1
|
Simpson BW, McLean AB, Trent MS. A conserved hub protein for coordinating peptidoglycan turnover that activates cell division amidases in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612460. [PMID: 39314424 PMCID: PMC11419085 DOI: 10.1101/2024.09.11.612460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Gram-negative bacteria produce a multilayered cell envelope in which their peptidoglycan is sandwiched between two membranes, an inner membrane made of glycerophospholipids and an asymmetric outer membrane with glycerophospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet. The Acinetobacter baumannii outer membrane contains lipooligosaccharide (LOS), a variant of LPS lacking O-antigen. LPS/LOS is typically essential, but A. baumannii can survive without LOS. Previously, we found that the peptidoglycan biogenesis protein NlpD becomes essential during LOS-deficiency. NlpD is typically redundant and is one of the cell's amidase activators for regulating peptidoglycan degradation, a process critical for cell division. We found that NlpD is essential under these conditions because a second putative amidase activator, termed WthA (cell w all turnover h ub protein A ), no longer functions in LOS-deficient cells. Mutants lacking WthA had severe cell division defects and were synthetically sick with loss of NlpD. Both Acinetobacter WthA and NlpD were found to activate an amidase activity of Oxa51, a chromosomally encoded β -lactamase. Further, WthA is homologous to Pseudomonas LbcA that impacts two other classes of peptidoglycan degradation enzymes, endopeptidases and lytic transglycosylases. WthA/LbcA homologs were identified across Proteobacteria, Bacteroidota, and Chlorobiota, suggesting they belong to a conserved family involved in regulation of peptidoglycan turnover. While Acinetobacter WthA may share functions of Pseudomonas LbcA, we found no evidence that LbcA is an amidase activator. Altogether, we have identified a missing player in Acinetobacter peptidoglycan biogenesis, a conserved hub protein that regulates multiple peptidoglycan turnover enzymes including cell division amidases. Significance Statement Peptidoglycan is a rigid layer that provides structural support to bacterial cells. Peptidoglycan must be degraded to make room for new synthesis and for cells to divide, a process termed turnover. Turnover enzymes are tightly regulated to prevent their activities from lysing the cell. The critical pathogen Acinetobacter baumannii was missing known peptidoglycan amidases, a class of turnover enzymes, and the key activator that controls their activity during cell division. We have identified WthA as having a role in cell division most likely as an amidase activator. WthA homologs were widely distributed in bacteria and the closely related LbcA in Pseudomonas impacts two other types of turnover enzymes. We explore the possible functions of this new family of proteins that serves as a hub for impacting peptidoglycan turnover.
Collapse
|
2
|
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
|
3
|
Simpson BW, Gilmore MC, McLean AB, Cava F, Trent MS. Escherichia coli CadB is capable of promiscuously transporting muropeptides and contributing to peptidoglycan recycling. J Bacteriol 2024; 206:e0036923. [PMID: 38169298 PMCID: PMC10810205 DOI: 10.1128/jb.00369-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
The bacterial peptidoglycan (PG) cell wall is remodeled during growth and division, releasing fragments called muropeptides. Muropeptides can be internalized and reused in a process called PG recycling. Escherichia coli is highly devoted to recycling muropeptides and is known to have at least two transporters, AmpG and OppBCDF, that import them into the cytoplasm. While studying mutants lacking AmpG, we unintentionally isolated mutations that led to the altered expression of a third transporter, CadB. CadB is normally upregulated under acidic pH conditions and is an antiporter for lysine and cadaverine. Here, we explored if CadB was altering PG recycling to assist in the absence of AmpG. Surprisingly, CadB overexpression was able to restore PG recycling when both AmpG and OppBCDF were absent. CadB was found to import freed PG peptides, a subpopulation of muropeptides, through a promiscuous activity. Altogether, our data support that CadB is a third transporter capable of contributing to PG recycling. IMPORTANCE Bacteria produce a rigid mesh cell wall. During growth, the cell wall is remodeled, which releases cell wall fragments. If released into the extracellular environment, cell wall fragments can trigger inflammation by the immune system of a host. Gastrointestinal bacteria, like Escherichia coli, have dedicated pathways to recycle almost all cell wall fragments they produce. E. coli contains two known recycling transporters, AmpG and Opp, that we previously showed are optimized for growth in different environments. Here, we identify that a third transporter, CadB, can also contribute to cell wall recycling. This work expands our understanding of cell wall recycling and highlights the dedication of organisms like E. coli to ensure high recycling in multiple growth environments.
