1
|
McConnell SA, Amer BR, Muroski J, Fu J, Chang C, Ogorzalek Loo RR, Loo JA, Osipiuk J, Ton-That H, Clubb RT. Protein Labeling via a Specific Lysine-Isopeptide Bond Using the Pilin Polymerizing Sortase from Corynebacterium diphtheriae. J Am Chem Soc 2018; 140:8420-8423. [PMID: 29927249 PMCID: PMC6230430 DOI: 10.1021/jacs.8b05200] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteins that are site-specifically modified with peptides and chemicals can be used as novel therapeutics, imaging tools, diagnostic reagents and materials. However, there are few enzyme-catalyzed methods currently available to selectively conjugate peptides to internal sites within proteins. Here we show that a pilus-specific sortase enzyme from Corynebacterium diphtheriae (CdSrtA) can be used to attach a peptide to a protein via a specific lysine-isopeptide bond. Using rational mutagenesis we created CdSrtA3M, a highly activated cysteine transpeptidase that catalyzes in vitro isopeptide bond formation. CdSrtA3M mediates bioconjugation to a specific lysine residue within a fused domain derived from the corynebacterial SpaA protein. Peptide modification yields greater than >95% can be achieved. We demonstrate that CdSrtA3M can be used in concert with the Staphylococcus aureus SrtA enzyme, enabling dual, orthogonal protein labeling via lysine-isopeptide and backbone-peptide bonds.
Collapse
Affiliation(s)
- Scott A. McConnell
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Brendan R. Amer
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - John Muroski
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Janine Fu
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Chungyu Chang
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Jerzy Osipiuk
- Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA
| | - Hung Ton-That
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| |
Collapse
|
2
|
Khare B, V L Narayana S. Pilus biogenesis of Gram-positive bacteria: Roles of sortases and implications for assembly. Protein Sci 2017; 26:1458-1473. [PMID: 28493331 DOI: 10.1002/pro.3191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/26/2022]
Abstract
Successful adherence, colonization, and survival of Gram-positive bacteria require surface proteins, and multiprotein assemblies called pili. These surface appendages are attractive pharmacotherapeutic targets and understanding their assembly mechanisms is essential for identifying a new class of 'anti-infectives' that do not elicit microbial resistance. Molecular details of the Gram-negative pilus assembly are available indepth, but the Gram-positive pilus biogenesis is still an emerging field and investigations continue to reveal novel insights into this process. Pilus biogenesis in Gram-positive bacteria is a biphasic process that requires enzymes called pilus-sortases for assembly and a housekeeping sortase for covalent attachment of the assembled pilus to the peptidoglycan cell wall. Emerging structural and functional data indicate that there are at least two groups of Gram-positive pili, which require either the Class C sortase or Class B sortase in conjunction with LepA/SipA protein for major pilin polymerization. This observation suggests two distinct modes of sortase-mediated pilus biogenesis in Gram-positive bacteria. Here we review the structural and functional biology of the pilus-sortases from select streptococcal pilus systems and their role in Gram-positive pilus assembly.
Collapse
Affiliation(s)
- Baldeep Khare
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
| | - Sthanam V L Narayana
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
| |
Collapse
|
3
|
Jacobitz AW, Naziga EB, Yi SW, McConnell SA, Peterson R, Jung ME, Clubb RT, Wereszczynski J. The "Lid" in the Streptococcus pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site. J Phys Chem B 2016; 120:8302-12. [PMID: 27109553 DOI: 10.1021/acs.jpcb.6b01930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many species of Gram-positive bacteria use sortase enzymes to assemble long, proteinaceous pili structures that project from the cell surface to mediate microbial adhesion. Sortases construct highly stable structures by catalyzing a transpeptidation reaction that covalently links pilin subunits together via isopeptide bonds. Most Gram-positive pili are assembled by class C sortases that contain a "lid", a structurally unique N-terminal extension that occludes the active site. It has been hypothesized that the "lid" in many sortases is mobile and thus capable of readily being displaced from the enzyme to facilitate substrate binding. Here, we show using NMR dynamics measurements, in vitro assays, and molecular dynamics simulations that the lid in the class C sortase from Streptococcus pneumoniae (SrtC1) adopts a rigid conformation in solution that is devoid of large magnitude conformational excursions that occur on mechanistically relevant time scales. Additionally, we show that point mutations in the lid induce dynamic behavior that correlates with increased hydrolytic activity and sorting signal substrate access to the active site cysteine residue. These results suggest that the lid of the S. pneumoniae SrtC1 enzyme has a negative regulatory function and imply that a significant energetic barrier must be surmounted by currently unidentified factors to dislodge it from the active site to initiate pilus biogenesis.
