of transport systems involved in the import of various molecules including amino acids, ions, sugars, and peptides. In the lactic acid bacteria Lactococcus lactis, the oligopeptide-binding protein A (OppA) binds peptides for import to support nitrogen metabolism and cell growth. The OppA protein is of great interest because it can bind peptides over a broad variety of lengths and sequences; however, current methods to study peptide binding have employed low throughput, endpoint, or low dynamic range techniques. Therefore, in this study, we developed a fluorescence anisotropy-based peptide-binding assay that can be readily employed to quantify OppA function. To test the utility of our assay, we characterized the pH dependence of oligopeptide binding because L. lactis is commonly used in fermentation and often must survive in low pH environments caused by lactic acid export. We determined that OppA affinity increases as pH or temperature decreases, and circular dichroism spectroscopy further indicated that acidic conditions increase the thermal stability of the protein, increasing the unfolding transition temperature by 10 °C from pH 8 to pH 6. Thus, our fluorescence anisotropy assay provides an easy technique to measure peptide binding, and it can be used to understand molecular aspects of OppA function under stress conditions experienced during fermentation and other biotechnology applications.
Collapse
Affiliation(s)
- Stevie Norcross
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
| | - Ashwin Sunderraj
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
| | - Mathew Tantama
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
- E-mail: . Phone: 765-494-5312
| |
Collapse
|
33
|
Tanaka KJ, Pinkett HW. Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket. J Biol Chem 2018; 294:1070-1082. [PMID: 30455346 DOI: 10.1074/jbc.ra118.004479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/14/2018] [Indexed: 11/06/2022] Open
Abstract
In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein (OppA) serves as the substrate-binding protein (SBP) of the oligopeptide transport system responsible for the import of peptides. We solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. Our novel hexapeptide complex demonstrates the flexibility of the nthiOppA-binding cavity to expand and accommodate the longer peptide while maintaining similar protein-peptide interactions of smaller peptide complexes. In addition to acquiring peptides from the host environment, as a heme auxotroph NTHi utilizes host hemoproteins as a source of essential iron. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. We observed nthiOppA shares this heme-binding characteristic and established heme specificity and affinity by surface plasmon resonance (SPR) of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the binding pocket, and using SPR competition assays, we observed that heme does not directly compete with peptide in the substrate-binding pocket. Additionally, we identified that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. Our results demonstrate the multisubstrate specificity of nthiOppA and the role of NTHi Cluster C proteins in the heme-uptake pathway for this pathogen.
Collapse
Affiliation(s)
- Kari J Tanaka
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Heather W Pinkett
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| |
Collapse
|
34
|
Tanaka KJ, Song S, Mason K, Pinkett HW. Selective substrate uptake: The role of ATP-binding cassette (ABC) importers in pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:868-877. [PMID: 28847505 PMCID: PMC5807212 DOI: 10.1016/j.bbamem.2017.08.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/11/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023]
Abstract
The uptake of nutrients, including metals, amino acids and peptides are required for many biological processes. Pathogenic bacteria scavenge these essential nutrients from microenvironments to survive within the host. Pathogens must utilize a myriad of mechanisms to acquire these essential nutrients from the host while mediating the effects of toxicity. Bacteria utilize several transport proteins, including ATP-binding cassette (ABC) transporters to import and expel substrates. ABC transporters, conserved across all organisms, are powered by the energy from ATP to move substrates across cellular membranes. In this review, we will focus on nutrient uptake, the role of ABC importers at the host-pathogen interface, and explore emerging therapies to combat pathogenesis. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
Collapse
Affiliation(s)
- Kari J Tanaka
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Saemee Song
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Kevin Mason
- The Research Institute at Nationwide Children's Hospital and The Ohio State University, College of Medicine, Department of Pediatrics, Center for Microbial Pathogenesis, Columbus, OH, USA
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
35
|
Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter. mBio 2017; 8:mBio.02047-17. [PMID: 29259089 PMCID: PMC5736914 DOI: 10.1128/mbio.02047-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Borrelia burgdorferi is an extreme amino acid (AA) auxotroph whose genome encodes few free AA transporters and an elaborate oligopeptide transport system (B. burgdorferi Opp [BbOpp]). BbOpp consists of five oligopeptide-binding proteins (OBPs), two heterodimeric permeases, and a heterodimeric nucleotide-binding domain (NBD). Homology modeling based on the crystal structure of liganded BbOppA4 revealed that each OBP likely binds a distinct range of peptides. Transcriptional analyses demonstrated that the OBPs are differentially and independently regulated whereas the permeases and NBDs are constitutively expressed. A conditional NBD mutant failed to divide in the absence of inducer and replicated in an IPTG (isopropyl-β-d-thiogalactopyranoside) concentration-dependent manner. NBD mutants grown without IPTG exhibited an elongated morphotype lacking division septa, often with flattening at the cell center due to the absence of flagellar filaments. Following cultivation in dialysis membrane chambers, NBD mutants recovered from rats not receiving IPTG also displayed an elongated morphotype. The NBD mutant was avirulent by needle inoculation, but infectivity was partially restored by oral administration of IPTG to infected mice. We conclude that peptides are a major source of AAs for B. burgdorferi both in vitro and in vivo and that peptide uptake is essential for regulation of morphogenesis, cell division, and virulence. Borrelia burgdorferi, the causative agent of Lyme disease, is an extreme amino acid (AA) auxotroph with a limited repertoire of annotated single-AA transporters. A major issue is how the spirochete meets its AA requirements as it transits between its arthropod vector and mammalian reservoir. While previous studies have confirmed that the B. burgdorferi oligopeptide transport (opp) system is capable of importing peptides, the importance of the system for viability and pathogenesis has not been established. Here, we evaluated the opp system structurally and transcriptionally to elucidate its ability to import a wide range of peptides during the spirochete’s enzootic cycle. Additionally, using a novel mutagenesis strategy to abrogate opp transporter function, we demonstrated that peptide uptake is essential for bacterial viability, morphogenesis, and infectivity. Our studies revealed a novel link between borrelial physiology and virulence and suggest that peptide uptake serves an intracellular signaling function regulating morphogenesis and division.
Collapse
|
36
|
Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
Collapse
Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| |
Collapse
|
37
|
Lewinson O, Livnat-Levanon N. Mechanism of Action of ABC Importers: Conservation, Divergence, and Physiological Adaptations. J Mol Biol 2017; 429:606-619. [PMID: 28104364 DOI: 10.1016/j.jmb.2017.01.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
The past decade has seen a remarkable surge in structural characterization of ATP binding cassette (ABC) transporters, which have spurred a more focused functional analysis of these elaborate molecular machines. As a result, it has become increasingly apparent that there is a substantial degree of mechanistic variation between ABC transporters that function as importers, which correlates with their physiological roles. Here, we summarize recent advances in ABC importers' structure-function studies and provide an explanation as to the origin of the different mechanisms of action.
Collapse
Affiliation(s)
- Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel.
| | - Nurit Livnat-Levanon
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel
| |
Collapse
|
38
|
Culurgioni S, Harris G, Singh AK, King SJ, Walsh MA. Structural Basis for Regulation and Specificity of Fructooligosaccharide Import in Streptococcus pneumoniae. Structure 2016; 25:79-93. [PMID: 27939783 PMCID: PMC5222590 DOI: 10.1016/j.str.2016.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/28/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022]
Abstract
Streptococcus pneumoniae is dependent on carbohydrate uptake for colonization and pathogenesis, and dedicates over a third of its transport systems to their uptake. The ability of the pneumococcus to utilize fructooligosaccharides (FOSs) is attributed to the presence of one of two types of FOS ATP-binding cassette (ABC) transporters. Strains encoding SfuABC are only able to utilize short-chain FOSs, while strains encoding FusABC can utilize both short- and long-chain FOSs. The crystal structures of the substrate-binding protein FusA in its open and closed conformations bound to FOSs, and solution scattering data of SfuA, delineate the structural basis for import of short- and long-chain FOSs. The structure of FusA identifies an EF hand-like calcium-binding motif. This is shown to be essential for translocation of FOSs in FusABC and forms the basis for the definition of a new class of substrate-binding proteins that regulate substrate translocation by calcium.