Collapse
Affiliation(s)
- Brent W. Simpson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Michael C. Gilmore
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Amanda Briann McLean
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
4
|
Simpson BW, Gilmore MC, McLean AB, Cava F, Trent MS. Escherichia coli utilizes multiple peptidoglycan recycling permeases with distinct strategies of recycling. Proc Natl Acad Sci U S A 2023; 120:e2308940120. [PMID: 37871219 PMCID: PMC10622912 DOI: 10.1073/pnas.2308940120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023] Open
Abstract
Bacteria produce a structural layer of peptidoglycan (PG) that enforces cell shape, resists turgor pressure, and protects the cell. As bacteria grow and divide, the existing layer of PG is remodeled and PG fragments are released. Enterics such as Escherichia coli go to great lengths to internalize and reutilize PG fragments. E. coli is estimated to break down one-third of its cell wall, yet only loses ~0 to 5% of meso-diaminopimelic acid, a PG-specific amino acid, per generation. Two transporters were identified early on to possibly be the primary permease that facilitates PG fragment recycling, i) AmpG and ii) the Opp ATP binding cassette transporter in conjunction with a PG-specific periplasmic binding protein, MppA. The contribution of each transporter to PG recycling has been debated. Here, we have found that AmpG and MppA/Opp are differentially regulated by carbon source and growth phase. In addition, MppA/Opp is uniquely capable of high-affinity scavenging of muropeptides from growth media, demonstrating that AmpG and MppA/Opp allow for different strategies of recycling PG fragments. Altogether, this work clarifies environmental contexts under which E. coli utilizes distinct permeases for PG recycling and explores how scavenging by MppA/Opp could be beneficial in mixed communities.
Collapse
Affiliation(s)
- Brent W. Simpson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA30602
| | - Michael C. Gilmore
- Laboratory for Molecular Infection Medicine Sweden, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, Umeå90187, Sweden
| | - Amanda Briann McLean
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA30602
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, Umeå90187, Sweden
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA30602
- Department of Microbiology, College of Art and Sciences, University of Georgia, Athens, GA30602
| |
Collapse
|
5
|
Drousiotis K, Herman R, Hawkhead J, Leech A, Wilkinson A, Thomas GH. Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001308. [PMID: 36920280 PMCID: PMC10191376 DOI: 10.1099/mic.0.001308] [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: 11/01/2022] [Accepted: 02/07/2023] [Indexed: 03/16/2023]
Abstract
Microbes that have evolved to live on lignocellulosic biomass face unique challenges in the effective and efficient use of this material as food. The bacterium Shewanella sp. ANA-3 has the potential to utilize arabinan and arabinoxylan, and uptake of the monosaccharide, l-arabinose, derived from these polymers, is known to be mediated by a single ABC transporter. We demonstrate that the substrate binding protein of this system, GafASw, binds specifically to l-arabinofuranose, which is the rare furanose form of l-arabinose found in lignocellulosic biomass. The structure of GafASw was resolved to 1.7 Å and comparison to Escherichia coli YtfQ (GafAEc) revealed binding site adaptations that confer specificity for furanose over pyranose forms of monosaccharides, while selecting arabinose over another related monosaccharide, galactose. The discovery of a bacterium with a natural predilection for a sugar found abundantly in certain lignocellulosic materials suggests an intimate connection in the enzymatic release and uptake of the sugar, perhaps to prevent other microbes scavenging this nutrient before it mutarotates to l-arabinopyranose. This biological discovery also provides a clear route to engineer more efficient utilization of plant biomass components in industrial biotechnology.
Collapse
Affiliation(s)
| | - Reyme Herman
- Department of Biology, University of York, PO Box 373, York, UK
| | - Judith Hawkhead
- Department of Biology, University of York, PO Box 373, York, UK
| | - Andrew Leech
- Biology Technology Facility, University of York, PO Box 373, York. YO10 5YW, UK
| | - Anthony Wilkinson
- Department of Chemistry, York Structural Biology Laboratory, University of York, PO Box 373, York. YO10 5YW, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, PO Box 373, York, UK
| |
Collapse
|
6
|
Thomas GH. Microbial Musings - Winter 2022. MICROBIOLOGY (READING, ENGLAND) 2022; 168:micro001310. [PMID: 36848206 PMCID: PMC10009517 DOI: 10.1099/mic.0.001310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 03/01/2023]
|
7
|
Hughes AM, Darby JF, Dodson EJ, Wilson SJ, Turkenburg JP, Thomas GH, Wilkinson AJ. Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748525 DOI: 10.1099/mic.0.001274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.