Collapse
Affiliation(s)
- Alex W Jacobitz
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Emmanuel B Naziga
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , 3440 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Sung Wook Yi
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Scott A McConnell
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Robert Peterson
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Michael E Jung
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Robert T Clubb
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , 3440 South Dearborn Street, Chicago, Illinois 60616, United States
| |
Collapse
|
4
|
Lazzarin M, Cozzi R, Malito E, Martinelli M, D'Onofrio M, Maione D, Margarit I, Rinaudo CD. Noncanonical sortase‐mediated assembly of pilus type 2b in group B
Streptococcus. FASEB J 2015. [DOI: 10.1096/fj.15-272500] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Roberta Cozzi
- Novartis Vaccines and Diagnostics, GlaxoSmithKlineSienaItaly
| | - Enrico Malito
- Novartis Vaccines and Diagnostics, GlaxoSmithKlineSienaItaly
| | | | - Mariapina D'Onofrio
- Nuclear Magnetic Resonance LaboratoryDepartment of BiotechnologyUniversity of VeronaVeronaItaly
| | - Domenico Maione
- Novartis Vaccines and Diagnostics, GlaxoSmithKlineSienaItaly
| | | | | |
Collapse
|
5
|
Shaik MM, Lombardi C, Maragno Trindade D, Fenel D, Schoehn G, Di Guilmi AM, Dessen A. A structural snapshot of type II pilus formation in Streptococcus pneumoniae. J Biol Chem 2015. [PMID: 26198632 DOI: 10.1074/jbc.m115.647834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pili are fibrous appendages expressed on the surface of a vast number of bacterial species, and their role in surface adhesion is important for processes such as infection, colonization, andbiofilm formation. The human pathogen Streptococcus pneumoniae expresses two different types of pili, PI-1 and PI-2, both of which require the concerted action of structural proteins and sortases for their polymerization. The type PI-1 streptococcal pilus is a complex, well studied structure, but the PI-2 type, present in a number of invasive pneumococcal serotypes, has to date remained less well understood. The PI-2 pilus consists of repeated units of a single protein, PitB, whose covalent association is catalyzed by cognate sortase SrtG-1 and partner protein SipA. Here we report the high resolution crystal structures of PitB and SrtG1 and use molecular modeling to visualize a "trapped" 1:1 complex between the two molecules. X-ray crystallography and electron microscopy reveal that the pneumococcal PI-2 backbone fiber is formed by PitB monomers associated in head-to-tail fashion and that short, flexible fibers can be formed even in the absence of coadjuvant proteins. These observations, obtained with a simple pilus biosynthetic system, are likely to be applicable to other fiber formation processes in a variety of Gram-positive organisms.
Collapse
Affiliation(s)
- Md Munan Shaik
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and
| | - Charlotte Lombardi
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and
| | - Daniel Maragno Trindade
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, 13083 São Paulo, Brazil
| | - Daphna Fenel
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and
| | - Guy Schoehn
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and
| | - Anne Marie Di Guilmi
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and
| | - Andréa Dessen
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France, CNRS, IBS, 38044 Grenoble, France, Commissariat à l'Energie Atomique, IBS, Grenoble, France, and Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, 13083 São Paulo, Brazil
| |
Collapse
|
6
|
Suryadinata R, Seabrook SA, Adams TE, Nuttall SD, Peat TS. Structural and biochemical analyses of a Clostridium perfringens sortase D transpeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1505-13. [PMID: 26143922 PMCID: PMC4498605 DOI: 10.1107/s1399004715009219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/14/2015] [Indexed: 01/08/2023]
Abstract
The assembly and anchorage of various pathogenic proteins on the surface of Gram-positive bacteria is mediated by the sortase family of enzymes. These cysteine transpeptidases catalyze a unique sorting signal motif located at the C-terminus of their target substrate and promote the covalent attachment of these proteins onto an amino nucleophile located on another protein or on the bacterial cell wall. Each of the six distinct classes of sortases displays a unique biological role, with sequential activation of multiple sortases often observed in many Gram-positive bacteria to decorate their peptidoglycans. Less is known about the members of the class D family of sortases (SrtD), but they have a suggested role in spore formation in an oxygen-limiting environment. Here, the crystal structure of the SrtD enzyme from Clostridium perfringens was determined at 1.99 Å resolution. Comparative analysis of the C. perfringens SrtD structure reveals the typical eight-stranded β-barrel fold observed in all other known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Biochemical approaches further reveal the specifics of the SrtD catalytic activity in vitro, with a significant preference for the LPQTGS sorting motif. Additionally, the catalytic activity of SrtD is most efficient at 316 K and can be further improved in the presence of magnesium cations. Since C. perfringens spores are heat-resistant and lead to foodborne illnesses, characterization of the spore-promoting sortase SrtD may lead to the development of new antimicrobial agents.