Collapse
Affiliation(s)
- Simone Culurgioni
- Diamond House, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Gemma Harris
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Anirudh K Singh
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Samantha J King
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Martin A Walsh
- Diamond House, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| |
Collapse
|
39
|
Scheepers GH, Lycklama A Nijeholt JA, Poolman B. An updated structural classification of substrate-binding proteins. FEBS Lett 2016; 590:4393-4401. [PMID: 27714801 DOI: 10.1002/1873-3468.12445] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/02/2016] [Accepted: 09/25/2016] [Indexed: 01/29/2023]
Abstract
Substrate-binding proteins (SBPs) play an important role in solute uptake and signal transduction. In 2010, Berntsson et al. classified the 114 organism-specific SBP structures available at that time and defined six protein clusters, based on their structural similarity. Since then, the number of unique SBP structures has increased almost fivefold, whereas the number of protein entries in the Protein Data Bank (PDB) nearly doubled. On the basis of the much larger dataset, we now subclassify the SBPs within the original clusters. Moreover, we propose a 7th cluster based on a small group of SBPs with structural features significantly different from those observed in the other proteins.
Collapse
Affiliation(s)
- Giel H Scheepers
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Jelger A Lycklama A Nijeholt
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| |
Collapse
|
40
|
Di DD, Jiang H, Tian LL, Kang JL, Zhang W, Yi XP, Ye F, Zhong Q, Ni B, He YY, Xia L, Yu Y, Cui BY, Mao X, Fan WX. Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330. BMC Genomics 2016; 17:741. [PMID: 27645563 PMCID: PMC5029015 DOI: 10.1186/s12864-016-3076-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/07/2016] [Indexed: 11/16/2022] Open
Abstract
Background Brucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain in China. It has been widely used for vaccination in China since 1971. Until now, the mechanisms underlie virulence attenuation of S2 are still unknown. Results In this paper, the whole genome sequencing of S2 was carried out by Illumina Hiseq2000 sequencing method. We further performed the comparative genomic analysis to find out the differences between S2 and the virulent Brucella suis strain 1330. We found premature stops in outer membrane autotransporter omaA and eryD genes. Single mutations were found in phosphatidylcholine synthase, phosphorglucosamine mutase, pyruvate kinase and FliF, which have been reported to be related to the virulence of Brucella or other bacteria. Of the other different proteins between S2 and 1330, such as Omp2b, periplasmic sugar-binding protein, and oligopeptide ABC transporter, no definitive implications related to bacterial virulence were found, which await further investigation. Conclusions The data presented here provided the rational basis for designing Brucella vaccines that could be used in other strains. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3076-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dong-Dong Di
- Laboratory of Zoonoses, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Hai Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Li-Li Tian
- Laboratory of Zoonoses, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Jing-Li Kang
- Laboratory of Zoonoses, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xin-Ping Yi
- Xinjiang Academy of Animal Science, Institute of Veterinary Research, Urumuqi, Xinjiang, China
| | - Feng Ye
- Xinjiang Academy of Animal Science, Institute of Veterinary Research, Urumuqi, Xinjiang, China
| | - Qi Zhong
- Xinjiang Academy of Animal Science, Institute of Veterinary Research, Urumuqi, Xinjiang, China
| | - Bo Ni
- Laboratory of Zoonoses, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - You-Yu He
- ZhongXin Biotechology Shanghai Co, Ltd. 12F, Building 1, 100 Qinzhou Road, Shanghai, China
| | - Lin Xia
- ZhongXin Biotechology Shanghai Co, Ltd. 12F, Building 1, 100 Qinzhou Road, Shanghai, China
| | - Yao Yu
- ZhongXin Biotechology Shanghai Co, Ltd. 12F, Building 1, 100 Qinzhou Road, Shanghai, China
| | - Bu-Yun Cui
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China.