Collapse
Affiliation(s)
- Adam M Hughes
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - John F Darby
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Eleanor J Dodson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Samuel J Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Johan P Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
8
|
Thomas GH. Microbial Musings - October 2020. MICROBIOLOGY-SGM 2020; 166:891-893. [PMID: 33124974 PMCID: PMC7660917 DOI: 10.1099/mic.0.000989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Peptidoglycan Sensing Prevents Quiescence and Promotes Quorum-Independent Colony Growth of Uropathogenic Escherichia coli. J Bacteriol 2020; 202:JB.00157-20. [PMID: 32778561 DOI: 10.1128/jb.00157-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/04/2020] [Indexed: 11/20/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the leading cause of human urinary tract infections (UTIs), and many patients experience recurrent infection after successful antibiotic treatment. The source of recurrent infections may be persistent bacterial reservoirs in vivo that are in a quiescent state and thus are not susceptible to antibiotics. Here, we show that multiple UPEC strains require a quorum to proliferate in vitro with glucose as the carbon source. At low cell density, the bacteria remain viable but enter a quiescent, nonproliferative state. Of the clinical UPEC isolates tested to date, 35% (51/145) enter this quiescent state, including isolates from the recently emerged, multidrug-resistant pandemic lineage ST131 (i.e., strain JJ1886) and isolates from the classic endemic lineage ST73 (i.e., strain CFT073). Moreover, quorum-dependent UPEC quiescence is prevented and reversed by small-molecule proliferants that stimulate colony formation. These proliferation cues include d-amino acid-containing peptidoglycan (PG) tetra- and pentapeptides, as well as high local concentrations of l-lysine and l-methionine. Peptidoglycan fragments originate from the peptidoglycan layer that supports the bacterial cell wall but are released as bacteria grow. These fragments are detected by a variety of organisms, including human cells, other diverse bacteria, and, as we show here for the first time, UPEC. Together, these results show that for UPEC, (i) sensing of PG stem peptide and uptake of l-lysine modulate the quorum-regulated decision to proliferate and (ii) quiescence can be prevented by both intra- and interspecies PG peptide signaling.IMPORTANCE Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs). During pathogenesis, UPEC cells adhere to and infiltrate bladder epithelial cells, where they may form intracellular bacterial communities (IBCs) or enter a nongrowing or slowly growing quiescent state. Here, we show in vitro that UPEC strains at low population density enter a reversible, quiescent state by halting division. Quiescent cells resume proliferation in response to sensing a quorum and detecting external signals, or cues, including peptidoglycan tetra- and pentapeptides.
Collapse
|
10
|
Herman R, Bennett-Ness C, Maqbool A, Afzal A, Leech A, Thomas GH. The Salmonella enterica serovar Typhimurium virulence factor STM3169 is a hexuronic acid binding protein component of a TRAP transporter. MICROBIOLOGY-SGM 2020; 166:981-987. [PMID: 32894213 PMCID: PMC7660916 DOI: 10.1099/mic.0.000967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The intracellular pathogen S. Typhimurium is a leading cause of foodborne illness across the world and is known to rely on a range of virulence factors to colonize the human host and cause disease. The gene coding for one such factor, stm3169, was determined to be upregulated upon macrophage entry and its disruption reduces survival in the macrophage. In this study we characterize the STM3169 protein, which forms the substrate binding protein (SBP) of an uncharacterized tripartite ATP-independent periplasmic (TRAP) transporter. Genome context analysis of the genes encoding this system in related bacteria suggests a function in sugar acid transport. We demonstrate that purified STM3169 binds d-glucuronic acid with high affinity and specificity. S. Typhimurium LT2 can use this sugar acid as a sole carbon source and the genes for a probable catabolic pathway are present in the genome. As this gene was previously implicated in macrophage survival, it suggests a role for d-glucuronate as an important carbon source for S. Typhimurium in this environment.