Collapse
Affiliation(s)
- Randy Suryadinata
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A. Seabrook
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Timothy E. Adams
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Stewart D. Nuttall
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thomas S. Peat
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| |
Collapse
|
7
|
Abstract
Pili of Gram-positive bacteria are unique structures on the bacterial surface, assembled from covalently linked polypeptide subunits. Pilus assembly proceeds by transpeptidation reactions catalyzed by sortases, followed by covalent anchoring of the filament in the peptidoglycan layer. Another distinctive property is the presence of intramolecular isopeptide bonds, conferring extraordinary chemical and mechanical stability to these elongated structures. Besides their function in cell adhesion and biofilm formation, this section discusses possible application of pilus constituents as vaccine components against Gram-positive pathogens.
Collapse
|
8
|
Abstract
Bioorthogonal, chemoselective ligation methods are an essential part of the tools utilized to investigate biochemical pathways. Specifically enzymatic approaches are valuable methods in this context due to the inherent specificity of the deployed enzymes and the mild conditions of the modification reactions. One of the most common strategies is based on the transpeptidation catalyzed by sortase A derived from Staphylococcus aureus. The procedure is well established and a wide variety of applications have been published to date. Here, implementations of sortase A, which range from protein labeling using fluorescence dyes and the preparation of cyclic proteins to the modification of entire cells, are summarized. Furthermore, there is a focus on the optimization approaches established to solve the drawbacks of sortase-mediated transpeptidation.
Collapse
Affiliation(s)
- Markus Ritzefeld
- Bielefeld University, Department of Chemistry, Organic and Bioorganic Chemistry (OCIII), Universitätsstrasse 25, 33615 Bielefeld (Germany).
| |
Collapse
|
9
|
Douillard FP, Rasinkangas P, von Ossowski I, Reunanen J, Palva A, de Vos WM. Functional identification of conserved residues involved in Lactobacillus rhamnosus strain GG sortase specificity and pilus biogenesis. J Biol Chem 2014; 289:15764-75. [PMID: 24753244 DOI: 10.1074/jbc.m113.542332] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In Gram-positive bacteria, sortase-dependent pili mediate the adhesion of bacteria to host epithelial cells and play a pivotal role in colonization, host signaling, and biofilm formation. Lactobacillus rhamnosus strain GG, a well known probiotic bacterium, also displays on its cell surface mucus-binding pilus structures, along with other LPXTG surface proteins, which are processed by sortases upon specific recognition of a highly conserved LPXTG motif. Bioinformatic analysis of all predicted LPXTG proteins encoded by the L. rhamnosus GG genome revealed a remarkable conservation of glycine residues juxtaposed to the canonical LPXTG motif. Here, we investigated and defined the role of this so-called triple glycine (TG) motif in determining sortase specificity during the pilus assembly and anchoring. Mutagenesis of the TG motif resulted in a lack or an alteration of the L. rhamnosus GG pilus structures, indicating that the TG motif is critical in pilus assembly and that they govern the pilin-specific and housekeeping sortase specificity. This allowed us to propose a regulatory model of the L. rhamnosus GG pilus biogenesis. Remarkably, the TG motif was identified in multiple pilus gene clusters of other Gram-positive bacteria, suggesting that similar signaling mechanisms occur in other, mainly pathogenic, species.
Collapse
Affiliation(s)
- François P Douillard
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and
| | - Pia Rasinkangas
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and
| | - Ingemar von Ossowski
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and
| | - Justus Reunanen
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and
| | - Airi Palva
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and
| | - Willem M de Vos
- From the Department of Veterinary Biosciences, University of Helsinki, Helsinki 00790, Finland and the Laboratory of Microbiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| |
Collapse
|