| | - Xiang Mao
- Chinese Academy of Agricultural Sciences, Shanghai Veterinary Research Institute, Shanghai, China.
| | - Wei-Xing Fan
- Laboratory of Zoonoses, China Animal Health and Epidemiology Center, Qingdao, Shandong, China.
| |
Collapse
|
41
|
The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity. Biochem Soc Trans 2016; 43:1011-7. [PMID: 26517916 DOI: 10.1042/bst20150135] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms. Most prokaryotes have many SBP-dependent ABC transporters that recognize a broad range of ligands from metal ions to amino acids, sugars and peptides. Herein, we review the structure and function of a number of more unusual SBPs, including an ABC transporter involved in the transport of rare furanose forms of sugars and an SBP that has evolved to specifically recognize the bacterial cell wall-derived murein tripeptide (Mtp). Both these examples illustrate that subtle changes in binding-site architecture, including changes in side chains not directly involved in ligand co-ordination, can result in significant alteration of substrate range in novel and unpredictable ways.
Collapse
|
42
|
Yoon HJ, Kim HJ, Mikami B, Yu YG, Lee HH. Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile. Extremophiles 2016; 20:723-31. [PMID: 27377296 DOI: 10.1007/s00792-016-0861-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/26/2016] [Indexed: 11/30/2022]
Abstract
Oligopeptide-binding proteins (Opps) are part of the ATP-binding cassette system, playing a crucial role in nutrient uptake and sensing the external environment in bacteria, including hyperthermophiles. Opps serve as a binding platform for diverse peptides; however, how these peptides are recognized by Opps is still largely unknown and few crystal structures of Opps from hyperthermophiles have been determined. To facilitate such an understanding, the crystal structure of a putative Opp, OppA from Thermotoga maritima (TmOppA), was solved at 2.6-Å resolution in the open conformation. TmOppA is composed of three domains. The N-terminal domain consists of twelve strands, nine helices, and four 310 helices, and the C-terminal domain consists of five strands, ten helices, and one 310 helix. These two domains are connected by the linker domain, which consists of two strands, three helices, and three 310 helices. Based on structural comparisons of TmOppA with other OppAs and binding studies, we suggest that TmOppA might be a periplasmic Opp. The most distinct feature of TmOppA is the insertion of two helices, which are lacking in other OppAs. A cavity volume between the N-terminal and C-terminal domains is suggested to be responsible for binding peptides of various lengths.
Collapse
Affiliation(s)
- Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Hee Jung Kim
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, 136-702, Korea
| | - Bunzo Mikami
- Laboratory of Quality Design and Exploitation, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, 611-0011, Japan
| | - Yeon Gyu Yu
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, 136-702, Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.
| |
Collapse
|
43
|
Enterococcal Sex Pheromones: Evolutionary Pathways to Complex, Two-Signal Systems. J Bacteriol 2016; 198:1556-1562. [PMID: 27021562 DOI: 10.1128/jb.00128-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Gram-positive bacteria carry out intercellular communication using secreted peptides. Important examples of this type of communication are the enterococcal sex pheromone systems, in which the transfer of conjugative plasmids is controlled by intercellular signaling among populations of donors and recipients. This review focuses on the pheromone response system of the conjugative plasmid pCF10. The peptide pheromones regulating pCF10 transfer act by modulating the ability of the PrgX transcription factor to repress the transcription of an operon encoding conjugation functions. Many Gram-positive bacteria regulate important processes, including the production of virulence factors, biofilm formation, sporulation, and genetic exchange using peptide-mediated signaling systems. The key master regulators of these systems comprise the RRNPP (RggRap/NprR/PlcR/PrgX) family of intracellular peptide receptors; these regulators show conserved structures. While many RRNPP systems include a core module of two linked genes encoding the regulatory protein and its cognate signaling peptide, the enterococcal sex pheromone plasmids have evolved to a complex system that also recognizes a second host-encoded signaling peptide. Additional regulatory genes not found in most RRNPP systems also modulate signal production and signal import in the enterococcal pheromone plasmids. This review summarizes several structural studies that cumulatively demonstrate that the ability of three pCF10 regulatory proteins to recognize the same 7-amino-acid pheromone peptide arose by convergent evolution of unrelated proteins from different families. We also focus on the selective pressures and structure/function constraints that have driven the evolution of pCF10 from a simple, single-peptide system resembling current RRNPPs in other bacteria to the current complex inducible plasmid transfer system.