Collapse
Affiliation(s)
- Reyme Herman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Cavan Bennett-Ness
- Present address: Institute of Genetics and Molecular Medicine, University of Edinburgh WGH, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Abbas Maqbool
- Present address: The Sainsbury Laboratory, Norwich NR4 7UH, UK
| | - Amna Afzal
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Andrew Leech
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
- *Correspondence: Gavin H. Thomas,
| |
Collapse
|
11
|
Chlamydia trachomatis Oligopeptide Transporter Performs Dual Functions of Oligopeptide Transport and Peptidoglycan Recycling. Infect Immun 2020; 88:IAI.00086-20. [PMID: 32094256 DOI: 10.1128/iai.00086-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Peptidoglycan, the sugar-amino acid polymer that composes the bacterial cell wall, requires a significant expenditure of energy to synthesize and is highly immunogenic. To minimize the loss of an energetically expensive metabolite and avoid host detection, bacteria often recycle their peptidoglycan, transporting its components back into the cytoplasm, where they can be used for subsequent rounds of new synthesis. The peptidoglycan-recycling substrate binding protein (SBP) MppA, which is responsible for recycling peptidoglycan fragments in Escherichia coli, has not been annotated for most intracellular pathogens. One such pathogen, Chlamydia trachomatis, has a limited capacity to synthesize amino acids de novo and therefore must obtain oligopeptides from its host cell for growth. Bioinformatics analysis suggests that the putative C. trachomatis oligopeptide transporter OppABCDF (OppABCDF Ct ) encodes multiple SBPs (OppA1 Ct , OppA2 Ct , and OppA3 Ct ). Intracellular pathogens often encode multiple SBPs, while only one, OppA, is encoded in the E. coli opp operon. We hypothesized that the putative OppABCDF transporter of C. trachomatis functions in both oligopeptide transport and peptidoglycan recycling. We coexpressed the putative SBP genes (oppA1Ct , oppA2Ct , oppA3Ct ) along with oppBCDFCt in an E. coli mutant lacking the Opp transporter and determined that all three chlamydial OppA subunits supported oligopeptide transport. We also demonstrated the in vivo functionality of the chlamydial Opp transporter in C. trachomatis Importantly, we found that one chlamydial SBP, OppA3 Ct , possessed dual substrate recognition properties and is capable of transporting peptidoglycan fragments (tri-diaminopimelic acid) in E. coli and in C. trachomatis These findings suggest that Chlamydia evolved an oligopeptide transporter to facilitate the acquisition of oligopeptides for growth while simultaneously reducing the accumulation of immunostimulatory peptidoglycan fragments in the host cell cytosol. The latter property reflects bacterial pathoadaptation that dampens the host innate immune response to Chlamydia infection.
Collapse
|
12
|
Sterling AJ, Snelling WJ, Naughton PJ, Ternan NG, Dooley JSG. Competent but complex communication: The phenomena of pheromone-responsive plasmids. PLoS Pathog 2020; 16:e1008310. [PMID: 32240270 PMCID: PMC7117660 DOI: 10.1371/journal.ppat.1008310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system for genetic exchange that allows antimicrobial-resistance determinants to spread within bacterial populations. The pCF10 plasmid system is the best characterised, and although other PRP systems are structurally similar, they lack exact functional homologues of pCF10-encoded genes. In this review, we provide an overview of the enterococcal PRP systems, incorporating functional details for the less-well-defined systems. We catalogue the virulence-associated elements of the PRPs that have been identified to date, and we argue that this reinforces the requirement for elucidation of the less studied systems.
Collapse
Affiliation(s)
- Amy J. Sterling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
- * E-mail:
| | - William J. Snelling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Patrick J. Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Nigel G. Ternan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - James S. G. Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| |
Collapse
|
13
|
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
|
14
|
Hughes A, Wilson S, Dodson EJ, Turkenburg JP, Wilkinson AJ. Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile. Acta Crystallogr F Struct Biol Commun 2019; 75:246-253. [PMID: 30950825 PMCID: PMC6450515 DOI: 10.1107/s2053230x1900178x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 12/21/2022] Open
Abstract
Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC-type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide-binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form. Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and compositions. Re-examination of the protein sequences together with structure comparisons prompts the proposal that CdAppA is not a versatile peptide-binding protein but instead may bind a restricted set of peptides. Meanwhile, CdOppA is likely to be the receptor protein for a nickel-uptake system.
Collapse
Affiliation(s)
- Adam Hughes
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Samuel Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Eleanor J. Dodson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| |
Collapse
|
15
|
Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. BIOLOGY 2018; 7:biology7020030. [PMID: 29783769 PMCID: PMC6022919 DOI: 10.3390/biology7020030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 01/28/2023]
Abstract
Periplasmic ligand-binding proteins (PBPs) bind ligands with a high affinity and specificity. They undergo a large conformational change upon ligand binding, and they have a robust protein fold. These physical features have made them ideal candidates for use in protein engineering projects to develop novel biosensors and signaling molecules. The Escherichia coli MppA (murein peptide permease A) PBP binds the murein tripeptide, l-alanyl-γ-d-glutamyl-meso-diaminopimelate, (l-Ala-γ-d-Glu-meso-Dap), which contains both a D-amino acid and a gamma linkage between two of the amino acids. We have solved a high-resolution X-ray crystal structure of E. coli MppA at 1.5 Å resolution in the unliganded, open conformation. Now, structures are available for this member of the PBP protein family in both the liganded/closed form and the unliganded/open form.
Collapse
|
16
|
Whiteley AT, Garelis NE, Peterson BN, Choi PH, Tong L, Woodward JJ, Portnoy DA. c-di-AMP modulates Listeria monocytogenes central metabolism to regulate growth, antibiotic resistance and osmoregulation. Mol Microbiol 2017; 104:212-233. [PMID: 28097715 DOI: 10.1111/mmi.13622] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2017] [Indexed: 12/26/2022]
Abstract
Cyclic diadenosine monophosphate (c-di-AMP) is a conserved nucleotide second messenger critical for bacterial growth and resistance to cell wall-active antibiotics. In Listeria monocytogenes, the sole diadenylate cyclase, DacA, is essential in rich, but not synthetic media and ΔdacA mutants are highly sensitive to the β-lactam antibiotic cefuroxime. In this study, loss of function mutations in the oligopeptide importer (oppABCDF) and glycine betaine importer (gbuABC) allowed ΔdacA mutants to grow in rich medium. Since oligopeptides were sufficient to inhibit growth of the ΔdacA mutant we hypothesized that oligopeptides act as osmolytes, similar to glycine betaine, to disrupt intracellular osmotic pressure. Supplementation with salt stabilized the ΔdacA mutant in rich medium and restored cefuroxime resistance. Additional suppressor mutations in the acetyl-CoA binding site of pyruvate carboxylase (PycA) rescued cefuroxime resistance and resulted in a 100-fold increase in virulence of the ΔdacA mutant. PycA is inhibited by c-di-AMP and these mutations prompted us to examine the role of TCA cycle enzymes. Inactivation of citrate synthase, but not down-stream enzymes suppressed ΔdacA phenotypes. These data suggested that c-di-AMP modulates central metabolism at the pyruvate node to moderate citrate production and indeed, the ΔdacA mutant accumulated six times the concentration of citrate present in wild-type bacteria.
Collapse
Affiliation(s)
- Aaron T Whiteley
- Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas E Garelis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Bret N Peterson
- Graduate Group in Microbiology, University of California, Berkeley, Berkeley, CA, USA
| | - Philip H Choi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
17
|
Genome scale identification, structural analysis, and classification of periplasmic binding proteins from Mycobacterium tuberculosis. Curr Genet 2016; 63:553-576. [DOI: 10.1007/s00294-016-0664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 01/26/2023]
|
18
|
Morimoto H, Kadoya R, Takahashi K, Kasahara Y. Proteome analysis of Pseudomonas putida F1 genes induced in soil environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:825-832. [PMID: 27452675 DOI: 10.1111/1758-2229.12445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Knowledge of the gene expression dynamics of a single soil bacterial strain contributes to the understanding of its behaviour, physiological state and surrounding microenvironment. Genes expressed in soil environments rather than in laboratory media are considered to particularly relevant. Here, we compared genome-wide gene expression profiles of the bacterium Pseudomonas putida F1 inoculated in three different types of nonsterile soils deduced using proteome analysis via sodium dodecyl sulfate-polyacrylamide gel electrophoresis combined with liquid chromatography-tandem mass spectrometry. Proteins commonly detected in all three samples and involved with bacterial growth and fundamental metabolism were excluded. Nine proteins were identified as specifically expressed in soil including an aldehyde dehydrogenase, a nitric oxide dioxygenase and five proteins encoded by a cluster of metabolism-associated genes. Expression factor analysis revealed that the nitric oxide dioxygenase-coding gene was induced by nitric oxide and the five clustered genes were induced under phosphate starvation. The expression of these genes can be attributed to response to soil environmental stimuli surrounding the F1 cells. These results strongly suggest that our soil metaproteome approach is useful for understanding the autecology and lifestyle of a single bacterial strain in soil environments and allows the prediction of the microenvironment surrounding the bacterial cells.