Collapse
|
44
|
Maurer M, de Beer SBA, Oostenbrink C. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Molecules 2016; 21:499. [PMID: 27092480 PMCID: PMC5881882 DOI: 10.3390/molecules21040499] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 03/30/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.
Collapse
Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| | - Stephanie B A de Beer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| |
Collapse
|
45
|
Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913. J Bacteriol 2015; 197:1125-34. [PMID: 25605306 DOI: 10.1128/jb.02600-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Peptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements. PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr). PsDppA alternates between an "open" and a "closed" form during substrate binding. Structural analyses of the 4 PsDppA-substrate complexes combined with mutational assays indicate that PsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake. IMPORTANCE Peptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unliganded PsDppA and PsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism of PsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism of PsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.
Collapse
|
46
|
Duar RM, Clark KJ, Patil PB, Hernández C, Brüning S, Burkey TE, Madayiputhiya N, Taylor SL, Walter J. Identification and characterization of intestinal lactobacilli strains capable of degrading immunotoxic peptides present in gluten. J Appl Microbiol 2014; 118:515-27. [PMID: 25376327 DOI: 10.1111/jam.12687] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/15/2014] [Accepted: 10/30/2014] [Indexed: 01/17/2023]
Abstract
AIM Identify and characterize bacteria from the proximal gastrointestinal tract of pigs capable of degrading immunogenic gluten peptides. METHODS AND RESULTS Bacteria were cultured from the small intestine of pigs fed a 20% gluten diet and from an enrichment media with the 18-mer peptide LQLQPFPQPQLPYPQPQL. Isolates were screened for the production of specialized proteolytic enzymes and the ability to degrade and remove metastable peptides from α-gliadin (16-mer and 33-mer) and ω-gliadin (17-mer), with established roles in the aetiology of coeliac disease. Degradation was determined by ELISA and mass spectrometry (UHPLC-MS/MS in MRM mode), and hydrolysis fragments were characterized by LC-MS/MS. Four strains from the species Lactobacillus ruminis, Lactobacillus johnsonii, Lactobacillus amylovorus and Lactobacillus salivarius showed the highest peptide-degrading activities. Strains displayed different degradation rates and cleavage patterns that resulted in reduction but not complete removal of immunotoxic epitopes. CONCLUSIONS We employed a unique enrichment process to select for bacteria adapted to the conditions of the proximal gastrointestinal tract with the ability to partially detoxify well-characterized peptides involved in coeliac disease. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides a basis for the selection of Lactobacillus strains for probiotic applications aimed to reduce epitope-containing gluten peptides before reaching the epithelium of the small intestine of patients with coeliac disease.