Collapse
Affiliation(s)
- Hajime Morimoto
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Ryosuke Kadoya
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Kazuhiro Takahashi
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| |
Collapse
|
19
|
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
|
20
|
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
|
21
|
Tavío MM, Aquili VD, Vila J, Poveda JB. Resistance to ceftazidime in Escherichia coli associated with AcrR, MarR and PBP3 mutations and overexpression of sdiA. J Med Microbiol 2014; 63:56-65. [DOI: 10.1099/jmm.0.063727-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mechanisms responsible for the increase in ceftazidime MIC in two Escherichia coli in vitro selected mutants, Caz/20-1 and Caz/20-2, were studied. OmpF loss and overexpression of acrB, acrD and acrF that were associated with acrR and marR mutations and sdiA overexpression, together with mutations A233T and I332V in FtSI (PBP3) resulted in ceftazidime resistance in Caz/20-2, multiplying by 128-fold the ceftazidime MIC in the parental clinical isolate PS/20. Absence of detectable β-lactamase hydrolytic activity in the crude extract of Caz/20-2 was observed, and coincided with Q191K and P209S mutations in AmpC and a nucleotide substitution at −28 in the ampC promoter, whereas β-lactamase hydrolytic activity in crude extracts of PS/20 and Caz/20-1 strains was detected. Nevertheless, a fourfold increase in ceftazidime MIC in Caz/20-1 compared with that in PS/20 was due to the increased transcript level of acrB derived from acrR mutation. The two Caz mutants and PS/20 showed the same mutations in AmpG and ParE.
Collapse
Affiliation(s)
- María M. Tavío
- Unidad de Epidemiología y Medicina Preventiva, Instituto Universitario de Sanidad Animal (IUSA), Universidad de Las Palmas de Gran Canaria, Arucas, Spain
- Microbiología, Departamento de Ciencias Clínicas, Facultad de Ciencias de la Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Virginia D. Aquili
- Microbiología, Departamento de Ciencias Clínicas, Facultad de Ciencias de la Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Jordi Vila
- Departamento de Microbiología, IDIBAPS, Facultad de Medicina, Universidad de Barcelona, Barcelona, Spain
| | - José B. Poveda
- Unidad de Epidemiología y Medicina Preventiva, Instituto Universitario de Sanidad Animal (IUSA), Universidad de Las Palmas de Gran Canaria, Arucas, Spain
| |
Collapse
|
22
|
Fortifying the wall: synthesis, regulation and degradation of bacterial peptidoglycan. Curr Opin Struct Biol 2013; 23:695-703. [DOI: 10.1016/j.sbi.2013.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/28/2013] [Accepted: 07/11/2013] [Indexed: 12/24/2022]
|
23
|
Basavanna S, Chimalapati S, Maqbool A, Rubbo B, Yuste J, Wilson RJ, Hosie A, Ogunniyi AD, Paton JC, Thomas G, Brown JS. The effects of methionine acquisition and synthesis on Streptococcus pneumoniae growth and virulence. PLoS One 2013; 8:e49638. [PMID: 23349662 PMCID: PMC3551916 DOI: 10.1371/journal.pone.0049638] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/16/2012] [Indexed: 11/19/2022] Open
Abstract
Bacterial pathogens need to acquire nutrients from the host, but for many nutrients their importance during infection remain poorly understood. We have investigated the importance of methionine acquisition and synthesis for Streptococcus pneumoniae growth and virulence using strains with gene deletions affecting a putative methionine ABC transporter lipoprotein (Sp_0149, metQ) and/or methionine biosynthesis enzymes (Sp_0585 - Sp_0586, metE and metF). Immunoblot analysis confirmed MetQ was a lipoprotein and present in all S. pneumoniae strains investigated. However, vaccination with MetQ did not prevent fatal S. pneumoniae infection in mice despite stimulating a strong specific IgG response. Tryptophan fluorescence spectroscopy and isothermal titration calorimetry demonstrated that MetQ has both a high affinity and specificity for L-methionine with a KD of ∼25 nM, and a ΔmetQ strain had reduced uptake of C14-methionine. Growth of the ΔmetQ/ΔmetEF strain was greatly impaired in chemically defined medium containing low concentrations of methionine and in blood but was partially restored by addition of high concentrations of exogenous methionine. Mixed infection models showed no attenuation of the ΔmetQ, ΔmetEF and ΔmetQ/ΔmetEF strains in their ability to colonise the mouse nasopharnyx. In a mouse model of systemic infection although significant infection was established in all mice, there were reduced spleen bacterial CFU after infection with the ΔmetQ/ΔmetEF strain compared to the wild-type strain. These data demonstrate that Sp_0149 encodes a high affinity methionine ABC transporter lipoprotein and that Sp_0585 – Sp_0586 are likely to be required for methionine synthesis. Although Sp_0149 and Sp_0585-Sp_0586 make a contribution towards full virulence, neither was essential for S. pneumoniae survival during infection.
Collapse
Affiliation(s)
- Shilpa Basavanna
- Department of Microbiology and Molecular Genetics, University of Texas-Houston Medical School, Houston, Texas, United States of America
| | - Suneeta Chimalapati
- Department of Medicine, Centre for Inflammation and Tissue Repair, University College Medical School, Rayne Institute, London, United Kingdom
| | - Abbas Maqbool
- Department of Biology (Area 10), University of York, York, United Kingdom
| | - Bruna Rubbo
- Department of Medicine, Centre for Inflammation and Tissue Repair, University College Medical School, Rayne Institute, London, United Kingdom
| | - Jose Yuste
- Centro de Investigaciones Biologicas, CSIC and CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Robert J. Wilson
- Department of Medicine, Centre for Inflammation and Tissue Repair, University College Medical School, Rayne Institute, London, United Kingdom
| | - Arthur Hosie
- Division of Science, University of Bedfordshire, Park Square, Luton, Bedfordshire, United Kingdom
| | - Abiodun D. Ogunniyi
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - James C. Paton
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Gavin Thomas
- Department of Biology (Area 10), University of York, York, United Kingdom
| | - Jeremy S. Brown
- Department of Medicine, Centre for Inflammation and Tissue Repair, University College Medical School, Rayne Institute, London, United Kingdom
- * E-mail:
| |
Collapse
|
24
|
MpaA is a murein-tripeptide-specific zinc carboxypeptidase that functions as part of a catabolic pathway for peptidoglycan-derived peptides in γ-proteobacteria. Biochem J 2013; 448:329-41. [PMID: 22970852 DOI: 10.1042/bj20121164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The murein peptide amidase MpaA is a cytoplasmic enzyme that processes peptides derived from the turnover of murein. We have purified the enzyme from Escherichia coli and demonstrated that it efficiently hydrolyses the γ-D-glutamyl-diaminopimelic acid bond in the murein tripeptide (L-Ala-γ-D-Glu-meso-Dap), with Km and kcat values of 0.41±0.05 mM and 38.3±10 s-1. However, it is unable to act on the murein tetrapeptide (L-Ala-γ-D-Glu-meso-Dap-D-Ala). E. coli MpaA is a homodimer containing one bound zinc ion per chain, as judged by mass spectrometric analysis and size-exclusion chromatography. To investigate the structure of MpaA we solved the crystal structure of the orthologous protein from Vibrio harveyi to 2.17 Å (1Å=0.1 nm). Vh_MpaA, which has identical enzymatic and biophysical properties to the E. coli enzyme, has high structural similarity to eukaryotic zinc carboxypeptidases. The structure confirms that MpaA is a dimeric zinc metalloprotein. Comparison of the structure of MpaA with those of other carboxypeptidases reveals additional structure that partially occludes the substrate-binding groove, perhaps explaining the narrower substrate specificity of the enzyme compared with other zinc carboxypeptidases. In γ-proteobacteria mpaA is often located adjacent to mppA which encodes a periplasmic transporter protein previously shown to bind murein tripeptide. We demonstrate that MppA can also bind murein tetrapeptide with high affinity. The genetic coupling of these genes and their related biochemical functions suggest that MpaA amidase and MppA transporter form part of a catabolic pathway for utilization of murein-derived peptides that operates in γ-proteobacteria in addition to the established murein recycling pathways.