Collapse
Affiliation(s)
- R M Duar
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA; Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Wium M, Botes A, Bellstedt DU. The identification of oppA gene homologues as part of the oligopeptide transport system in mycoplasmas. Gene 2014; 558:31-40. [PMID: 25528211 DOI: 10.1016/j.gene.2014.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/03/2014] [Accepted: 12/16/2014] [Indexed: 11/27/2022]
Abstract
The lack of an annotated oppA gene as part of many oligopeptide permease (opp) operons has questioned the necessity of the oligopeptide-binding domain (OppA) as a part of the Opp transport system in mycoplasmas. This study investigated the occurrence of an oppA gene as part of the oppBCDF operon in 42 mycoplasma genomes. Except for hemoplasma, all mycoplasmas were found to possess one or more copies of the oppBCDF operon and with the help of similarity searches their oppA genes could be identified. Phylogenetic analysis of the combined OppABCDF amino acid sequences allowed them to be grouped into three types. Each type has a unique set of conserved motifs, which are likely to reflect substrate preference and adaption strategies. Our approach allowed the identification of oppA gene homologues for all mycoplasma opp operons and thereby provides a method for re-evaluating the current annotation of oppA genes in mycoplasma genomes.
Collapse
Affiliation(s)
- Martha Wium
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Annelise Botes
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
48
|
Lebrette H, Brochier-Armanet C, Zambelli B, de Reuse H, Borezée-Durant E, Ciurli S, Cavazza C. Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins. Structure 2014; 22:1421-32. [PMID: 25199691 DOI: 10.1016/j.str.2014.07.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/16/2014] [Accepted: 07/13/2014] [Indexed: 10/24/2022]
Abstract
In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.
Collapse
Affiliation(s)
- Hugo Lebrette
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France; CNRS, IBS, 38044 Grenoble, France; CEA, IBS, 38044 Grenoble, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy
| | - Hilde de Reuse
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Elise Borezée-Durant
- INRA, UMR 1319 Micalis, 78350 Jouy en Josas, France; Agro ParisTech, UMR Micalis, 78350 Jouy en Josas, France
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy.
| | - Christine Cavazza
- University Grenoble Alpes, LCBM, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France.
| |
Collapse
|
49
|
Negami T, Shimizu K, Terada T. Coarse-grained molecular dynamics simulations of protein-ligand binding. J Comput Chem 2014; 35:1835-45. [PMID: 25043724 DOI: 10.1002/jcc.23693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/06/2014] [Accepted: 07/09/2014] [Indexed: 01/25/2023]
Abstract
Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.
Collapse
Affiliation(s)
- Tatsuki Negami
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | | | | |
Collapse
|
50
|
Newstead S. Molecular insights into proton coupled peptide transport in the PTR family of oligopeptide transporters. Biochim Biophys Acta Gen Subj 2014; 1850:488-99. [PMID: 24859687 PMCID: PMC4331665 DOI: 10.1016/j.bbagen.2014.05.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 12/15/2022]
Abstract
Background Cellular uptake of small peptides is an important physiological process mediated by the PTR family of proton-coupled peptide transporters. In bacteria peptides can be used as a source of amino acids and nitrogen. Similarly in humans peptide transport is the principle route for the uptake and retention of dietary protein in the form of short di- and tri-peptides for cellular metabolism. Scope of the review Recent crystal structures of bacterial PTR family transporters, combined with biochemical studies of transport have revealed key molecular details underpinning ligand promiscuity and the mechanism of proton-coupled transport within the family. Major conclusions Pairs of salt bridge interactions between transmembrane helices work in tandem to orchestrate alternating access transport within the PTR family. Key roles for residues conserved between bacterial and eukaryotic homologues suggest a conserved mechanism of peptide recognition and transport that in some cases has been subtly modified in individual species. General significance Physiological studies on PepT1 and PepT2, the mammalian members of this family, have identified these transporters as being responsible for the uptake of many pharmaceutically important drug molecules, including antibiotics and antiviral medications and demonstrated their promiscuity can be used for improving the oral bioavailability of poorly absorbed compounds. The insights gained from recent structural studies combined with previous physiological and biochemical analyses are rapidly advancing our understanding of this medically important transporter superfamily. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins. Crystal structures of PTR family transporters Identification of mechanistically important salt bridge interactions. Conservation of key functional residues between bacterial and mammalian homologues. High resolution structural information on peptide binding.
Collapse
Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| |
Collapse
|