Collapse
|
25
|
Synthetic tripeptides as alternate substrates of murein peptide ligase (Mpl). Biochimie 2012; 95:1120-6. [PMID: 23270797 DOI: 10.1016/j.biochi.2012.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
Abstract
Murein peptide ligase (Mpl) is an enzyme found in Gram-negative bacteria. It catalyses the addition of tripeptide L-Ala-γ-D-Glu-meso-diaminopimelate to nucleotide precursor UDP-N-acetylmuramic acid during the recycling of peptidoglycan. Although not essential, this enzyme represents an interesting target for antibacterial compounds through the synthesis of alternate substrates whose incorporation into peptidoglycan might be deleterious for the bacterial cell. Therefore, we have synthesised 10 tripeptides L-Ala-γ-D-Glu-Xaa in which Xaa represents amino acids different from diaminopimelic acid. Tripeptide with Xaa = ε-D-Lys proved to be an excellent substrate of Escherichia coli Mpl in vitro. Tripeptides with Xaa = p-amino- or p-nitro-L-phenylalanine were poor substrates, while tripeptides with Xaa = D- or L-2-aminopimelate, DL-2-aminoheptanoic acid, L-Glu, L-norleucine, L-norvaline, L-2-aminobutyric acid or L-Ala were not substrates at all. Although a good Mpl substrate, the D-Lys-containing tripeptide was devoid of antibacterial activity against E. coli, presumably owing to poor uptake.
Collapse
|
26
|
Berntsson RPA, Schuurman-Wolters GK, Dunny G, Slotboom DJ, Poolman B. Structure and mode of peptide binding of pheromone receptor PrgZ. J Biol Chem 2012; 287:37165-70. [PMID: 22948145 DOI: 10.1074/jbc.m112.386334] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present the crystal structure of the pheromone receptor protein PrgZ from Enterococcus faecalis in complex with the heptapeptide cCF10 (LVTLVFV), which is used in signaling between conjugative recipient and donor cells. Comparison of PrgZ with homologous oligopeptide-binding proteins (AppA and OppA) explains the high specificity of PrgZ for hydrophobic heptapeptides versus the promiscuity of peptide binding in the homologous proteins.
Collapse
Affiliation(s)
- Ronnie P-A Berntsson
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
27
|
Gao J, Li X, Feng Y, Zhang B, Miao S, Wang L, Wang N. Purification and crystallization of the ABC-type transport substrate-binding protein OppA from Thermoanaerobacter tengcongensis. Biochem Biophys Res Commun 2012; 423:45-9. [PMID: 22627134 DOI: 10.1016/j.bbrc.2012.05.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 05/14/2012] [Indexed: 11/29/2022]
Abstract
Di- and oligopeptide- binding protein OppAs play important roles in solute and nutrient uptake, sporulation, biofilm formation, cell wall muropeptides recycling, peptide-dependent quorum-sensing responses, adherence to host cells, and a variety of other biological processes. Soluble OppA from Thermoanaerobacter tengcongensis was expressed in Escherichia coli. The protein was found to be >95% pure with SDS-PAGE after a series of purification steps and the purity was further verified by mass spectrometry. The protein was crystallized using the sitting-drop vapour-diffusion method with PEG 400 as the precipitant. Crystal diffraction extended to 2.25 Å. The crystal belonged to space group C222(1), with unit-cell parameters of a=69.395, b=199.572, c=131.673 Å, and α=β=γ=90°.
Collapse
Affiliation(s)
- Jinlan Gao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
28
|
Boudreau MA, Fisher JF, Mobashery S. Messenger functions of the bacterial cell wall-derived muropeptides. Biochemistry 2012; 51:2974-90. [PMID: 22409164 DOI: 10.1021/bi300174x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial muropeptides are soluble peptidoglycan structures central to recycling of the bacterial cell wall and messengers in diverse cell signaling events. Bacteria sense muropeptides as signals that antibiotics targeting cell-wall biosynthesis are present, and eukaryotes detect muropeptides during the innate immune response to bacterial infection. This review summarizes the roles of bacterial muropeptides as messengers, with a special emphasis on bacterial muropeptide structures and the relationship of structure to the biochemical events that the muropeptides elicit. Muropeptide sensing and recycling in both Gram-positive and Gram-negative bacteria are discussed, followed by muropeptide sensing by eukaryotes as a crucial event in the innate immune response of insects (via peptidoglycan-recognition proteins) and mammals (through Nod-like receptors) to bacterial invasion.
Collapse
Affiliation(s)
- Marc A Boudreau
- Department of Chemistry and Biochemistry, Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | |
Collapse
|
29
|
Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides. J Mol Biol 2011; 414:75-85. [DOI: 10.1016/j.jmb.2011.09.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/20/2011] [Accepted: 09/26/2011] [Indexed: 11/18/2022]
|